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Journal articles on the topic 'Animal genomics'

To see the other types of publications on this topic, follow the link: Animal genomics.

Author: Grafiati

Published: 10 December 2022

Last updated: 28 January 2023

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1

Song, Luting, and Wen Wangs. "Genomes and evolutionary genomics of animals." Current Zoology 59, no. 1 (February 1, 2013): 87–98. http://dx.doi.org/10.1093/czoolo/59.1.87.

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Abstract Alongside recent advances and booming applications of DNA sequencing technologies, a great number of complete genome sequences for animal species are available to researchers. Hundreds of animals have been involved in whole genome sequencing, and at least 87 non-human animal species’ complete or draft genome sequences have been published since 1998. Based on these technological advances and the subsequent accumulation of large quantity of genomic data, evolutionary genomics has become one of the most rapidly advancing disciplines in biology. Scientists now can perform a number of comparative and evolutionary genomic studies for animals, to identify conserved genes or other functional elements among species, genomic elements that confer animals their own specific characteristics and new phenotypes for adaptation. This review deals with the current ge-nomic and evolutionary research on non-human animals, and displays a comprehensive landscape of genomes and the evolutionary genomics of non-human animals. It is very helpful to a better understanding of the biology and evolution of the myriad forms within the animal kingdom.

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2

Tellam, R. "Animal Genomics." Australian Veterinary Journal 82, no. 7 (July 2004): 425. http://dx.doi.org/10.1111/j.1751-0813.2004.tb11134.x.

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3

Lopez, Jose V., Bishoy Kamel, Mónica Medina, Timothy Collins, and Iliana B. Baums. "Multiple Facets of Marine Invertebrate Conservation Genomics." Annual Review of Animal Biosciences 7, no. 1 (February 15, 2019): 473–97. http://dx.doi.org/10.1146/annurev-animal-020518-115034.

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Conservation genomics aims to preserve the viability of populations and the biodiversity of living organisms. Invertebrate organisms represent 95% of animal biodiversity; however, few genomic resources currently exist for the group. The subset of marine invertebrates includes the most ancient metazoan lineages and possesses codes for unique gene products and possible keys to adaptation. The benefits of supporting invertebrate conservation genomics research (e.g., likely discovery of novel genes, protein regulatory mechanisms, genomic innovations, and transposable elements) outweigh the various hurdles (rare, small, or polymorphic starting materials). Here we review best conservation genomics practices in the laboratory and in silico when applied to marine invertebrates and also showcase unique features in several case studies of acroporid corals, crown-of-thorns starfish, apple snails, and abalone. Marine conservation genomics should also address how diversity can lead to unique marine innovations, the impact of deleterious variation, and how genomic monitoring and profiling could positively affect broader conservation goals (e.g., value of baseline data for in situ/ex situ genomic stocks).

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4

Ponce de León, F. Abel, and Gustavo A. Gutierrez. "Genomics and animal production." Revista Peruana de Biología 27, no. 1 (March 4, 2020): 015–20. http://dx.doi.org/10.15381/rpb.v27i1.17574.

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Developing countries have the challenge of achieving food security in a world context that is affected by climate change and global population growth. Molecular Genetics and genomics are proposed as technologies that will help to achieve sustainable food security. Technologies that have been developed in the last decade such as the development of genetic markers, genetic maps, genomic selection, next-generation sequencing, and DNA editing systems are discussed. Examples of some discoveries and achievements are provided.

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Smith, Timothy P. "226 Genomics in animal agriculture: current technologies and applications." Journal of Animal Science 97, Supplement_3 (December 2019): 55–56. http://dx.doi.org/10.1093/jas/skz258.113.

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Abstract The early impact of genomic research on animal agriculture was relatively modest, as it proved difficult to translate quantitative trait loci mapping to industrial application. Fortunately, developments in technology have facilitated the application of genomics to animal agriculture, which has led to more substantial impacts on many commercially produced animal species. A brief look back on the history of genomic research will be presented, followed by an overview of recent developments in genomic technologies. Examples of application of genomic research, focusing on beef cattle and comparative genomics with other bovinae specie, and the current status of some new genomic resources emerging for sheep, pigs, and goats, will also be presented.

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Burton, Jeanne L., and Guilherme J. M. Rosa. "Physiological genomics special issue on animal functional genomics." Physiological Genomics 28, no. 1 (December 2006): 1–4. http://dx.doi.org/10.1152/physiolgenomics.00220.2006.

