Journal articles: 'Genome structure'

1

Khaitovich, A. B. "CORONAVIRUS (GENOME STRUCTURE, REPLICATION)." Crimea Journal of Experimental and Clinical Medicine 10, no. 4 (2021): 78–95. http://dx.doi.org/10.37279/2224-6444-2020-10-4-78-95.

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The overview presented in the article is a continuation of the publication on coronaviruses. The paper examines modern data on the structure of the genome and the replication process in various types of coronaviruses that cause diseases in humans and are of medical importance. The structure of the genomes of coronaviruses and the functions of genes that encode the structure of viral particles are presented; describes the function of structural genes and auxiliary genes; the role of genes encoding non-structural proteins in the structure of the viral particle and replication of coronaviruses is shown. The analysis of published studies made it possible to comparatively characterize the genomes of highly dangerous coronaviruses: SARS-CoV, MERS-CoV, SARS-CoV-2, describe their differences in structure and in the process of replication. The review analyzes the structure of the genome and the replication process of coronaviruses at the molecular level, taking into account the characteristics of different types of coronaviruses. To analyze the genetic structures and replication of coronaviruses, modern literary sources, articles in the world’s leading medical and biological journals were used.

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Mauger, David M., Michael Golden, Daisuke Yamane, Sara Williford, Stanley M. Lemon, Darren P. Martin, and Kevin M. Weeks. "Functionally conserved architecture of hepatitis C virus RNA genomes." Proceedings of the National Academy of Sciences 112, no. 12 (March 9, 2015): 3692–97. http://dx.doi.org/10.1073/pnas.1416266112.

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Hepatitis C virus (HCV) infects over 170 million people worldwide and is a leading cause of liver disease and cancer. The virus has a 9,650-nt, single-stranded, messenger-sense RNA genome that is infectious as an independent entity. The RNA genome has evolved in response to complex selection pressures, including the need to maintain structures that facilitate replication and to avoid clearance by cell-intrinsic immune processes. Here we used high-throughput, single-nucleotide resolution information to generate and functionally test data-driven structural models for three diverse HCV RNA genomes. We identified, de novo, multiple regions of conserved RNA structure, including all previously characterized cis-acting regulatory elements and also multiple novel structures required for optimal viral fitness. Well-defined RNA structures in the central regions of HCV genomes appear to facilitate persistent infection by masking the genome from RNase L and double-stranded RNA-induced innate immune sensors. This work shows how structure-first comparative analysis of entire genomes of a pathogenic RNA virus enables comprehensive and concise identification of regulatory elements and emphasizes the extensive interrelationships among RNA genome structure, viral biology, and innate immune responses.

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Fujishiro, Shin, Naoko Tokuda, and Masaki Sasai. "2P267 Computational chromosome conformation sampling of human diploid genome(21B. Genome biology:Genome structure,Poster)." Seibutsu Butsuri 54, supplement1-2 (2014): S239. http://dx.doi.org/10.2142/biophys.54.s239_3.

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Bernaola-Galván, Pedro, Pedro Carpena, Cristina Gómez-Martín, and Jose L. Oliver. "Compositional Structure of the Genome: A Review." Biology 12, no. 6 (June 13, 2023): 849. http://dx.doi.org/10.3390/biology12060849.

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As the genome carries the historical information of a species’ biotic and environmental interactions, analyzing changes in genome structure over time by using powerful statistical physics methods (such as entropic segmentation algorithms, fluctuation analysis in DNA walks, or measures of compositional complexity) provides valuable insights into genome evolution. Nucleotide frequencies tend to vary along the DNA chain, resulting in a hierarchically patchy chromosome structure with heterogeneities at different length scales that range from a few nucleotides to tens of millions of them. Fluctuation analysis reveals that these compositional structures can be classified into three main categories: (1) short-range heterogeneities (below a few kilobase pairs (Kbp)) primarily attributed to the alternation of coding and noncoding regions, interspersed or tandem repeats densities, etc.; (2) isochores, spanning tens to hundreds of tens of Kbp; and (3) superstructures, reaching sizes of tens of megabase pairs (Mbp) or even larger. The obtained isochore and superstructure coordinates in the first complete T2T human sequence are now shared in a public database. In this way, interested researchers can use T2T isochore data, as well as the annotations for different genome elements, to check a specific hypothesis about genome structure. Similarly to other levels of biological organization, a hierarchical compositional structure is prevalent in the genome. Once the compositional structure of a genome is identified, various measures can be derived to quantify the heterogeneity of such structure. The distribution of segment G+C content has recently been proposed as a new genome signature that proves to be useful for comparing complete genomes. Another meaningful measure is the sequence compositional complexity (SCC), which has been used for genome structure comparisons. Lastly, we review the recent genome comparisons in species of the ancient phylum Cyanobacteria, conducted by phylogenetic regression of SCC against time, which have revealed positive trends towards higher genome complexity. These findings provide the first evidence for a driven progressive evolution of genome compositional structure.

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Zhang, Hui, Yao Xiong, Wenhai Xiao, and Yi Wu. "Investigation of Genome Biology by Synthetic Genome Engineering." Bioengineering 10, no. 2 (February 20, 2023): 271. http://dx.doi.org/10.3390/bioengineering10020271.

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Synthetic genomes were designed based on an understanding of natural genomic information, offering an opportunity to engineer and investigate biological systems on a genome-wide scale. Currently, the designer version of the M. mycoides genome and the E. coli genome, as well as most of the S. cerevisiae genome, have been synthesized, and through the cycles of design–build–test and the following engineering of synthetic genomes, many fundamental questions of genome biology have been investigated. In this review, we summarize the use of synthetic genome engineering to explore the structure and function of genomes, and highlight the unique values of synthetic genomics.

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Makałowski, W. "The human genome structure and organization." Acta Biochimica Polonica 48, no. 3 (September 30, 2001): 587–98. http://dx.doi.org/10.18388/abp.2001_3893.

