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Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation (2018)
Journal Article
Joseph, S., O'Connor, R. E., Al Mutery, A., Watson, M., Larkin, D. M., & Griffin, D. (2018). Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation. Diversity, 10(4), 113. https://doi.org/10.3390/d10040113

Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its k... Read More about Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation.

Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation (2018)
Journal Article
Yurchenko, A. A., Daetwyler, H. D., Yudin, N., Schnabel, R. D., Vander Jagt, C. J., Soloshenko, V., …Larkin, D. M. (2018). Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation. https://doi.org/10.1038/s41598-018-31304-w

Domestication and selective breeding has resulted in over 1000 extant cattle breeds. Many of these breeds do not excel in important traits but are adapted to local environments. These adaptations are a valuable source of genetic material for efforts... Read More about Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation.

Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly (2018)
Journal Article
Rando, H., Farré, M., Robson, M., Won, N., Johnson, J., Buch, R., …Kukekova, A. (2018). Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly. Genes, 9(6), 308. https://doi.org/10.3390/genes9060308

The genome of a red fox (Vulpes vulpes) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which... Read More about Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly.

Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs (2018)
Journal Article
O'Connor, R. E., Romanov, M. N., Kiazim, L. G., Barrett, P. M., Farre Belmonte, M., Damas, J., …Griffin, D. K. (2018). Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs. Nature Communications, 9(1), 1883. https://doi.org/10.1038/s41467-018-04267-9

Genomic organisation of extinct lineages can be inferred from extant chromosome-level genome assemblies. Here, we apply bioinformatic and molecular cytogenetic approaches to determine the genomic structure of the diapsid common ancestor. We then infe... Read More about Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs.

Chromosome Segregation Is Biased by Kinetochore Size (2018)
Journal Article
Drpic, D., Almeida, A. C., Aguiar, P., Renda, F., Damas, J., Lewin, H. A., …Maiato, H. (2018). Chromosome Segregation Is Biased by Kinetochore Size. Current Biology, 28(9), 1344-1365. https://doi.org/10.1016/j.cub.2018.03.023

Chromosome missegregation during mitosis or meiosis is a hallmark of cancer and the main cause of prenatal death in humans. The gain or loss of specific chromosomes is thought to be random, with cell viability being essentially determined by selectio... Read More about Chromosome Segregation Is Biased by Kinetochore Size.

Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000RAD and 15000RAD (2018)
Journal Article
Perelman, P. L., Pichler, R., Gaggl, A., Larkin, D. M., Raudsepp, T., Alshanbari, F., …Periasamy, K. (2018). Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000RAD and 15000RAD. Scientific Reports, 8(1), https://doi.org/10.1038/s41598-018-20223-5

The availability of genomic resources including linkage information for camelids has been very limited. Here, we describe the construction of a set of two radiation hybrid (RH) panels (5000RAD and 15000RAD) for the dromedary (Camelus dromedarius) as... Read More about Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000RAD and 15000RAD.

A compendium and functional characterization of mammalian genes involved in adaptation to Arctic or Antarctic environments (2017)
Journal Article
Yudin, N. S., Larkin, D. M., & Ignatieva, E. V. (2017). A compendium and functional characterization of mammalian genes involved in adaptation to Arctic or Antarctic environments. BMC Genetics, 18, https://doi.org/10.1186/s12863-017-0580-9

Many mammals are well adapted to surviving in extremely cold environments. These species have likely accumulated genetic changes that help them efficiently cope with low temperatures. It is not known whether the same genes related to cold adaptation... Read More about A compendium and functional characterization of mammalian genes involved in adaptation to Arctic or Antarctic environments.

Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds (2017)
Journal Article
Yurchenko, A., Yudin, N., Aitnazarov, R., Plyusnina, A., Brukhin, V., Soloshenko, V., …Larkin, D. M. (2017). Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds. Heredity, 120(2), 125-137. https://doi.org/10.1038/s41437-017-0024-3

One of the most economically important areas within the Russian agricultural sector is dairy and beef cattle farming contributing about $11 billion to the Russian economy annually. Trade connections, selection and breeding have resulted in the establ... Read More about Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds.