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7

Giuffra, Elisabetta, and Christopher K. Tuggle. "Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap." Annual Review of Animal Biosciences 7, no. 1 (February 15, 2019): 65–88. http://dx.doi.org/10.1146/annurev-animal-020518-114913.

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Functional annotation of genomes is a prerequisite for contemporary basic and applied genomic research, yet farmed animal genomics is deficient in such annotation. To address this, the FAANG (Functional Annotation of Animal Genomes) Consortium is producing genome-wide data sets on RNA expression, DNA methylation, and chromatin modification, as well as chromatin accessibility and interactions. In addition to informing our understanding of genome function, including comparative approaches to elucidate constrained sequence or epigenetic elements, these annotation maps will improve the precision and sensitivity of genomic selection for animal improvement. A scientific community–driven effort has already created a coordinated data collection and analysis enterprise crucial for the success of this global effort. Although it is early in this continuing process, functional data have already been produced and application to genetic improvement reported. The functional annotation delivered by the FAANG initiative will add value and utility to the greatly improved genome sequences being established for domesticated animal species.

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8

Passamonti, Matilde Maria, Elisa Somenzi, Mario Barbato, Giovanni Chillemi, Licia Colli, Stéphane Joost, Marco Milanesi, et al. "The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock." Animals 11, no. 10 (September 28, 2021): 2833. http://dx.doi.org/10.3390/ani11102833.

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Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.

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9

Hien, Le Thi Thu, Nguyen Tuong Van, Kim Thi Phuong Oanh, Nguyen Dang Ton, Huynh Thi Thu Hue, Nguyen Thuy Duong, Pham Le Bich Hang, and Nguyen Hai Ha. "Genomics and big data: Research, development and applications." Vietnam Journal of Biotechnology 19, no. 3 (October 13, 2021): 393–410. http://dx.doi.org/10.15625/1811-4989/16158.

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Recent years, genomics and big data analytics have been widely applied and have significant impacts in various important areas of social life worldwide. The development of the next-generation sequencing (NGS) technologies, such as whole-genome sequencing (WGS), whole-exome sequencing (WES), transcriptome, and/or targeted sequencing, has enabled quickly generating the genomes of interested living organisms. Around the world many nations have invested in and promoted the development of genomics and big data analytics. A number of well-established projects on sequencing of human, animal, plant, and microorganism genomes to generate vast amounts of genomic data have been conducted independently or as collaborative efforts by national or international research networks of scientists specializing in different technical fields of genomics, bioinformatics, computational and statistical biology, automation, artificial intelligence, etc. Complicated and large genomic datasets have been effectively established, storage, managed, and used. Vietnam supports this new field of study through setting up governmental authorized institutions and conducting genomic research projects of human and other endemic organisms. In this paper, the research, development, and applications of genomic big data are reviewed with focusing on: (i) Available sequencing technologies for generating genomic datasets; (ii) Genomics and big data initiatives worldwide; (iii) Genomics and big data analytics in selected countries and Vietnam; (iv) Genomic data applications in key areas including medicine for human health care, agriculture - forestry, food safety, and environment.

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van Oers, Kees, and Jakob C. Mueller. "Evolutionary genomics of animal personality." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1560 (December 27, 2010): 3991–4000. http://dx.doi.org/10.1098/rstb.2010.0178.

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Research on animal personality can be approached from both a phenotypic and a genetic perspective. While using a phenotypic approach one can measure present selection on personality traits and their combinations. However, this approach cannot reconstruct the historical trajectory that was taken by evolution. Therefore, it is essential for our understanding of the causes and consequences of personality diversity to link phenotypic variation in personality traits with polymorphisms in genomic regions that code for this trait variation. Identifying genes or genome regions that underlie personality traits will open exciting possibilities to study natural selection at the molecular level, gene–gene and gene–environment interactions, pleiotropic effects and how gene expression shapes personality phenotypes. In this paper, we will discuss how genome information revealed by already established approaches and some more recent techniques such as high-throughput sequencing of genomic regions in a large number of individuals can be used to infer micro-evolutionary processes, historical selection and finally the maintenance of personality trait variation. We will do this by reviewing recent advances in molecular genetics of animal personality, but will also use advanced human personality studies as case studies of how molecular information may be used in animal personality research in the near future.