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Genetic information of human is encoded in two genomes: nuclear and mitochondrial. Both of them reflect molecular evolution of human starting from the beginning of life (about 4.5 billion years ago) until the origin of Homo sapiens species about 100,000 years ago. From this reason human genome contains some features that are common for different groups of organisms and some features that are unique for Homo sapiens. 3.2 x 10(9) base pairs of human nuclear genome are packed into 23 chromosomes of different size. The smallest chromosome - 21st contains 5 x 10(7) base pairs while the biggest one -1st contains 2.63 x 10(8) base pairs. Despite the fact that the nucleotide sequence of all chromosomes is established, the organisation of nuclear genome put still questions: for example: the exact number of genes encoded by the human genome is still unknown giving estimations from 30 to 150 thousand genes. Coding sequences represent a few percent of human nuclear genome. The majority of the genome is represented by repetitiVe sequences (about 50%) and noncoding unique sequences. This part of the genome is frequently wrongly called "junk DNA". The distribution of genes on chromosomes is irregular, DNA fragments containing low percentage of GC pairs code lower number of genes than the fragments of high percentage of GC pairs.

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Mukherjee, Partha, Youakim Badr, Srushti Karvekar, and Shanmugapriya Viswanathan. "Coronavirus Genome Sequence Similarity and Protein Sequence Classification." Journal of Digital Science 3, no. 2 (December 28, 2021): 3–18. http://dx.doi.org/10.33847/2686-8296.3.2_1.

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The world currently is going through a serious pandemic due to the coronavirus disease (COVID-19). In this study, we investigate the gene structure similarity of coronavirus genomes isolated from COVID-19 patients, Severe Acute Respiratory Syndrome (SARS) patients and bats genes. We also explore the extent of similarity between their genome structures to find if the new coronavirus is similar to either of the other genome structures. Our experimental results show that there is 82.42% similarity between the CoV-2 genome structure and the bat genome structure. Moreover, we have used a bidirectional Gated Recurrent Unit (GRU) model as the deep learning technique and an improved variant of Recurrent Neural networks (i.e., Bidirectional Long Short Term Memory model) to classify the protein families of these genomes to isolate the prominent protein family accession. The accuracy of Gated Recurrent Unit (GRU) is 98% for labeled protein sequences against the protein families. By comparing the performance of the Gated Recurrent Unit (GRU) model with the Bidirectional Long Short Term Memory (Bi-LSTM) model results, we found that the GRU model is 1.6% more accurate than the Bi-LSTM model for our multiclass protein classification problem. Our experimental results would be further support medical research purposes in targeting the protein family similarity to better understand the coronavirus genomic structure.

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8

Lloyd, Vett K., and Kathleen Fitzpatrick. "Genome and chromosome structure: Twelve dynamic and evolving genomes." Fly 2, no. 3 (May 19, 2008): 141–44. http://dx.doi.org/10.4161/fly.6379.

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9

Cassidy, Liam D., and Ashok R. Venkitaraman. "Genome instability mechanisms and the structure of cancer genomes." Current Opinion in Genetics & Development 22, no. 1 (February 2012): 10–13. http://dx.doi.org/10.1016/j.gde.2012.02.003.

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10

Zhou, Tianming, Ruochi Zhang, and Jian Ma. "The 3D Genome Structure of Single Cells." Annual Review of Biomedical Data Science 4, no. 1 (July 20, 2021): 21–41. http://dx.doi.org/10.1146/annurev-biodatasci-020121-084709.

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The spatial organization of the genome in the cell nucleus is pivotal to cell function. However, how the 3D genome organization and its dynamics influence cellular phenotypes remains poorly understood. The very recent development of single-cell technologies for probing the 3D genome, especially single-cell Hi-C (scHi-C), has ushered in a new era of unveiling cell-to-cell variability of 3D genome features at an unprecedented resolution. Here, we review recent developments in computational approaches to the analysis of scHi-C, including data processing, dimensionality reduction, imputation for enhancing data quality, and the revealing of 3D genome features at single-cell resolution. While much progress has been made in computational method development to analyze single-cell 3D genomes, substantial future work is needed to improve data interpretation and multimodal data integration, which are critical to reveal fundamental connections between genome structure and function among heterogeneous cell populations in various biological contexts.

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11

Andrzejewska, Angelika, Małgorzata Zawadzka, Julita Gumna, David J. Garfinkel, and Katarzyna Pachulska-Wieczorek. "In vivostructure of the Ty1 retrotransposon RNA genome." Nucleic Acids Research 49, no. 5 (February 23, 2021): 2878–93. http://dx.doi.org/10.1093/nar/gkab090.

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AbstractLong terminal repeat (LTR)-retrotransposons constitute a significant part of eukaryotic genomes and influence their function and evolution. Like other RNA viruses, LTR-retrotransposons efficiently utilize their RNA genome to interact with host cell machinery during replication. Here, we provide the first genome-wide RNA secondary structure model for a LTR-retrotransposon in living cells. Using SHAPE probing, we explore the secondary structure of the yeast Ty1 retrotransposon RNA genome in its native in vivo state and under defined in vitro conditions. Comparative analyses reveal the strong impact of the cellular environment on folding of Ty1 RNA. In vivo, Ty1 genome RNA is significantly less structured and more dynamic but retains specific well-structured regions harboring functional cis-acting sequences. Ribosomes participate in the unfolding and remodeling of Ty1 RNA, and inhibition of translation initiation stabilizes Ty1 RNA structure. Together, our findings support the dual role of Ty1 genomic RNA as a template for protein synthesis and reverse transcription. This study also contributes to understanding how a complex multifunctional RNA genome folds in vivo, and strengthens the need for studying RNA structure in its natural cellular context.

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12

White, K. Andrew. "Regulation of RNA Virus Processes by Viral Genome Structure." Proceedings 50, no. 1 (June 16, 2020): 68. http://dx.doi.org/10.3390/proceedings2020050068.

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The genomes of RNA viruses contain a variety of RNA sequences and structures that regulate different steps in virus reproduction. Events that are controlled by RNA elements include (i) the translation of viral proteins, (ii) the replication of viral RNA genomes, and (iii) the transcription of viral subgenomic mRNAs. Studies of members of the family Tombusviridae, which possess plus-strand RNA genomes, have revealed novel ways in which the RNA genome structure is utilized to control different viral processes. Recent advances in our understanding of RNA-based viral regulation in select tombusvirids will be presented.

