Relevant bibliographies by topics / Genome-wide re-sequencing

Academic literature on the topic 'Genome-wide re-sequencing'

Author: Grafiati
Published: 10 December 2022
Last updated: 28 January 2023

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Contents

Consult the lists of relevant articles, books, theses, conference reports, and other scholarly sources on the topic 'Genome-wide re-sequencing.'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Journal articles on the topic "Genome-wide re-sequencing"

1

Singh, P., A. Benjak, S. Carat, M. Kai, P. Busso, C. Avanzi, A. Paniz-Mondolfi, et al. "Genome-wide re-sequencing of multidrug-resistant Mycobacterium leprae Airaku-3." Clinical Microbiology and Infection 20, no. 10 (October 2014): O619—O622. http://dx.doi.org/10.1111/1469-0691.12609.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Lin, Miaomiao, Jinbao Fang, Chungen Hu, Xiujuan Qi, Shihang Sun, Jinyong Chen, Leiming Sun, and Yunpeng Zhong. "Genome-wide DNA polymorphisms in four Actinidia arguta genotypes based on whole-genome re-sequencing." PLOS ONE 15, no. 4 (April 10, 2020): e0219884. http://dx.doi.org/10.1371/journal.pone.0219884.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Yu, Xiaomin, Xujun Fu, Qinghua Yang, Hangxia Jin, Longming Zhu, and Fengjie Yuan. "Genome-Wide Variation Analysis of Four Vegetable Soybean Cultivars Based on Re-Sequencing." Plants 11, no. 1 (December 23, 2021): 28. http://dx.doi.org/10.3390/plants11010028.

Full text
Abstract:
Vegetable soybean is a type of value-added specialty soybean, served as a fresh vegetable or snack in China. Due to the difference from other types, it is important to understand the genetic structure and diversity of vegetable soybean for further utilization in breeding programs. The four vegetable cultivars, Taiwan-75, Zhexiandou No. 8, Zhexian No. 9 and Zhexian No. 10 are popular soybean varieties planted in Zhejiang province, and have large pods and intermediate maturity. The clustering showed a close relationship of these four cultivars in simple sequence repeat analysis. To reveal the genome variation of vegetable soybean, these four improved lines were analyzed by whole-genome re-sequencing. The average sequencing depth was 7X and the coverage ratio of each cultivar was at least more than 94%. Compared with the reference genome, a large number of single-nucleotide polymorphisms, insertion/deletions and structure variations were identified with different chromosome distributions. The average heterozygosity rate of the single-nucleotide polymorphisms was 11.99% of these four cultivars. According to the enrichment analysis, there were 23,371 genes identified with putative modifications, and a total of 282 genes were related to carbohydrate metabolic processes. These results provide useful information for genetic research and future breeding, which can facilitate the selection procedures in vegetable soybean breeding.
APA, Harvard, Vancouver, ISO, and other styles
4

Hoggart, Clive J., John C. Whittaker, Maria De Iorio, and David J. Balding. "Simultaneous Analysis of All SNPs in Genome-Wide and Re-Sequencing Association Studies." PLoS Genetics 4, no. 7 (July 25, 2008): e1000130. http://dx.doi.org/10.1371/journal.pgen.1000130.

Full text
APA, Harvard, Vancouver, ISO, and other styles
5

WANG, Kai, Ping-xian WU, De-juan CHEN, Jie ZHOU, Xi-di YANG, An-an JIANG, Ji-deng MA, et al. "Genome-wide scan for selection signatures based on whole-genome re-sequencing in Landrace and Yorkshire pigs." Journal of Integrative Agriculture 20, no. 7 (July 2021): 1898–906. http://dx.doi.org/10.1016/s2095-3119(20)63488-8.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

Liu, Z., H. Sun, W. Lai, M. Hu, Y. Zhang, C. Bai, J. Liu, H. Ren, F. Li, and S. Yan. "Genome‐wide re‐sequencing reveals population structure and genetic diversity of Bohai Black cattle." Animal Genetics 53, no. 1 (November 16, 2021): 133–36. http://dx.doi.org/10.1111/age.13155.