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Kyselová, Jitka, Ladislav Tichý, and Kateřina Jochová. "The role of molecular genetics in animal breeding: A minireview." Czech Journal of Animal Science 66, No. 4 (March 26, 2021): 107–11. http://dx.doi.org/10.17221/251/2020-cjas.

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Current animal breeding approaches are strongly associated with the development of sophisticated molecular genetics methods and techniques. Worldwide expansion of genomic selection can be achieved by the identification of genetic DNA markers and implementation of the microarray (“chip”) technology. Further advancement was associated with next-generation sequencing methods, high-throughput genotyping platforms, targeted genome editing techniques, and studies of epigenetic mechanisms. The remarkable development of “omics” technologies, such as genomics, epigenomics, transcriptomics, proteomics and metabolomics, has enabled individual genomic prediction of animal performance, identification of disease-causing genes and biomarkers for the prevention and treatment and overall qualitative progress in animal production.

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12

Steiner, Cynthia C., Andrea S. Putnam, Paquita E. A. Hoeck, and Oliver A. Ryder. "Conservation Genomics of Threatened Animal Species." Annual Review of Animal Biosciences 1, no. 1 (January 2013): 261–81. http://dx.doi.org/10.1146/annurev-animal-031412-103636.

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13

Blackburn, Harvey D., Ted Manahan, Carrie S. Wilson, Wenkai Fu, Eduardo Cajueiro, Milton G. Thomas, and Samuel Paiva. "333 Animal –GRIN a platform for animal genetic information." Journal of Animal Science 97, Supplement_3 (December 2019): 49. http://dx.doi.org/10.1093/jas/skz258.098.

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Abstract An information system, Animal-GRIN, has been constructed as part of the U.S., Brazilian, and Canadian livestock genetic resource programs. It is designed to provide information to gene bank managers, the research community, and livestock producers about livestock breeds and subpopulations acquired in gene bank collections. The system was developed using a range of free software tools, including: MySQL, Ruby on Rails, Java Script, etc. The system is dynamic and publically accessible (https://nrrc.ars.usda.gov/A-GRIN). Exemplary information in Animal-GRIN consists of: animal identifiers, number and type of samples in the collection, pedigrees, coefficients of genetic relationships between animals within a breed, breeding values, phenotypes, and geographic source. To meet the national need for the long term archiving of genomic information developed with public funds, Animal-GRIN was expanded to store and make publically available genomic information (SNP) from any SNP chip, including custom products. Researchers are encouraged to submit their data upon completion of their publically funded projects. With the drill down concept, users can search the database for genomic information, physical samples associated with the genomic information, and phenotypic information on specific animals. Once animals of interest are found, on-line tools enable users to request either germplasm samples or genomic data. Progress in meeting genetic security for a breed’s collection can also be viewed. To date the U.S. collection has 52,639 animals with almost a million samples representing 36 species, 167 breeds, and 331 subpopulations and these have been entered into Animal-GRIN. Genomic data has been acquired on 1,899 animals representing 36 breeds. The next phase of Animal-GRIN development will be development of landscape genomics components. Acquisition of germplasm samples and associated genomic information are a continuing effort.

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14

López-Escardó, David, Xavier Grau-Bové, Amy Guillaumet-Adkins, Marta Gut, Michael E. Sieracki, and Iñaki Ruiz-Trillo. "Reconstruction of protein domain evolution using single-cell amplified genomes of uncultured choanoflagellates sheds light on the origin of animals." Philosophical Transactions of the Royal Society B: Biological Sciences 374, no. 1786 (October 7, 2019): 20190088. http://dx.doi.org/10.1098/rstb.2019.0088.

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Understanding the origins of animal multicellularity is a fundamental biological question. Recent genome data have unravelled the role that co-option of pre-existing genes played in the origin of animals. However, there were also some important genetic novelties at the onset of Metazoa. To have a clear understanding of the specific genetic innovations and how they appeared, we need the broadest taxon sampling possible, especially among early-branching animals and their unicellular relatives. Here, we take advantage of single-cell genomics to expand our understanding of the genomic diversity of choanoflagellates, the sister-group to animals. With these genomes, we have performed an updated and taxon-rich reconstruction of protein evolution from the Last Eukaryotic Common Ancestor (LECA) to animals. Our novel data re-defines the origin of some genes previously thought to be metazoan-specific, like the POU transcription factor, which we show appeared earlier in evolution. Moreover, our data indicate that the acquisition of new genes at the stem of Metazoa was mainly driven by duplications and protein domain rearrangement processes at the stem of Metazoa. Furthermore, our analysis allowed us to reveal protein domains that are essential to the maintenance of animal multicellularity. Our analyses also demonstrate the utility of single-cell genomics from uncultured taxa to address evolutionary questions. This article is part of a discussion meeting issue ‘Single cell ecology’.