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13

Khaitovich, A. B., and P. A. Yermachkova. "CORONAVIRUS (GENOME STRUCTURE, REPLICATION)." Crimea Journal of Experimental and Clinical Medicine 11, no. 1 (2022): 61–75. http://dx.doi.org/10.37279/2224-6444-2021-11-1-61-75.

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The publication analyzes studies on identified mutations and their impact on the variability of coronaviruses; on the identified genotypes (lines, clusters, clades) in SARS-CoV-2, which are important for: assessing the biological properties of coronaviruses; determination of the epidemiological pathways for the introduction and spread of the virus; studying the evolution and origin of the virus; determining the effect of the virus on clinical manifestations; drug development that targets some of the targets of the virus. The work describes the genotypes (clusters, types, lines) of SARS-CoV-2 and their geographical and temporal distribution.

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14

Rusk, Nicole. "Variability in genome structure." Nature Methods 16, no. 5 (April 30, 2019): 359. http://dx.doi.org/10.1038/s41592-019-0410-2.

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15

Ondřej, M. "Structure of Plant Genome." Biotechnology & Biotechnological Equipment 8, no. 1 (January 1994): 3–6. http://dx.doi.org/10.1080/13102818.1994.10818744.

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16

Bernardi, Giorgio. "Genome structure and evolution." Journal of Molecular Evolution 33, no. 1 (July 1991): 3. http://dx.doi.org/10.1007/bf02100189.

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Bernardi, G. "Genome structure and evolution:Foreword." Journal of Molecular Evolution 33, no. 4 (October 1991): 402. http://dx.doi.org/10.1007/bf02102870.

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Bernardi, Giorgio. "Genome structure and evolution." Journal of Molecular Evolution 37, no. 2 (August 1993): 91–92. http://dx.doi.org/10.1007/bf02407343.

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19

Saint Girons, I., S. J. Norris, U. Göbel, J. Meyer, E. M. Walker, and R. Zuerner. "Genome structure of spirochetes." Research in Microbiology 143, no. 6 (January 1992): 615–21. http://dx.doi.org/10.1016/0923-2508(92)90119-9.

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20

Philipp, Wolfgang J., David C. Schwartz, Amalio Telenti, and Stewart T. Cole. "Mycobacterial genome structure (minireview)." Electrophoresis 19, no. 4 (April 1998): 573–76. http://dx.doi.org/10.1002/elps.1150190418.

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21

Nicolas Calderon, Kevin, Johan Fabian Galindo, and Clara Isabel Bermudez-Santana. "Evaluation of Conserved RNA Secondary Structures within and between Geographic Lineages of Zika Virus." Life 11, no. 4 (April 14, 2021): 344. http://dx.doi.org/10.3390/life11040344.

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Zika virus (ZIKV), without a vaccine or an effective treatment approved to date, has globally spread in the last century. The infection caused by ZIKV in humans has changed progressively from mild to subclinical in recent years, causing epidemics with greater infectivity, tropism towards new tissues and other related symptoms as a product of various emergent ZIKV–host cell interactions. However, it is still unknown why or how the RNA genome structure impacts those interactions in differential evolutionary origin strains. Moreover, the genomic comparison of ZIKV strains from the sequence-based phylogenetic analysis is well known, but differences from RNA structure comparisons have barely been studied. Thus, in order to understand the RNA genome variability of lineages of various geographic distributions better, 410 complete genomes in a phylogenomic scanning were used to study the conservation of structured RNAs. Our results show the contemporary landscape of conserved structured regions with unique conserved structured regions in clades or in lineages within circulating ZIKV strains. We propose these structures as candidates for further experimental validation to establish their potential role in vital functions of the viral cycle of ZIKV and their possible associations with the singularities of different outbreaks that lead to ZIKV populations to acquire nucleotide substitutions, which is evidence of the local structure genome differentiation.

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Jackman, Shaun D., Lauren Coombe, René L. Warren, Heather Kirk, Eva Trinh, Tina MacLeod, Stephen Pleasance, et al. "Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure." Genome Biology and Evolution 12, no. 7 (May 25, 2020): 1174–79. http://dx.doi.org/10.1093/gbe/evaa108.

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Abstract Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the complete 5.5-Mb mitochondrial genome of Sitka spruce (Picea sitchensis), to date, one of the largest mitochondrial genomes of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads based on sequence homology to the white spruce mitochondrial genome. The assembly graph shows a multipartite genome structure, composed of one smaller 168-kb circular segment of DNA, and a larger 5.4-Mb single component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination.

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Boyd, Patricia S., Janae B. Brown, Joshua D. Brown, Jonathan Catazaro, Issac Chaudry, Pengfei Ding, Xinmei Dong, et al. "NMR Studies of Retroviral Genome Packaging." Viruses 12, no. 10 (September 30, 2020): 1115. http://dx.doi.org/10.3390/v12101115.

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Nearly all retroviruses selectively package two copies of their unspliced RNA genomes from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs. Over the past four decades, combinations of genetic experiments, phylogenetic analyses, nucleotide accessibility mapping, in silico RNA structure predictions, and biophysical experiments were employed to understand how retroviral genomes are selected for packaging. Genetic studies provided early clues regarding the protein and RNA elements required for packaging, and nucleotide accessibility mapping experiments provided insights into the secondary structures of functionally important elements in the genome. Three-dimensional structural determinants of packaging were primarily derived by nuclear magnetic resonance (NMR) spectroscopy. A key advantage of NMR, relative to other methods for determining biomolecular structure (such as X-ray crystallography), is that it is well suited for studies of conformationally dynamic and heterogeneous systems—a hallmark of the retrovirus packaging machinery. Here, we review advances in understanding of the structures, dynamics, and interactions of the proteins and RNA elements involved in retroviral genome selection and packaging that are facilitated by NMR.

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Andrews, Ryan J., Julien Roche, and Walter N. Moss. "ScanFold: an approach for genome-wide discovery of local RNA structural elements—applications to Zika virus and HIV." PeerJ 6 (December 18, 2018): e6136. http://dx.doi.org/10.7717/peerj.6136.