Full text
APA, Harvard, Vancouver, ISO, and other styles
7

E, Guangxin, B. ‐G Yang, W. ‐D Basang, Y. ‐B Zhu, T. ‐W An, and X. ‐L Luo. "Screening for signatures of selection of Tianzhu white yak using genome‐wide re‐sequencing." Animal Genetics 50, no. 5 (June 27, 2019): 534–38. http://dx.doi.org/10.1111/age.12817.

Full text
APA, Harvard, Vancouver, ISO, and other styles
8

Marques, João P., Fernando A. Seixas, Liliana Farelo, Colin M. Callahan, Jeffrey M. Good, W. Ian Montgomery, Neil Reid, Paulo C. Alves, Pierre Boursot, and José Melo-Ferreira. "An Annotated Draft Genome of the Mountain Hare (Lepus timidus)." Genome Biology and Evolution 12, no. 1 (December 13, 2019): 3656–62. http://dx.doi.org/10.1093/gbe/evz273.

Full text
Abstract:
Abstract Hares (genus Lepus) provide clear examples of repeated and often massive introgressive hybridization and striking local adaptations. Genomic studies on this group have so far relied on comparisons to the European rabbit (Oryctolagus cuniculus) reference genome. Here, we report the first de novo draft reference genome for a hare species, the mountain hare (Lepus timidus), and evaluate the efficacy of whole-genome re-sequencing analyses using the new reference versus using the rabbit reference genome. The genome was assembled using the ALLPATHS-LG protocol with a combination of overlapping pair and mate-pair Illumina sequencing (77x coverage). The assembly contained 32,294 scaffolds with a total length of 2.7 Gb and a scaffold N50 of 3.4 Mb. Re-scaffolding based on the rabbit reference reduced the total number of scaffolds to 4,205 with a scaffold N50 of 194 Mb. A correspondence was found between 22 of these hare scaffolds and the rabbit chromosomes, based on gene content and direct alignment. We annotated 24,578 protein coding genes by combining ab-initio predictions, homology search, and transcriptome data, of which 683 were solely derived from hare-specific transcriptome data. The hare reference genome is therefore a new resource to discover and investigate hare-specific variation. Similar estimates of heterozygosity and inferred demographic history profiles were obtained when mapping hare whole-genome re-sequencing data to the new hare draft genome or to alternative references based on the rabbit genome. Our results validate previous reference-based strategies and suggest that the chromosome-scale hare draft genome should enable chromosome-wide analyses and genome scans on hares.
APA, Harvard, Vancouver, ISO, and other styles
9

Huemer, Peter, Jean Haxaire, Kyung Min Lee, Marko Mutanen, Oleg Pekarsky, Stefano Scalercio, and László Ronkay. "Revision of the genus Hoplodrina Boursin, 1937 (Lepidoptera, Noctuidae, Xyleninae). I. Hoplodrina octogenaria (Goeze, 1781) and its sister species H. alsinides (Costantini, 1922) sp. rev. in Europe." ZooKeys 927 (April 16, 2020): 75–97. http://dx.doi.org/10.3897/zookeys.927.51142.

Full text
Abstract:
The taxonomic status of the European Hoplodrina octogenaria (Goeze, 1781) is discussed and its partly sympatric sister species, Hoplodrina alsinides (Costantini, 1922) sp. rev., is separated and re-described based on morphological and molecular taxonomic evidence. The adults and their genitalia are illustrated and DNA barcodes, as well as genome-wide single nucleotide polymorphism data collected by fractional genome sequencing (ddRAD), of the two species are provided.
APA, Harvard, Vancouver, ISO, and other styles
10

Eklöf, Helena, Carolina Bernhardsson, and Pär K. Ingvarsson. "Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies." Forests 11, no. 11 (November 10, 2020): 1185. http://dx.doi.org/10.3390/f11111185.