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15

Van Eenennaam, Alison L., Kent A. Weigel, Amy E. Young, Matthew A. Cleveland, and Jack C. M. Dekkers. "Applied Animal Genomics: Results from the Field." Annual Review of Animal Biosciences 2, no. 1 (February 2014): 105–39. http://dx.doi.org/10.1146/annurev-animal-022513-114119.

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16

Wang, Guo-Dong, Hai-Bing Xie, Min-Sheng Peng, David Irwin, and Ya-Ping Zhang. "Domestication Genomics: Evidence from Animals." Annual Review of Animal Biosciences 2, no. 1 (February 2014): 65–84. http://dx.doi.org/10.1146/annurev-animal-022513-114129.

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17

Oldenbroek, J. Kor. "The Use of Genomic Information for the Conservation of Animal Genetic Diversity." Animals 11, no. 11 (November 10, 2021): 3208. http://dx.doi.org/10.3390/ani11113208.

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The conservation of genetic diversity, both among and within breeds, is a costly process. Therefore, choices between breeds and animals within breeds are unavoidable, either for conservation in vitro (gene banks) or in vivo (maintaining small populations alive). Nowadays, genomic information on breeds and individual animals is the standard for the choices to be made in conservation. Genomics may accurately measure the genetic distances among breeds and the relationships among animals within breeds. Homozygosity at loci and at parts of chromosomes is used to measure inbreeding. In addition, genomics can be used to detect potentially valuable rare alleles and haplotypes, their carriers in these breeds and can facilitate in vivo or in vitro conservations of these genomic regions.

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18

Cakir, M., M. Bellgard, R. Appels, and M. Francki. "Looking through genomics: concepts and technologies for plant and animal genomics." Functional & Integrative Genomics 4, no. 2 (May 1, 2004): 71–73. http://dx.doi.org/10.1007/s10142-004-0115-0.

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19

Slagboom, P. E., M. Beekman, W. M. Passtoors, J. Deelen, A. A. M. Vaarhorst, J. M. Boer, E. B. van den Akker, et al. "Genomics of human longevity." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1561 (January 12, 2011): 35–42. http://dx.doi.org/10.1098/rstb.2010.0284.

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In animal models, single-gene mutations in genes involved in insulin/IGF and target of rapamycin signalling pathways extend lifespan to a considerable extent. The genetic, genomic and epigenetic influences on human longevity are expected to be much more complex. Strikingly however, beneficial metabolic and cellular features of long-lived families resemble those in animals for whom the lifespan is extended by applying genetic manipulation and, especially, dietary restriction. Candidate gene studies in humans support the notion that human orthologues from longevity genes identified in lower species do contribute to longevity but that the influence of the genetic variants involved is small. Here we discuss how an integration of novel study designs, labour-intensive biobanking, deep phenotyping and genomic research may provide insights into the mechanisms that drive human longevity and healthy ageing, beyond the associations usually provided by molecular and genetic epidemiology. Although prospective studies of humans from the cradle to the grave have never been performed, it is feasible to extract life histories from different cohorts jointly covering the molecular changes that occur with age from early development all the way up to the age at death. By the integration of research in different study cohorts, and with research in animal models, biological research into human longevity is thus making considerable progress.

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Canchaya, Carlos, Caroline Proux, Ghislain Fournous, Anne Bruttin, and Harald Brüssow. "Prophage Genomics." Microbiology and Molecular Biology Reviews 67, no. 2 (June 2003): 238–76. http://dx.doi.org/10.1128/mmbr.67.2.238-276.2003.