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In addition to encoding RNA primary structures, genomes also encode RNA secondary and tertiary structures that play roles in gene regulation and, in the case of RNA viruses, genome replication. Methods for the identification of functional RNA structures in genomes typically rely on scanning analysis windows, where multiple partially-overlapping windows are used to predict RNA structures and folding metrics to deduce regions likely to form functional structure. Separate structural models are produced for each window, where the step size can greatly affect the returned model. This makes deducing unique local structures challenging, as the same nucleotides in each window can be alternatively base paired. We are presenting here a new approach where all base pairs from analysis windows are considered and weighted by favorable folding. This results in unique base pairing throughout the genome and the generation of local regions/structures that can be ranked by their propensity to form unusually thermodynamically stable folds. We applied this approach to the Zika virus (ZIKV) and HIV-1 genomes. ZIKV is linked to a variety of neurological ailments including microcephaly and Guillain–Barré syndrome and its (+)-sense RNA genome encodes two, previously described, functionally essential structured RNA regions. HIV, the cause of AIDS, contains multiple functional RNA motifs in its genome, which have been extensively studied. Our approach is able to successfully identify and model the structures of known functional motifs in both viruses, while also finding additional regions likely to form functional structures. All data have been archived at the RNAStructuromeDB (www.structurome.bb.iastate.edu), a repository of RNA folding data for humans and their pathogens.

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Zhou, Chenxi, Tania Duarte, Rocio Silvestre, Genoveva Rossel, Robert O. M. Mwanga, Awais Khan, Andrew W. George, et al. "Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes." Gates Open Research 2 (September 5, 2018): 41. http://dx.doi.org/10.12688/gatesopenres.12856.1.

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Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an I. triloba line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the species from the Convolvulaceae Ipomoea section Batatas revealed that the most closely related diploid wild species of the hexaploid sweetpotato is I. trifida. Conclusions: Nanopore long reads are helpful in construction of cp genome assemblies, especially in solving the two long inverted repeats. We are generally able to extract cp sequences from WGS data of sufficiently high coverage for assembly of cp genomes. The cp genomes can be used to investigate the population structure and the phylogenetic relationship for the sweetpotato.

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Zhou, Chenxi, Tania Duarte, Rocio Silvestre, Genoveva Rossel, Robert O. M. Mwanga, Awais Khan, Andrew W. George, et al. "Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes." Gates Open Research 2 (July 21, 2020): 41. http://dx.doi.org/10.12688/gatesopenres.12856.2.

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Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an I. triloba line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the species from the Convolvulaceae Ipomoea section Batatas revealed that the most closely related diploid wild species of the hexaploid sweetpotato is I. trifida. Conclusions: Nanopore long reads are helpful in construction of cp genome assemblies, especially in solving the two long inverted repeats. We are generally able to extract cp sequences from WGS data of sufficiently high coverage for assembly of cp genomes. The cp genomes can be used to investigate the population structure and the phylogenetic relationship for the sweetpotato.

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Mohanta, Tapan Kumar, Awdhesh Kumar Mishra, and Ahmed Al-Harrasi. "The 3D Genome: From Structure to Function." International Journal of Molecular Sciences 22, no. 21 (October 27, 2021): 11585. http://dx.doi.org/10.3390/ijms222111585.

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The genome is the most functional part of a cell, and genomic contents are organized in a compact three-dimensional (3D) structure. The genome contains millions of nucleotide bases organized in its proper frame. Rapid development in genome sequencing and advanced microscopy techniques have enabled us to understand the 3D spatial organization of the genome. Chromosome capture methods using a ligation approach and the visualization tool of a 3D genome browser have facilitated detailed exploration of the genome. Topologically associated domains (TADs), lamin-associated domains, CCCTC-binding factor domains, cohesin, and chromatin structures are the prominent identified components that encode the 3D structure of the genome. Although TADs are the major contributors to 3D genome organization, they are absent in Arabidopsis. However, a few research groups have reported the presence of TAD-like structures in the plant kingdom.

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Campbell, Matthew A., James T. Van Leuven, Russell C. Meister, Kaitlin M. Carey, Chris Simon, and John P. McCutcheon. "Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont Hodgkinia." Proceedings of the National Academy of Sciences 112, no. 33 (May 18, 2015): 10192–99. http://dx.doi.org/10.1073/pnas.1421386112.

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Comparative genomics from mitochondria, plastids, and mutualistic endosymbiotic bacteria has shown that the stable establishment of a bacterium in a host cell results in genome reduction. Although many highly reduced genomes from endosymbiotic bacteria are stable in gene content and genome structure, organelle genomes are sometimes characterized by dramatic structural diversity. Previous results from Candidatus Hodgkinia cicadicola, an endosymbiont of cicadas, revealed that some lineages of this bacterium had split into two new cytologically distinct yet genetically interdependent species. It was hypothesized that the long life cycle of cicadas in part enabled this unusual lineage-splitting event. Here we test this hypothesis by investigating the structure of the Ca. Hodgkinia genome in one of the longest-lived cicadas, Magicicada tredecim. We show that the Ca. Hodgkinia genome from M. tredecim has fragmented into multiple new chromosomes or genomes, with at least some remaining partitioned into discrete cells. We also show that this lineage-splitting process has resulted in a complex of Ca. Hodgkinia genomes that are 1.1-Mb pairs in length when considered together, an almost 10-fold increase in size from the hypothetical single-genome ancestor. These results parallel some examples of genome fragmentation and expansion in organelles, although the mechanisms that give rise to these extreme genome instabilities are likely different.

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Sorimachi, Kenji. "Evolution based on genome structure: the “diagonal genome universe”." Natural Science 02, no. 10 (2010): 1104–12. http://dx.doi.org/10.4236/ns.2010.210137.

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Ulloa, Mauricio, Ibrokhim Y. Abdurakhmonov, Claudia Perez-M., Richard Percy, and James McD Stewart. "Genetic diversity and population structure of cotton (Gossypium spp.) of the New World assessed by SSR markers." Botany 91, no. 4 (April 2013): 251–59. http://dx.doi.org/10.1139/cjb-2012-0192.

