Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers

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

doi:10.1073/pnas.1905298116

RECONSTRUCTION OF THE PUTATIVE SAURIAN KARYOTYPE AND THE HYPOTHETICAL CHROMOSOME REARRANGEMENTS THAT OCCURRED ALONG THE DINOSUAR LINEAGE
Journal Article
O'Connor, R. E., Romanov, M. N., Farré, M., Larkin, D. M., & Griffin, D. K. RECONSTRUCTION OF THE PUTATIVE SAURIAN KARYOTYPE AND THE HYPOTHETICAL CHROMOSOME REARRANGEMENTS THAT OCCURRED ALONG THE DINOSUAR LINEAGE. Chromosome Research, 23(2), 379-380

AVIAN ANCESTRAL KARYOTYPE RECONSTRUCTION AND DIFFERENTIAL RATES OF INTER-AND INTRA-CHROMOSOMAL CHANGE IN DIFFERENT LINEAGES
Journal Article
Romanov, M. N., Farré, M., Lithgow, P. E., O'Connor, R., Fowler, K. E., Skinner, B. M., …Griffin, D. K. AVIAN ANCESTRAL KARYOTYPE RECONSTRUCTION AND DIFFERENTIAL RATES OF INTER-AND INTRA-CHROMOSOMAL CHANGE IN DIFFERENT LINEAGES. Chromosome Research, 23(2), 414-414

Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax
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Fang, X. D., Nevo, E., Han, L. J., Levanon, E. Y., Zhao, J., Avivi, A., …Wang, J. Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax. Nature Communications, 5, https://doi.org/10.1038/ncomms4966

AVIAN CYTOGENETICS GOES FUNCTIONAL
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Griffin, D. K., Farré, M., Lithgow, P., O'Connor, R., Fowler, K. E., Romanov, M., & Larkin, D. M. AVIAN CYTOGENETICS GOES FUNCTIONAL. Chromosome Research, 22(3), 423-424

Reference-assisted chromosome assembly
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Kim, J., Larkin, D. M., Asan, Q. C., Zhang, Y. F., Ge, R. L., Auvil, L., …Maj, J. Reference-assisted chromosome assembly. https://doi.org/10.1073/pnas.1220349110

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., …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

Analyses of pig genomes provide insight into porcine demography and evolution
Journal Article
Larkin, D. M. Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491(7424), 393-398. https://doi.org/10.1038/nature11622

AMNIOTE EVOLUTION: THE ROLE OF CHROMOSOME REARRANGEMENTS
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Farré, M., Narayan, J., Slavov, G. T., Auvil, L., Lewin, H. A., & Larkin, D. M. AMNIOTE EVOLUTION: THE ROLE OF CHROMOSOME REARRANGEMENTS. Chromosome Research, 23(2), 366-366

GENOMIC SIGNATURES OF EVOLUTIONARY RESHUFFLING IN MAMMALS
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Capilla, L., Sanchez-Guillen, R. A., Farré, M., Larkin, D. M., Ventura, J., & Ruiz-Herrera, A. GENOMIC SIGNATURES OF EVOLUTIONARY RESHUFFLING IN MAMMALS. Chromosome Research, 23(2), 375-375

Third Report on Chicken Genes and Chromosomes 2015
Journal Article
Schmid, M., Smith, J., Burt, D. W., Aken, B. L., Antin, P. B., Archibald, A. L., …Larkin, D. M. (in press). Third Report on Chicken Genes and Chromosomes 2015. Cytogenetic and Genome Research, 145, 78-179. https://doi.org/10.1159/000430927

Population structure and history of the Welsh sheep breeds determined by whole genome genotyping
Journal Article
Beynon, S. E., Slavov, G. T., Farré, M., Sunduimijid, B., Waddams, K., Davies, B., …Larkin, D. M. (in press). Population structure and history of the Welsh sheep breeds determined by whole genome genotyping. BMC Genetics, 16(65), https://doi.org/10.1186/s12863-015-0216-x

Synteny Explorer: An Interactive Visualization Application for Teaching Genome Evolution
Journal Article
Bryan, C., Guterman, G., Ma, K., Lewin, H., Larkin, D. M., Kim, J., …Farre Belmonte, M. Synteny Explorer: An Interactive Visualization Application for Teaching Genome Evolution. IEEE Transactions on Visualization and Computer Graphics, 23(1), 711-720. https://doi.org/10.1109/TVCG.2016.2598460

Novel insights into chromosome evolution in birds, archosaurs, and reptiles
Journal Article
Farré, M., Narayan, J., Slavov, G. T., Damas, J., Auvil, L., Li, C., …Larkin, D. M. (in press). Novel insights into chromosome evolution in birds, archosaurs, and reptiles. Genome Biology and Evolution, 8(8), 2442-2451. https://doi.org/10.1093/gbe/evw166

Homologous synteny blocks (HSBs) and evolutionary breakpoint regions (EBRs) in mammalian chromosomes are enriched for distinct DNA features, contributing to distinct phenotypes. To reveal HSB and EBR roles in avian evolution, we performed a sequence-... Read More about Novel insights into chromosome evolution in birds, archosaurs, and reptiles.

Contrasting origin of B chromosomes in two cervids (Siberian roe deer and grey brocket deer) unravelled by chromosome-specific DNA sequencing
Journal Article
Makunin, A., Kichigin, I. G., Larkin, D. M., O'Brien, P. C. M., Ferguson-Smith, M. A., Yang, F., …Trifonov, V. (in press). Contrasting origin of B chromosomes in two cervids (Siberian roe deer and grey brocket deer) unravelled by chromosome-specific DNA sequencing. BMC Genomics, 17(1), 618. https://doi.org/10.1186/s12864-016-2933-6

Turning back the evolutionary clock
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Larkin, D. M. Turning back the evolutionary clock

G-Anchor: a novel approach for whole-genome comparative mapping utilising evolutionary conserved DNA sequences
Journal Article
Lenis, V. E., Swain, M., & Larkin, D. M. (in press). G-Anchor: a novel approach for whole-genome comparative mapping utilising evolutionary conserved DNA sequences. GigaScience, 7(5), https://doi.org/10.1093/gigascience/giy017

Here we introduce G-Anchor, a new, fast, and efficient pipeline that uses a strictly limited but highly effective set of local sequence alignments to anchor (or map) an animal genome to another species’ reference genome. G-Anchor makes novel use of a... Read More about G-Anchor: a novel approach for whole-genome comparative mapping utilising evolutionary conserved DNA sequences.

Shared signatures of selection related to adaptation and acclimation in local cattle and sheep breeds from Russia
Journal Article
Yudin, N., & Larkin, D. M. Shared signatures of selection related to adaptation and acclimation in local cattle and sheep breeds from Russia. Russian Journal of Genetics, 55(8), 1008-1014. https://doi.org/10.1134/S1022795419070159

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., …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.

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