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SUMMARY The majority of the bacterial genome sequences deposited in the National Center for Biotechnology Information database contain prophage sequences. Analysis of the prophages suggested that after being integrated into bacterial genomes, they undergo a complex decay process consisting of inactivating point mutations, genome rearrangements, modular exchanges, invasion by further mobile DNA elements, and massive DNA deletion. We review the technical difficulties in defining such altered prophage sequences in bacterial genomes and discuss theoretical frameworks for the phage-bacterium interaction at the genomic level. The published genome sequences from three groups of eubacteria (low- and high-G+C gram-positive bacteria and γ-proteobacteria) were screened for prophage sequences. The prophages from Streptococcus pyogenes served as test case for theoretical predictions of the role of prophages in the evolution of pathogenic bacteria. The genomes from further human, animal, and plant pathogens, as well as commensal and free-living bacteria, were included in the analysis to see whether the same principles of prophage genomics apply for bacteria living in different ecological niches and coming from distinct phylogenetical affinities. The effect of selection pressure on the host bacterium is apparently an important force shaping the prophage genomes in low-G+C gram-positive bacteria and γ-proteobacteria.

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Hori, Hiroshi, and Nori Satoh. "[Comparative Genomics of Animals]." Zoological Science 22, no. 12 (December 2005): 1377–79. http://dx.doi.org/10.2108/zsj.22.1377.

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22

Liu, Fuyun, Yuli Li, Hongwei Yu, Lingling Zhang, Jingjie Hu, Zhenmin Bao, and Shi Wang. "MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca." Nucleic Acids Research 49, no. D1 (October 22, 2020): D988—D997. http://dx.doi.org/10.1093/nar/gkaa918.

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Abstract Mollusca represents the second largest animal phylum but remains poorly explored from a genomic perspective. While the recent increase in genomic resources holds great promise for a deep understanding of molluscan biology and evolution, access and utilization of these resources still pose a challenge. Here, we present the first comprehensive molluscan genomics database, MolluscDB (http://mgbase.qnlm.ac), which compiles and integrates current molluscan genomic/transcriptomic resources and provides convenient tools for multi-level integrative and comparative genomic analyses. MolluscDB enables a systematic view of genomic information from various aspects, such as genome assembly statistics, genome phylogenies, fossil records, gene information, expression profiles, gene families, transcription factors, transposable elements and mitogenome organization information. Moreover, MolluscDB offers valuable customized datasets or resources, such as gene coexpression networks across various developmental stages and adult tissues/organs, core gene repertoires inferred for major molluscan lineages, and macrosynteny analysis for chromosomal evolution. MolluscDB presents an integrative and comprehensive genomics platform that will allow the molluscan community to cope with ever-growing genomic resources and will expedite new scientific discoveries for understanding molluscan biology and evolution.

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C.M. Dekkers, Jack. "Application of Genomics Tools to Animal Breeding." Current Genomics 13, no. 3 (April 1, 2012): 207–12. http://dx.doi.org/10.2174/138920212800543057.

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San-Jose, Luis M., and Alexandre Roulin. "Genomics of coloration in natural animal populations." Philosophical Transactions of the Royal Society B: Biological Sciences 372, no. 1724 (May 22, 2017): 20160337. http://dx.doi.org/10.1098/rstb.2016.0337.

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Animal coloration has traditionally been the target of genetic and evolutionary studies. However, until very recently, the study of the genetic basis of animal coloration has been mainly restricted to model species, whereas research on non-model species has been either neglected or mainly based on candidate approaches, and thereby limited by the knowledge obtained in model species. Recent high-throughput sequencing technologies allow us to overcome previous limitations, and open new avenues to study the genetic basis of animal coloration in a broader number of species and colour traits, and to address the general relevance of different genetic structures and their implications for the evolution of colour. In this review, we highlight aspects where genome-wide studies could be of major utility to fill in the gaps in our understanding of the biology and evolution of animal coloration. The new genomic approaches have been promptly adopted to study animal coloration although substantial work is still needed to consider a larger range of species and colour traits, such as those exhibiting continuous variation or based on reflective structures. We argue that a robust advancement in the study of animal coloration will also require large efforts to validate the functional role of the genes and variants discovered using genome-wide tools. This article is part of the themed issue ‘Animal coloration: production, perception, function and application’.

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Scott, M. P. "Developmental genomics of the most dangerous animal." Proceedings of the National Academy of Sciences 104, no. 29 (July 9, 2007): 11865–66. http://dx.doi.org/10.1073/pnas.0704795104.

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Fadiel, A. "Farm animal genomics and informatics: an update." Nucleic Acids Research 33, no. 19 (October 24, 2005): 6308–18. http://dx.doi.org/10.1093/nar/gki931.