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A global analysis of cotton (Gossypium spp.) genetic diversity is the first step to understanding its geographical distribution, dissemination, genetic relatedness, and population structure. To assess the genetic diversity and population structure in Gossypium species, 111 cotton accessions representing five allotetraploids (AD1–AD5 genomes), 23 Asiatic diploids of the Old World (A1 and A2 genomes), and 82 diploids of the New World subgenus Houzingenia (D1–D11 genomes) species were assessed using simple sequence repeats (SSR) markers with wide genome coverage. The mean genetic distance (GD) between the two most important New World tetraploid cottons (Upland (Gossypium hirsutum L.) and Pima (Gossypium barbadense L.)) was 0.39. Among the three shrub type sections (Houzingenia, Integrifolia, and Caducibracteolata) and three arborescent sections (Erioxylum, Selera, and Austroamericana), the GD ranged between 0.19 and 0.41. Phylogenetic analyses clustered all species into distinct phylogenetic groups, which were consistent with genomic origin, evolutionary history, and geographic distribution or ecotypes of these accessions, suggesting the existence of clear structured strata. With all of the genomes, the highest statistical analysis of Structure test through measurements of ad hoc (ΔK) occurred at K = 2, with group Q1 with the Old World diploid A genomes and with group Q2 with all the New World diploids of the D genome. AD genome accessions shared nearly equal alleles from both Q1 and Q2 groups. With all of the diploids of the New World D genomes, the highest value of ΔK occurred at K = 5. These results are consistent with the fundamental knowledge of tetraploid AD-genome formation and the rapid radiation of the American diploid cotton linage that took place somewhere in southwestern Mexico, followed by a differentiation–speciation during angiosperm evolution. In addition, SSR markers provide an alternative solution for distinguishing phylogenetic relationships between accessions of different ecotypes and for elucidating population structure of cottons of the New World.

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Alzahrani, Dhafer, Enas Albokhari, Abidina Abba, and Samaila Yaradua. "The first complete chloroplast genome sequences in Resedaceae: Genome structure and comparative analysis." Science Progress 104, no. 4 (October 2021): 003685042110599. http://dx.doi.org/10.1177/00368504211059973.

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Caylusea hexagyna and Ochradenus baccatus are two species in the Resedaceae family. In this study, we analysed the complete plastid genomes of these two species using high-throughput sequencing technology and compared their genomic data. The length of the plastid genome of C. hexagyna was 154,390 bp while that of O. baccatus was 153,380 bp. The lengths of the inverted repeats (IR) regions were 26,526 bp and 26,558 bp, those of the large single copy (LSC) regions were 83,870 bp and 83,023 bp; and those of the small single copy (SSC) regions were 17,468 bp and 17,241 bp in C. hexagyna and O. baccatus, respectively. Both genomes consisted of 113 genes: 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Repeat analysis showed that the plastid genome included all types of repeats, with more frequent occurrences of palindromic sequences. Comparative studies of SSR markers showed that there were 256 markers in C. hexagyna and 255 in O. baccatus; the majority of the SSRs in these plastid genomes were mononucleotide repeats (A/T). All the clusters in the phylogenetic tree had high support. This study reported the first complete plastid genomes of the genera Caylusea and Ochradenus and the first for the Resedaceae family.

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Mazur, Andrzej, and Piotr Koper. "Rhizobial plasmids — replication, structure and biological role." Open Life Sciences 7, no. 4 (August 1, 2012): 571–86. http://dx.doi.org/10.2478/s11535-012-0058-8.

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AbstractSoil bacteria, collectively named rhizobia, can establish mutualistic relationships with legume plants. Rhizobia often have multipartite genome architecture with a chromosome and several extrachromosomal replicons making these bacteria a perfect candidate for plasmid biology studies. Rhizobial plasmids are maintained in the cells using a tightly controlled and uniquely organized replication system. Completion of several rhizobial genome-sequencing projects has changed the view that their genomes are simply composed of the chromosome and cryptic plasmids. The genetic content of plasmids and the presence of some important (or even essential) genes contribute to the capability of environmental adaptation and competitiveness with other bacteria. On the other hand, their mosaic structure results in the plasticity of the genome and demonstrates a complex evolutionary history of plasmids. In this review, a genomic perspective was employed for discussion of several aspects regarding rhizobial plasmids comprising structure, replication, genetic content, and biological role. A special emphasis was placed on current post-genomic knowledge concerning plasmids, which has enriched the view of the entire bacterial genome organization by the discovery of plasmids with a potential chromosome-like role.

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Szlachta, Karol, Arkadi Manukyan, Heather M. Raimer, Sandeep Singh, Anita Salamon, Wenying Guo, Kirill S. Lobachev, and Yuh-Hwa Wang. "Topoisomerase II contributes to DNA secondary structure-mediated double-stranded breaks." Nucleic Acids Research 48, no. 12 (June 5, 2020): 6654–71. http://dx.doi.org/10.1093/nar/gkaa483.

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Abstract DNA double-stranded breaks (DSBs) trigger human genome instability, therefore identifying what factors contribute to DSB induction is critical for our understanding of human disease etiology. Using an unbiased, genome-wide approach, we found that genomic regions with the ability to form highly stable DNA secondary structures are enriched for endogenous DSBs in human cells. Human genomic regions predicted to form non-B-form DNA induced gross chromosomal rearrangements in yeast and displayed high indel frequency in human genomes. The extent of instability in both analyses is in concordance with the structure forming ability of these regions. We also observed an enrichment of DNA secondary structure-prone sites overlapping transcription start sites (TSSs) and CCCTC-binding factor (CTCF) binding sites, and uncovered an increase in DSBs at highly stable DNA secondary structure regions, in response to etoposide, an inhibitor of topoisomerase II (TOP2) re-ligation activity. Importantly, we found that TOP2 deficiency in both yeast and human leads to a significant reduction in DSBs at structure-prone loci, and that sites of TOP2 cleavage have a greater ability to form highly stable DNA secondary structures. This study reveals a direct role for TOP2 in generating secondary structure-mediated DNA fragility, advancing our understanding of mechanisms underlying human genome instability.

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Durrant, Matthew G., and Ami S. Bhatt. "Microbiome genome structure drives function." Nature Microbiology 4, no. 6 (May 22, 2019): 912–13. http://dx.doi.org/10.1038/s41564-019-0473-y.

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Vinson, Valda. "The structure of the genome." Science 361, no. 6405 (August 30, 2018): 888.4–888. http://dx.doi.org/10.1126/science.361.6405.888-d.