Full text
Abstract:
Conifer genomes are characterized by their large size and high abundance of repetitive material, making large-scale genotyping in conifers complicated and expensive. One of the consequences of this is that it has been difficult to generate data on genome-wide levels of genetic variation. To date, researchers have mainly employed various complexity reduction techniques to assess genetic variation across the genome in different conifer species. These methods tend to capture variation in a relatively small subset of a typical conifer genome and it is currently not clear how representative such results are. Here we take advantage of data generated in the first large-scale re-sequencing effort in Norway spruce and assess how well two commonly used complexity reduction methods, targeted capture probes and genotyping by sequencing perform in capturing genome-wide variation in Norway spruce. Our results suggest that both methods perform reasonably well for assessing genetic diversity and population structure in Norway spruce (Picea abies (L.) H. Karst.). Targeted capture probes were slightly more effective than GBS, likely due to them targeting known genomic regions whereas the GBS data contains a substantially greater fraction of repetitive regions, which sometimes can be problematic for assessing genetic diversity. In conclusion, both methods are useful for genotyping large numbers of samples and they greatly reduce the cost involved with genotyping a species with such a complex genome as Norway spruce.
APA, Harvard, Vancouver, ISO, and other styles
More sources

Dissertations / Theses on the topic "Genome-wide re-sequencing"

1

Pagani, Luca. "Through the layers of the Ethiopian genome : a survey of human genetic variation based on genome-wide genotyping and re-sequencing data." Thesis, University of Cambridge, 2013. https://www.repository.cam.ac.uk/handle/1810/251330.

Full text
Abstract:
Understanding our evolutionary history as a species has since long been one of the most attracting and controversial themes of the scientific investigation. From its geographical position, outstanding fossil record and richness of human diversity, the Horn of Africa and, particularly, the Ethiopian region offers an unmatched opportunity to investigate our origins from a genetic perspective. To carry out a genome-wide survey of this region, 13 out of the estimated 80 extant Ethiopian populations were typed on an Illumina Omni 1M SNP array. The results showed a good concordance between genetic and linguistic stratification and, overall, a complex population structure placing the Ethiopians in between North and Sub Saharan Africans, due to the recent non African gene flow which was dated at around 3000 years ago. Furthermore the SNP array data unveiled putative traces of the out of Africa migrations as well as, in two of the typed populations, signatures of genetic adaptation to high altitude. To obtain an unbiased, high resolution representation of the Ethiopian genetic landscape, 25 individuals from each of five populations were newly collected and sequenced on an Illumina HiSeq platform. These populations were chosen, from among the ones typed on the SNP array, to represent the main components of Ethiopian genetic diversity. Of the 25 samples per population, 24 were sequenced at low depth to generate a broad list of genetic variants, while one sample from each was sequenced at high depth to provide a higher resolution list of variants peculiar to each analysed population. The 125 Ethiopian genomes thus sequenced, while overall consistent with the genotyping results, described the Ethiopian populations in a less biased way than the SNP array data. Furthermore estimation of past effective population size fluctuations from the individual genomes unveiled a unique pattern in the ancestry of the Ethiopian populations in the early stages of human evolution. These results provide a data resource which can be used in future analyses.
APA, Harvard, Vancouver, ISO, and other styles

Book chapters on the topic "Genome-wide re-sequencing"

1

Krishnan, S. Gopala, Daniel L. E. Waters, and Robert J. Henry. "A Method for Discovery of Genome-Wide SNP Between Any Two Genotypes from Whole-Genome Re-sequencing Data." In Methods in Molecular Biology, 287–94. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-715-0_24.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Landau, Alejandra, Franco Lencina, María Elizabeth Petterson, María Gabriela Pacheco, Susana Costoya, Vanina Brizuela, and Alberto Prina. "The barley chloroplast mutator (cpm) mutant, an extraordinary source of plastome variability." In Mutation breeding, genetic diversity and crop adaptation to climate change, 271–79. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0027.