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Luo, Shu-Jin, Yue-Chen Liu, and Xiao Xu. "Tigers of the World: Genomics and Conservation." Annual Review of Animal Biosciences 7, no. 1 (February 15, 2019): 521–48. http://dx.doi.org/10.1146/annurev-animal-020518-115106.

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Of all the big cats, or perhaps of all the endangered wildlife, the tiger may be both the most charismatic and most well-recognized flagship species in the world. The rapidly changing field of molecular genetics, particularly advances in genome sequencing technologies, has provided new tools to reconstruct what characterizes a tiger. Here we review how applications of molecular genomic tools have been used to depict the tiger's ancestral roots, phylogenetic hierarchy, demographic history, morphological diversity, and genetic patterns of diversification on both temporal and geographical scales. Tiger conservation, stabilization, and management are important areas that benefit from use of these genome resources for developing survival strategies for this charismatic megafauna both in situ and ex situ.

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Rothschild, Max F., and Graham S. Plastow. "Impact of genomics on animal agriculture and opportunities for animal health." Trends in Biotechnology 26, no. 1 (January 2008): 21–25. http://dx.doi.org/10.1016/j.tibtech.2007.10.001.

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Waples, Robin S., Kerry A. Naish, and Craig R. Primmer. "Conservation and Management of Salmon in the Age of Genomics." Annual Review of Animal Biosciences 8, no. 1 (February 15, 2020): 117–43. http://dx.doi.org/10.1146/annurev-animal-021419-083617.

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Salmon were among the first nonmodel species for which systematic population genetic studies of natural populations were conducted, often to support management and conservation. The genomics revolution has improved our understanding of the evolutionary ecology of salmon in two major ways: ( a) Large increases in the numbers of genetic markers (from dozens to 104–106) provide greater power for traditional analyses, such as the delineation of population structure, hybridization, and population assignment, and ( b) qualitatively new insights that were not possible with traditional genetic methods can be achieved by leveraging detailed information about the structure and function of the genome. Studies of the first type have been more common to date, largely because it has taken time for the necessary tools to be developed to fully understand the complex salmon genome. We expect that the next decade will witness many new studies that take full advantage of salmonid genomic resources.

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Dhanapal, Arun Prabhu, and Mahalingam Govindaraj. "Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement." Genetics Research International 2015 (March 19, 2015): 1–15. http://dx.doi.org/10.1155/2015/684321.

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The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences. The importance of databases keeps increasing as the volume of datasets from direct and indirect genomics, as well as other omics approaches, keeps expanding in recent years. The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants. The utilization of these databases in applied crop improvement program is still being achieved widely; otherwise, the end for sequencing is not far away.

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Brown, Louise, and Frans van der Ouderaa. "Nutritional genomics: food industry applications from farm to fork." British Journal of Nutrition 97, no. 6 (June 2007): 1027–35. http://dx.doi.org/10.1017/s0007114507691983.

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Nutritional genomics is a new and promising science area which can broadly be defined as the application of high throughput genomics (transcriptomics, proteomics, metabolomics/metabonomics) and functional genomic technologies to the study of nutritional sciences and food technology. First utilised in the food industry by plant biotechnologists to manipulate plant biosynthetic pathways, the use of genomic technologies has now spread within the agriculture sector, unleashing a host of new applications (e.g. approaches for producing novel, non-transgenic plant varietals; identification of genetic markers to guide plant and animal breeding programmes; exploration of diet–gene interactions for enhancing product quality and plant/animal health). Beyond agriculture, genomic technologies are also contributing to the improvement of food processing, food safety and quality assurance as well as the development of functional food products and the evolution of new health management concepts such as ‘personalised nutrition’, an emerging paradigm in which the diet of an individual is customised, based on their own genomic information, to optimise health and prevent disease. In this review the relevance of nutritional genomics to the food industry will be considered and examples given on how this science area is starting to be leveraged for economic benefits and to improve human nutrition and health.

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Armstrong, Joel, Ian T. Fiddes, Mark Diekhans, and Benedict Paten. "Whole-Genome Alignment and Comparative Annotation." Annual Review of Animal Biosciences 7, no. 1 (February 15, 2019): 41–64. http://dx.doi.org/10.1146/annurev-animal-020518-115005.