X Chromosome Evolution in Cetartiodactyla (2017)
Journal Article
Proskuryakova, A. A., Kulemzina, A. I., Perelman, P. L., Makunin, I. A., Larkin, D. M., Farré, M., …Graphodatsky, S. A. (2017). X Chromosome Evolution in Cetartiodactyla. Genes, 8(9), 216. https://doi.org/10.3390/genes8090216

The phenomenon of a remarkable conservation of the X chromosome in eutherian mammals has been first described by Susumu Ohno in 1964. A notable exception is the cetartiodactyl X chromosome, which varies widely in morphology and G-banding pattern betw... Read More about X Chromosome Evolution in Cetartiodactyla.

Reconstruction and evolutionary history of eutherian chromosomes (2017)
Journal Article
Kim, J., Farre Belmonte, M., Auvil, L. S., Capitanu, B., Larkin, D. M., Ma, J., & Lewin, H. A. (2017). Reconstruction and evolutionary history of eutherian chromosomes. Proceedings of the National Academy of Sciences, 114(27), E5379-E5388. https://doi.org/10.1073/pnas.1702012114

Whole-genome assemblies of 19 placental mammals and two outgroup species were used to reconstruct the order and orientation of syntenic fragments in chromosomes of the eutherian ancestor and six other descendant ancestors leading to human. For ancest... Read More about Reconstruction and evolutionary history of eutherian chromosomes.

Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set (2017)
Journal Article
Damas, J., O'Connor, R., Farré, M., Lenis, V. P. E., Martell, H. J., Mandawala, A., …Larkin, D. M. (2017). Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Research, 27, 697-708. https://doi.org/10.1101/gr.213660.116

Most recent initiatives to sequence and assemble new species’ genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist... Read More about Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set.

The genomes and history of domestic animals (2017)
Journal Article
Larkin, D. M., & Yudin, N. S. (2017). The genomes and history of domestic animals. Molecular Genetics, Microbiology and Virology, 31(4), 197-202. https://doi.org/10.3103/S0891416816040054

This paper reviews how mammalian genomes are utilized in modern genetics for the detection of genes and polymorphisms (mutations) within domesticated animal (mostly livestock) genomes that are related to traits of economic importance to humans. Examp... Read More about The genomes and history of domestic animals.

Identification of a nonsense mutation in APAF1 that is likely causal for a decrease in reproductive efficiency in Holstein dairy cattle (2016)
Journal Article
Adams, H. A., Sonstegard, T. S., VanRaden, P. M., Null, D. J., Van Tassell, C. P., Larkin, D. M., & Lewin, H. A. (2016). Identification of a nonsense mutation in APAF1 that is likely causal for a decrease in reproductive efficiency in Holstein dairy cattle. Journal of Dairy Science, 99(8), 6693-6701. https://doi.org/10.3168/jds.2015-10517

Comparative genomics reveals insights into avian genome evolution and adaptation (2014)
Journal Article
Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., & Lee, C. (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311-1320. https://doi.org/10.1126/science.1251385

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is prin... Read More about Comparative genomics reveals insights into avian genome evolution and adaptation.

Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor (2014)
Journal Article
Romanov, M. N., Farré, M., Lithgow, P. E., Fowler, K. E., Skinner, B. M., O'Connor, R., …Griffin, D. K. (2014). Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics, 15, https://doi.org/10.1186/1471-2164-15-1060

AVIAN CHROMONOMICS GOES FUNCTIONAL
Journal Article
Griffin, D. K., Farré, M., Lithgow, P., O'Connor, R., Fowler, K. E., Romanov, M. N., & Larkin, D. M. AVIAN CHROMONOMICS GOES FUNCTIONAL. Chromosome Research, 23(2), 367-367

The Genome 10K Project: A Way Forward Further
Journal Article
Koepfli, K. P., Paten, B., Antunes, A., Belov, K., Bustamante, C., Castoe, T. A., …O'Brien, S. J. The Genome 10K Project: A Way Forward Further. Annual Review of Animal Biosciences, 3, 57-111. https://doi.org/10.1146/annurev-animal-090414-014900

The Genome 10K Project was established in 2009 by a consortium of biologists and genome scientists determined to facilitate the sequencing and analysis of the complete genomes of 10,000 vertebrate species. Since then the number of selected and initia... Read More about The Genome 10K Project: A Way Forward Further.