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Martin-Didonet, Claudia C. G., Leda S. Chubatsu, Emanuel M. Souza, Margareth Kleina, Fabiane G. M. Rego, Liu U. Rigo, M. Geoffrey Yates, and Fabio O. Pedrosa. "Genome Structure of the GenusAzospirillum." Journal of Bacteriology 182, no. 14 (July 15, 2000): 4113–16. http://dx.doi.org/10.1128/jb.182.14.4113-4116.2000.

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ABSTRACT Azospirillum species are plant-associated diazotrophs of the alpha subclass of Proteobacteria. The genomes of five of the six Azospirillum species were analyzed by pulsed-field gel electrophoresis. All strains possessed several megareplicons, some probably linear, and 16S ribosomal DNA hybridization indicated multiple chromosomes in genomes ranging in size from 4.8 to 9.7 Mbp. The nifHDK operon was identified in the largest replicon.

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Spaan, W., D. Cavanagh, and M. C. Horzinek. "Coronaviruses: Structure and Genome Expression." Journal of General Virology 69, no. 12 (December 1, 1988): 2939–52. http://dx.doi.org/10.1099/0022-1317-69-12-2939.

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Samudrala, Ram. "Modeling genome structure and function." Pure and Applied Chemistry 74, no. 6 (January 1, 2002): 907–14. http://dx.doi.org/10.1351/pac200274060907.

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The ongoing genomics revolution has led to the creation and enumeration of all the genes encoded within several organisms. The next steps are to catalog all proteins, their structures, and their functions in different contexts. At the same time, scientists have been pursuing experimental and theoretical approaches to integrate this information to gain understanding of the behavior of entire systems. In this work, we provide a framework for obtaining structures for all tractable protein sequences encoded by a genome, and using the resulting structures to aid in understanding function. Our aim is to integrate the output produced with other genomic and proteomic data to create a comprehensive picture of systems and organismal biology.

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Zhang, Qinfen, Yuanzhu Gao, Matthew L. Baker, Shanshan Liu, Xudong Jia, Haidong Xu, Jianguo He, Jason T. Kaelber, Shaoping Weng, and Wen Jiang. "The structure of a 12-segmented dsRNA reovirus: New insights into capsid stabilization and organization." PLOS Pathogens 19, no. 4 (April 21, 2023): e1011341. http://dx.doi.org/10.1371/journal.ppat.1011341.

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Infecting a wide range of hosts, members of Reovirales (formerly Reoviridae) consist of a genome with different numbers of segmented double stranded RNAs (dsRNA) encapsulated by a proteinaceous shell and carry out genome replication and transcription inside the virion. Several cryo-electron microscopy (cryo-EM) structures of reoviruses with 9, 10 or 11 segmented dsRNA genomes have revealed insights into genome arrangement and transcription. However, the structure and genome arrangement of 12-segmented Reovirales members remain poorly understood. Using cryo-EM, we determined the structure of mud crab reovirus (MCRV), a 12-segmented dsRNA virus that is a putative member of Reovirales in the non-turreted Sedoreoviridae family, to near-atomic resolutions with icosahedral symmetry (3.1 Å) and without imposing icosahedral symmetry (3.4 Å). These structures revealed the organization of the major capsid proteins in two layers: an outer T = 13 layer consisting of VP12 trimers and unique VP11 clamps, and an inner T = 1 layer consisting of VP3 dimers. Additionally, ten RNA dependent RNA polymerases (RdRp) were well resolved just below the VP3 layer but were offset from the 5-fold axes and arranged with D5 symmetry, which has not previously been seen in other members of Reovirales. The N-termini of VP3 were shown to adopt four unique conformations; two of which anchor the RdRps, while the other two conformations are likely involved in genome organization and capsid stability. Taken together, these structures provide a new level of understanding for capsid stabilization and genome organization of segmented dsRNA viruses.

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Brickner, Jason. "Genetic and epigenetic control of the spatial organization of the genome." Molecular Biology of the Cell 28, no. 3 (February 2017): 364–69. http://dx.doi.org/10.1091/mbc.e16-03-0149.

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Eukaryotic genomes are spatially organized within the nucleus by chromosome folding, interchromosomal contacts, and interaction with nuclear structures. This spatial organization is observed in diverse organisms and both reflects and contributes to gene expression and differentiation. This leads to the notion that the arrangement of the genome within the nucleus has been shaped and conserved through evolutionary processes and likely plays an adaptive function. Both DNA-binding proteins and changes in chromatin structure influence the positioning of genes and larger domains within the nucleus. This suggests that the spatial organization of the genome can be genetically encoded by binding sites for DNA-binding proteins and can also involve changes in chromatin structure, potentially through nongenetic mechanisms. Here I briefly discuss the results that support these ideas and their implications for how genomes encode spatial organization.

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Poblete, Simón, and Horacio V. Guzman. "Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models." Viruses 13, no. 8 (August 6, 2021): 1555. http://dx.doi.org/10.3390/v13081555.

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Three-dimensional RNA domain reconstruction is important for the assembly, disassembly and delivery functionalities of a packed proteinaceus capsid. However, to date, the self-association of RNA molecules is still an open problem. Recent chemical probing reports provide, with high reliability, the secondary structure of diverse RNA ensembles, such as those of viral genomes. Here, we present a method for reconstructing the complete 3D structure of RNA genomes, which combines a coarse-grained model with a subdomain composition scheme to obtain the entire genome inside proteinaceus capsids based on secondary structures from experimental techniques. Despite the amount of sampling involved in the folded and also unfolded RNA molecules, advanced microscope techniques can provide points of anchoring, which enhance our model to include interactions between capsid pentamers and RNA subdomains. To test our method, we tackle the satellite tobacco mosaic virus (STMV) genome, which has been widely studied by both experimental and computational communities. We provide not only a methodology to structurally analyze the tertiary conformations of the RNA genome inside capsids, but a flexible platform that allows the easy implementation of features/descriptors coming from both theoretical and experimental approaches.

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Xia, Lei, Han Wang, Xiaokun Zhao, Hesbon Ochieng Obel, Xiaqing Yu, Qunfeng Lou, Jinfeng Chen, and Chunyan Cheng. "Chloroplast Pan-Genomes and Comparative Transcriptomics Reveal Genetic Variation and Temperature Adaptation in the Cucumber." International Journal of Molecular Sciences 24, no. 10 (May 18, 2023): 8943. http://dx.doi.org/10.3390/ijms24108943.