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Rapidly improving sequencing technology coupled with computational developments in sequence assembly are making reference-quality genome assembly economical. Hundreds of vertebrate genome assemblies are now publicly available, and projects are being proposed to sequence thousands of additional species in the next few years. Such dense sampling of the tree of life should give an unprecedented new understanding of evolution and allow a detailed determination of the events that led to the wealth of biodiversity around us. To gain this knowledge, these new genomes must be compared through genome alignment (at the sequence level) and comparative annotation (at the gene level). However, different alignment and annotation methods have different characteristics; before starting a comparative genomics analysis, it is important to understand the nature of, and biases and limitations inherent in, the chosen methods. This review is intended to act as a technical but high-level overview of the field that should provide this understanding. We briefly survey the state of the genome alignment and comparative annotation fields and potential future directions for these fields in a new, large-scale era of comparative genomics.

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Oliveira, Guilherme, Nilton B. Rodrigues, Alvaro J. Romanha, and Diana Bahia. "Genome and genomics of schistosomes." Canadian Journal of Zoology 82, no. 2 (February 1, 2004): 375–90. http://dx.doi.org/10.1139/z03-220.

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Schistosomes infect over 200 million people and 600 million are at risk. Genomics and post-genomic studies of schistosomes will contribute greatly to developing new reagents for diagnostic purposes and new vaccines that are of interest to the biotechnology industry. In this review, the most recent advances in these fields as well as new projects and future perspectives will de described. A vast quantity of data is publicly available, including short cDNA and genomic sequences, complete large genomic fragments, and the mitochondrial genomes of three species of the genus Schistosoma. The physical structure of the genome is being studied by physically mapping large genomic fragments and characterizing the highly abundant repetitive DNA elements. Bioinformatic manipulations of the data have already been carried out, mostly dealing with the functional analysis of the genes described. Specific search tools have also been developed. Sequence variability has been used to better understand the phylogeny of the species and for population studies, and new polymorphic genomic markers are currently being developed. The information generated has been used for the development of post-genomic projects. A small microarray detected genes that were differentially expressed between male and female worms. The identification of two-dimensional spots by mass spectrometry has also been demonstrated.

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Piórkowska, Katarzyna, and Katarzyna Ropka-Molik. "Pig Genomics and Genetics." Genes 12, no. 11 (October 25, 2021): 1692. http://dx.doi.org/10.3390/genes12111692.

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Tuggle, Christopher K., and Elisabetta Giuffra. "29 Introduction to functional annotation of animal genomes consortium." Journal of Animal Science 97, Supplement_2 (July 2019): 17. http://dx.doi.org/10.1093/jas/skz122.031.

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Abstract The annotation of the functional components of genomes is required for both basic and applied genomic research, yet farmed animal genomics are deficient in such annotation. This talk will introduce the Functional Annotation of ANimal Genomes (FAANG) consortium, which was initiated in 2014 to address this knowledge deficit. An overarching theme of early FAANG efforts is the collaborative approach required for such comprehensive research, thus another emphasis of this talk will be our community efforts to develop the environment for successful FAANG research. FAANG scientists have created a coordinated data collection and analysis enterprise crucial for success of this global effort, and funding of ~$20 million has been secured for current projects in several species, with an anticipated doubling of this support during 2019. Member FAANG consortium labs are producing genome-wide datasets on RNA expression, DNA methylation, chromatin modification, chromatin accessibility, and chromatin interactions for many agriculturally relevant animal species. The goal of a first-generation global chromatin state map for cattle, chicken, pig, and potentially other species is projected for completion in the next 3–5 years. These data will be used both to better understand animal genome function at the epigenetic level, as well as improve the precision and sensitivity of genomic selection for animal improvement. The functional annotation delivered by the FAANG initiative will add value and utility to the greatly improved genome sequences being established for domesticated animal species.

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Shaffer, H. Bradley, Müge Gidiş, Evan McCartney-Melstad, Kevin M. Neal, Hilton M. Oyamaguchi, Marisa Tellez, and Erin M. Toffelmier. "Conservation Genetics and Genomics of Amphibians and Reptiles." Annual Review of Animal Biosciences 3, no. 1 (February 16, 2015): 113–38. http://dx.doi.org/10.1146/annurev-animal-022114-110920.

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SMITH, J., A. GHEYAS, and D. W. BURT. "Animal genomics and infectious disease resistance in poultry." Revue Scientifique et Technique de l'OIE 35, no. 1 (April 1, 2016): 105–19. http://dx.doi.org/10.20506/rst.35.1.2421.

