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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., Holl, H. M., Brooks, S. A., Burger, P. A., & 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., Lhasaranov, B., Popov, R., Paronyan, I. A., Plemyashov, K. 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., Kukekova, V. A., Lynn Johnson, J., Lemskaya, A. N., Beklemisheva, R. V., Roelke-Parker, E. M., Bellizzi, J., Ryder, A. O., O’Brien, J. S., & 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., Fowler, K. E., Joseph, S., Swain, M. T., Griffin, D. K., & 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., Fonseka, G., Backstrom, N., Matsuda, Y., Nishida, C., Houde, P., Jarvis, E. D., Ellegren, H., Burt, D. W., Larkin, D. M., & 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
Presentation / Conference Contribution
Griffin, D. K., Farré, M., Lithgow, P., O'Connor, R., Fowler, K. E., Romanov, M. N., & Larkin, D. M. AVIAN CHROMONOMICS GOES FUNCTIONAL

Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers
Journal Article
Darolti, I., Wright, A. E., Sandkam, B. A., Morris, J., Bloch, N. I., Farré, M., Fuller, R. C., Bourne, G. R., Larkin, D. M., Breden, F., & Mank, J. E. (in press). Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers. https://doi.org/10.1073/pnas.1905298116

Morphologically and functionally distinct X and Y chromosomes have repeatedly evolved across the tree of life. However, the extent of differentiation between the sex chromosomes varies substantially across species. As sex chromosomes diverge, the Y c... Read More about Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers.

Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle
Journal Article
Larkin, D. M., Daetwyler, H. D., Hernandez, A. G., Wright, C. L., Hetrick, L. A., Boucek, L., Bachman, S. L., Band, M. R., Akraiko, T. V., Cohen-Zinder, M., Thimmapuram, J., Macleod, I. M., Harkins, T. T., McCague, J. E., Goddard, M. E., Hayes, B. J., & Lewin, H. A. (in press). Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle. https://doi.org/10.1073/pnas.1114546109

AVIAN CYTOGENETICS GOES FUNCTIONAL
Presentation / Conference Contribution
Griffin, D. K., Farré, M., Lithgow, P., O'Connor, R., Fowler, K. E., Romanov, M., & Larkin, D. M. AVIAN CYTOGENETICS GOES FUNCTIONAL

Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax
Journal Article
Fang, X. D., Nevo, E., Han, L. J., Levanon, E. Y., Zhao, J., Avivi, A., Larkin, D. M., Jiang, X. T., Feranchuk, S., Zhu, Y. B., Fishman, A., Feng, Y., Sher, N., Xiong, Z. Q., Hankeln, T., Huang, Z. Y., Gorbunova, V., Zhang, L., Zhao, W., Wildman, D. E., …Wang, J. Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax. Nature Communications, 5, https://doi.org/10.1038/ncomms4966