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Although whole genome sequencing, genetic variation mapping, and pan-genome studies have been done on a large group of cucumber nuclear genomes, organelle genome information is largely unclear. As an important component of the organelle genome, the chloroplast genome is highly conserved, which makes it a useful tool for studying plant phylogeny, crop domestication, and species adaptation. Here, we have constructed the first cucumber chloroplast pan-genome based on 121 cucumber germplasms, and investigated the genetic variations of the cucumber chloroplast genome through comparative genomic, phylogenetic, haplotype, and population genetic structure analysis. Meanwhile, we explored the changes in expression of cucumber chloroplast genes under high- and low-temperature stimulation via transcriptome analysis. As a result, a total of 50 complete chloroplast genomes were successfully assembled from 121 cucumber resequencing data, ranging in size from 156,616–157,641 bp. The 50 cucumber chloroplast genomes have typical quadripartite structures, consisting of a large single copy (LSC, 86,339–86,883 bp), a small single copy (SSC, 18,069–18,363 bp), and two inverted repeats (IRs, 25,166–25,797 bp). Comparative genomic, haplotype, and population genetic structure results showed that there is more genetic variation in Indian ecotype cucumbers compared to other cucumber cultivars, which means that many genetic resources remain to be explored in Indian ecotype cucumbers. Phylogenetic analysis showed that the 50 cucumber germplasms could be classified into 3 types: East Asian, Eurasian + Indian, and Xishuangbanna + Indian. The transcriptomic analysis showed that matK were significantly up-regulated under high- and low-temperature stresses, further demonstrating that cucumber chloroplasts respond to temperature adversity by regulating lipid metabolism and ribosome metabolism. Further, accD has higher editing efficiency under high-temperature stress, which may contribute to the heat tolerance. These studies provide useful insight into genetic variation in the chloroplast genome, and established the foundation for exploring the mechanisms of temperature-stimulated chloroplast adaptation.

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Sharma, Manoj K., Rita Sharma, Peijian Cao, Jerry Jenkins, Laura E. Bartley, Morgan Qualls, Jane Grimwood, Jeremy Schmutz, Daniel Rokhsar, and Pamela C. Ronald. "A Genome-Wide Survey of Switchgrass Genome Structure and Organization." PLoS ONE 7, no. 4 (April 12, 2012): e33892. http://dx.doi.org/10.1371/journal.pone.0033892.

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Wu, Xiaobing, Tao Zheng, Zhigang Jiang, and Lei Wei. "The mitochondrial genome structure of the clouded leopard (Neofelis nebulosa)." Genome 50, no. 2 (February 2007): 252–57. http://dx.doi.org/10.1139/g06-143.

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The complete 16 844 bp mitochondrial genome of Neofelis nebulosa has been sequenced and compared with the complete mitochondrial genomes of Felis catus and the Acinonyx jubatus . The base composition of the mitochondrial genome of N. nebulosa is as follows: A, 5343 bp (31.7%); C, 4441 bp (26.4%); G, 2491 bp (14.8%); T, 4569 bp (27.1%). The genome complement and the gene order of this mitochondrial genome was found to be typical of those reported for other mammals. Several unusual features of this genome, however, were found. First, in protein-coding regions, AT bias in the genome was not prevalent in the third position of codons, as it is in most other mammals, but was found in the second position of codons. Second, in tRNA regions, tRNASer (AGY), which lacked the “DHU” arm, could not be folded into the typical cloverleaf-shaped structure. Third, in the control region, no repetitive sequences (RS)-2 were found. However, RS-2 repetitive motifs usually occurr in the control regions of most great cats. In addition, 4 variable sites were found in CSB-3 of the control region. Fourth, AT content in the control region of the mtDNA from the clouded leopard was lower than it is in other regions.

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Seemann, Stefan E., Aashiq H. Mirza, Claus H. Bang-Berthelsen, Christian Garde, Mikkel Christensen-Dalsgaard, Christopher T. Workman, Flemming Pociot, Niels Tommerup, Jan Gorodkin, and Walter L. Ruzzo. "Does rapid sequence divergence preclude RNA structure conservation in vertebrates?" Nucleic Acids Research 50, no. 5 (February 21, 2022): 2452–63. http://dx.doi.org/10.1093/nar/gkac067.

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Abstract Accelerated evolution of any portion of the genome is of significant interest, potentially signaling positive selection of phenotypic traits and adaptation. Accelerated evolution remains understudied for structured RNAs, despite the fact that an RNA’s structure is often key to its function. RNA structures are typically characterized by compensatory (structure-preserving) basepair changes that are unexpected given the underlying sequence variation, i.e., they have evolved through negative selection on structure. We address the question of how fast the primary sequence of an RNA can change through evolution while conserving its structure. Specifically, we consider predicted and known structures in vertebrate genomes. After careful control of false discovery rates, we obtain 13 de novo structures (and three known Rfam structures) that we predict to have rapidly evolving sequences—defined as structures where the primary sequences of human and mouse have diverged at least twice as fast (1.5 times for Rfam) as nearby neutrally evolving sequences. Two of the three known structures function in translation inhibition related to infection and immune response. We conclude that rapid sequence divergence does not preclude RNA structure conservation in vertebrates, although these events are relatively rare.

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Oakley, Aaron J. "Hidden Glutathione Transferases in the Human Genome." Biomolecules 13, no. 8 (August 12, 2023): 1240. http://dx.doi.org/10.3390/biom13081240.

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With the development of accurate protein structure prediction algorithms, artificial intelligence (AI) has emerged as a powerful tool in the field of structural biology. AI-based algorithms have been used to analyze large amounts of protein sequence data including the human proteome, complementing experimental structure data found in resources such as the Protein Data Bank. The EBI AlphaFold Protein Structure Database (for example) contains over 230 million structures. In this study, these data have been analyzed to find all human proteins containing (or predicted to contain) the cytosolic glutathione transferase (cGST) fold. A total of 39 proteins were found, including the alpha-, mu-, pi-, sigma-, zeta- and omega-class GSTs, intracellular chloride channels, metaxins, multisynthetase complex components, elongation factor 1 complex components and others. Three broad themes emerge: cGST domains as enzymes, as chloride ion channels and as protein–protein interaction mediators. As the majority of cGSTs are dimers, the AI-based structure prediction algorithm AlphaFold-multimer was used to predict structures of all pairwise combinations of these cGST domains. Potential homo- and heterodimers are described. Experimental biochemical and structure data is used to highlight the strengths and limitations of AI-predicted structures.