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COWLED, C., and L. F. WANG. "Animal genomics in natural reservoirs of infectious diseases." Revue Scientifique et Technique de l'OIE 35, no. 1 (April 1, 2016): 159–74. http://dx.doi.org/10.20506/rst.35.1.2425.

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Yamamura, Ken-ichi. "Animal Model as a tool for Medical Genomics." Ensho Saisei 23, no. 5 (2003): 269–74. http://dx.doi.org/10.2492/jsir.23.269.

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Bagnato, Alessandro, and Andrea Rosati. "From the Editors—Animal selection: The genomics revolution." Animal Frontiers 2, no. 1 (January 1, 2012): 1–2. http://dx.doi.org/10.2527/af.2011-0033.

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van Arendonk, J. A. M., and A. E. Liinamo. "Animal breeding and genomics: Perspectives for dog breeding." Veterinary Journal 170, no. 1 (July 2005): 3–5. http://dx.doi.org/10.1016/j.tvjl.2004.05.006.

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Else, Holly. "Genomics institute to close world-leading animal facility." Nature 569, no. 7758 (May 2019): 612. http://dx.doi.org/10.1038/d41586-019-01685-7.

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Harlizius, Barbara, Rik van Wijk, and Jan W. M. Merks. "Genomics for food safety and sustainable animal production." Journal of Biotechnology 113, no. 1-3 (September 2004): 33–42. http://dx.doi.org/10.1016/j.jbiotec.2004.03.021.

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Frantz, Laurent A. F., Daniel G. Bradley, Greger Larson, and Ludovic Orlando. "Animal domestication in the era of ancient genomics." Nature Reviews Genetics 21, no. 8 (April 7, 2020): 449–60. http://dx.doi.org/10.1038/s41576-020-0225-0.

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Plastow, Graham Stuart. "Genomics to benefit livestock production: improving animal health." Revista Brasileira de Zootecnia 45, no. 6 (June 2016): 349–54. http://dx.doi.org/10.1590/s1806-92902016000600010.

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Appels, Rudi, Johan Nystrom, Hollie Webster, and Gabriel Keeble-Gagnere. "Discoveries and advances in plant and animal genomics." Functional & Integrative Genomics 15, no. 2 (March 2015): 121–29. http://dx.doi.org/10.1007/s10142-015-0434-3.

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Albertin, Caroline B., and Oleg Simakov. "Cephalopod Biology: At the Intersection Between Genomic and Organismal Novelties." Annual Review of Animal Biosciences 8, no. 1 (February 15, 2020): 71–90. http://dx.doi.org/10.1146/annurev-animal-021419-083609.

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Cephalopods are resourceful marine predators that have fascinated generations of researchers as well as the public owing to their advanced behavior, complex nervous system, and significance in evolutionary studies. Recent advances in genomics have accelerated the pace of cephalopod research. Many traditional areas focusing on evolution, development, behavior, and neurobiology, primarily on the morphological level, are now transitioning to molecular approaches. This review addresses the recent progress and impact of genomic and other molecular resources on research in cephalopods. We outline several key directions in which significant progress in cephalopod research is expected and discuss its impact on our understanding of the genetic background behind cephalopod biology and beyond.

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Pérez‐Enciso, Miguel. "Breeding beyond genomics." Journal of Animal Breeding and Genetics 138, no. 3 (April 22, 2021): 275–76. http://dx.doi.org/10.1111/jbg.12547.

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Kadarmideen, Haja N., Peter von Rohr, and Luc L. G. Janss. "From genetical genomics to systems genetics: potential applications in quantitative genomics and animal breeding." Mammalian Genome 17, no. 6 (June 2006): 548–64. http://dx.doi.org/10.1007/s00335-005-0169-x.

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JACKSON, ANDREW P. "Genome evolution in trypanosomatid parasites." Parasitology 142, S1 (July 28, 2014): S40—S56. http://dx.doi.org/10.1017/s0031182014000894.

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SUMMARYA decade of genome sequencing has transformed our understanding of how trypanosomatid parasites have evolved and provided fresh impetus to explaining the origins of parasitism in the Kinetoplastida. In this review, I will consider the many ways in which genome sequences have influenced our view of genomic reduction in trypanosomatids; how species-specific genes, and the genomic domains they occupy, have illuminated the innovations in trypanosomatid genomes; and how comparative genomics has exposed the molecular mechanisms responsible for innovation and adaptation to a parasitic lifestyle.

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