Full text
Abstract:
Abstract The plastome is usually considered a highly conserved genome. Compared with the nuclear genome, it is small and has different genetic rules. Through different molecular methods (TILLING, candidate gene sequencing, amplicon massive sequencing and plastome re-sequencing) applied to barley chloroplast mutator (cpm) seedlings, we detected more than 60 polymorphisms affecting a wide variety of plastid genes and several intergenic regions. The genes affected belonged mostly to the plastid genetic machinery and the photosynthetic apparatus, but there were also genes like matK, whose functions are so far not clearly established. Among the isolated mutants, we found the first infA gene mutant in higher plants, two mutants in ycf3 locus and the first psbA gene mutant in barley. The latter is used in breeding barley cultivars where PSII is tolerant to toxic herbicides. Most of the molecular changes were substitutions, and small indels located in microsatellites. However, particular combinations of polymorphisms observed in the rpl23 gene and pseudogene suggest that, besides an increased rate of mutations, an augmented rate of illegitimate recombination also occurred. Although a few substitutions were observed in the mitochondria of cpm plants, we have not yet determined the implications of the cpm for mitochondrial stability. The spectrum of plastome polymorphisms highly suggests that the cpm gene is involved in plastid DNA repair, more precisely taking part in the mismatch repair system. All results show that the cpm mutant is an extraordinary source of plastome variability for plant research and/or plant breeding. This mutant also provides an interesting experimental system in which to investigate the mechanisms responsible for maintaining plastid stability.
APA, Harvard, Vancouver, ISO, and other styles
3

Zhou, Li-bin, Yan Du, Zhuo Feng, Tao Cui, Xia Chen, Shan-wei Luo, Yu-ze Chen, et al. "Comparative study of mutations induced by carbon-ion beams and gamma-ray irradiations in Arabidopsis thaliana at the genome-wide scale." In Mutation breeding, genetic diversity and crop adaptation to climate change, 451–58. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0046.

Full text
Abstract:
Abstract Mutation breeding induced by irradiation with highly energetic photons and ion beams is one of the important methods to improve plant varieties, but the mutagenic effects and molecular mechanisms are often not entirely clear. Traditional research is focused on phenotype screening, chromosome aberration tests and genetic variation analysis of specific genes. The whole genome sequencing technique provides a new method to understand and undertake the comprehensive identification of mutations caused by irradiations with different linear energy transfer (LET). In this study, ten Arabidopsis thaliana M3 lines induced by carbon-ion beams (CIB) and ten M3 lines induced by gamma-rays were re-sequenced by using the Illumina HiSeq sequencing platform, and the single base substitutions (SBSs) and small insertions or deletions (indels) were analysed comparatively. It was found that the ratio of SBSs to small indels for M3 lines induced by CIB was 2.57:1, whereas the ratio was 1.78:1 for gamma-rays. The ratios of deletions to insertions for carbon ions and gamma-rays were 4.8:1 and 2.8:1, respectively. The single-base indels were more prevalent than those equal to or greater than 2 bp in both CIB and gamma-ray induced M3 lines. Among the detected SBSs, the ratio of transitions to transversions induced by carbon-ion irradiation was 1.01 and 1.42 for gamma-rays; these values differ greatly from the 2.41 reported for spontaneous substitutions. This study provides novel data on molecular characteristics of CIB and gamma-ray induced mutations at the genome-wide scale. It can also provide valuable clues for explaining the potential mechanism of plant mutation breeding by irradiations with different LETs.
APA, Harvard, Vancouver, ISO, and other styles

Reports on the topic "Genome-wide re-sequencing"

1

Gur, Amit, Edward Buckler, Joseph Burger, Yaakov Tadmor, and Iftach Klapp. Characterization of genetic variation and yield heterosis in Cucumis melo. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7600047.bard.