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Livingstone, Kevin D., Vincent K. Lackney, James R. Blauth, Rik van Wijk, and Molly Kyle Jahn. "Genome Mapping in Capsicum and the Evolution of Genome Structure in the Solanaceae." Genetics 152, no. 3 (July 1, 1999): 1183–202. http://dx.doi.org/10.1093/genetics/152.3.1183.

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Abstract We have created a genetic map of Capsicum (pepper) from an interspecific F2 population consisting of 11 large (76.2–192.3 cM) and 2 small (19.1 and 12.5 cM) linkage groups that cover a total of 1245.7 cM. Many of the markers are tomato probes that were chosen to cover the tomato genome, allowing comparison of this pepper map to the genetic map of tomato. Hybridization of all tomato-derived probes included in this study to positions throughout the pepper map suggests that no major losses have occurred during the divergence of these genomes. Comparison of the pepper and tomato genetic maps showed that 18 homeologous linkage blocks cover 98.1% of the tomato genome and 95.0% of the pepper genome. Through these maps and the potato map, we determined the number and types of rearrangements that differentiate these species and reconstructed a hypothetical progenitor genome. We conclude there have been 30 breaks as part of 5 translocations, 10 paracentric inversions, 2 pericentric inversions, and 4 disassociations or associations of genomic regions that differentiate tomato, potato, and pepper, as well as an additional reciprocal translocation, nonreciprocal translocation, and a duplication or deletion that differentiate the two pepper mapping parents.

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Zhao, Xinmei, Chenglong Liu, Lijuan He, Zhiyong Zeng, Anda Zhang, Hui Li, Zhangli Hu, and Sulin Lou. "Structure and Phylogeny of Chloroplast and Mitochondrial Genomes of a Chlorophycean Algae Pectinodesmus pectinatus (Scenedesmaceae, Sphaeropleales)." Life 12, no. 11 (November 17, 2022): 1912. http://dx.doi.org/10.3390/life12111912.

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Pectinodesmus pectinatus is a green alga of commercial interest in sewage purification. Clarification of its organelle genomes is helpful for genetic manipulation, taxonomic revisions and evolutionary research. Here, de novo sequencing was used to determine chloroplast genome and mitochondrial genome of P. pectinatus strain F34. The chloroplast genome was composed of a large single-copy (LSC) region of 99,156 bp, a small single-copy (SSC) region of 70,665 bp, and a pair of inverted repeats (IRs) with a length of 13,494 bp each separated by LSC and SSC. The chloroplast genome contained 69 protein-coding genes, 25 transfer-RNA (tRNA) genes, 3 ribosomal RNA (rRNA) genes. The mitochondrial genome was 32,195 bp in length and consisted of 46 unique genes, including 16 protein-coding genes, 27 tRNA genes and 3 rRNA genes. The predominant mutations in organelle genomes were T/A to G/C transitions. Phylogenic analysis indicated P. pectinatus was a sister species to Tetradesmus obliquus and Hariotina sp. within the Pectinodesmus genus. In analysis with CGView Comparison Tool, P. pectinatus organelle genomes displayed the highest sequence similarity with that of T. obliquus. These findings advanced research on the taxonomy and phylogeny of Chlorophyceae algae and particularly revealed the role of P. pectinatus in microalgae evolution.

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Zirkel, Anne, and Argyris Papantonis. "Transcription as a force partitioning the eukaryotic genome." Biological Chemistry 395, no. 11 (November 1, 2014): 1301–5. http://dx.doi.org/10.1515/hsz-2014-0196.

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Abstract Eukaryotic genomes – until recently dealt with as if they were a cohort of linear DNA molecules – are perplexed three-dimensional structures, the exact conformation of which profoundly affects genome function. Recent advances in molecular biology and DNA sequencing technologies have led to a new understanding of the folding of chromatin in the nucleus. Changes in chromatin structure underlie deployment of new gene expression programs during development, differentiation, or disease. In this review, we revisit data pointing to, arguably, the major force that shapes genomes: transcription of DNA into RNA.

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Liang, Daqu, Haoyun Wang, Jun Zhang, Yuanxiang Zhao, and Feng Wu. "Complete Chloroplast Genome Sequence of Fagus longipetiolata Seemen (Fagaceae): Genome Structure, Adaptive Evolution, and Phylogenetic Relationships." Life 12, no. 1 (January 9, 2022): 92. http://dx.doi.org/10.3390/life12010092.

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Fagus longipetiolata Seemen is a deciduous tree of the Fagus genus in Fagaceae, which is endemic to China. In this study, we successfully sequenced the cp genome of F. longipetiolata, compared the cp genomes of the Fagus genus, and reconstructed the phylogeny of Fagaceae. The results showed that the cp genome of F. longipetiolata was 158,350 bp, including a pair of inverted repeat (IRA and IRB) regions with a length of 25,894 bp each, a large single-copy (LSC) region of 87,671 bp, and a small single-copy (SSC) region of 18,891 bp. The genome encoded 131 unique genes, including 81 protein-coding genes, 37 transfer RNA genes (tRNAs), 8 ribosomal RNA genes (rRNAs), and 5 pseudogenes. In addition, 33 codons and 258 simple sequence repeats (SSRs) were identified. The cp genomes of Fagus were relatively conserved, especially the IR regions, which showed the best conservation, and no inversions or rearrangements were found. The five regions with the largest variations were the rps12, rpl32, ccsA, trnW-CCA, and rps3 genes, which spread over in LSC and SSC. The comparison of gene selection pressure indicated that purifying selection was the main selective pattern maintaining important biological functions in Fagus cp genomes. However, the ndhD, rpoA, and ndhF genes of F. longipetiolata were affected by positive selection. Phylogenetic analysis revealed that F. longipetiolata and F. engleriana formed a close relationship, which partially overlapped in their distribution in China. Our analysis of the cp genome of F. longipetiolata would provide important genetic information for further research into the classification, phylogeny and evolution of Fagus.

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Journal articles on the topic 'Genome structure'

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