Full text
Abstract:
Project objectives: 1) Characterization of variation for yield heterosis in melon using Half-Diallele (HDA) design. 2) Development and implementation of image-based yield phenotyping in melon. 3) Characterization of genetic, epigenetic and transcriptional variation across 25 founder lines and selected hybrids. The epigentic part of this objective was modified during the course of the project: instead of characterization of chromatin structure in a single melon line through genome-wide mapping of nucleosomes using MNase-seq approach, we took advantage of rapid advancements in single-molecule sequencing and shifted the focus to Nanoporelong-read sequencing of all 25 founder lines. This analysis provides invaluable information on genome-wide structural variation across our diversity 4) Integrated analyses and development of prediction models Agricultural heterosis relates to hybrids that outperform their inbred parents for yield. First generation (F1) hybrids are produced in many crop species and it is estimated that heterosis increases yield by 15-30% globally. Melon (Cucumismelo) is an economically important species of The Cucurbitaceae family and is among the most important fleshy fruits for fresh consumption Worldwide. The major goal of this project was to explore the patterns and magnitude of yield heterosis in melon and link it to whole genome sequence variation. A core subset of 25 diverse lines was selected from the Newe-Yaar melon diversity panel for whole-genome re-sequencing (WGS) and test-crosses, to produce structured half-diallele design of 300 F1 hybrids (MelHDA25). Yield variation was measured in replicated yield trials at the whole-plant and at the rootstock levels (through a common-scion grafted experiments), across the F1s and parental lines. As part of this project we also developed an algorithmic pipeline for detection and yield estimation of melons from aerial-images, towards future implementation of such high throughput, cost-effective method for remote yield evaluation in open-field melons. We found extensive, highly heritable root-derived yield variation across the diallele population that was characterized by prominent best-parent heterosis (BPH), where hybrids rootstocks outperformed their parents by 38% and 56 % under optimal irrigation and drought- stress, respectively. Through integration of the genotypic data (~4,000,000 SNPs) and yield analyses we show that root-derived hybrids yield is independent of parental genetic distance. However, we mapped novel root-derived yield QTLs through genome-wide association (GWA) analysis and a multi-QTLs model explained more than 45% of the hybrids yield variation, providing a potential route for marker-assisted hybrid rootstock breeding. Four selected hybrid rootstocks are further studied under multiple scion varieties and their validated positive effect on yield performance is now leading to ongoing evaluation of their commercial potential. On the genomic level, this project resulted in 3 layers of data: 1) whole-genome short-read Illumina sequencing (30X) of the 25 founder lines provided us with 25 genome alignments and high-density melon HapMap that is already shown to be an effective resource for QTL annotation and candidate gene analysis in melon. 2) fast advancements in long-read single-molecule sequencing allowed us to shift focus towards this technology and generate ~50X Nanoporesequencing of the 25 founders which in combination with the short-read data now enable de novo assembly of the 25 genomes that will soon lead to construction of the first melon pan-genome. 3) Transcriptomic (3' RNA-Seq) analysis of several selected hybrids and their parents provide preliminary information on differentially expressed genes that can be further used to explain the root-derived yield variation. Taken together, this project expanded our view on yield heterosis in melon with novel specific insights on root-derived yield heterosis. To our knowledge, thus far this is the largest systematic genetic analysis of rootstock effects on yield heterosis in cucurbits or any other crop plant, and our results are now translated into potential breeding applications. The genomic resources that were developed as part of this project are putting melon in the forefront of genomic research and will continue to be useful tool for the cucurbits community in years to come.
APA, Harvard, Vancouver, ISO, and other styles
You might also be interested in the extended bibliographies on the topic 'Genome-wide re-sequencing' for particular source types:
Journal articles
We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!

To the bibliography