Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor

Journal article

Romanov, M., Farré, M., Lithgow, P., Fowler, K., Skinner, B., O'Connor, R., Fonseka, G., Backström, N., Matsuda, Y., Nishida, C., Houde, P., Jarvis, E., Hanson, E., Burt, D., Larkin, D. and Griffin, D. 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 (1060). https://doi.org/10.1186/1471-2164-15-1060
AuthorsRomanov, M., Farré, M., Lithgow, P., Fowler, K., Skinner, B., O'Connor, R., Fonseka, G., Backström, N., Matsuda, Y., Nishida, C., Houde, P., Jarvis, E., Hanson, E., Burt, D., Larkin, D. and Griffin, D.
Abstract

Background
The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed.

Results
Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n = 80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes.

Conclusions
Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g. in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.

Year2014
JournalBMC Genomics
Journal citation15 (1060)
PublisherBioMed Central
ISSN1471-2164
Digital Object Identifier (DOI)https://doi.org/10.1186/1471-2164-15-1060
Publication dates
Print11 Dec 2014
Publication process dates
Deposited18 Dec 2014
Accepted27 Nov 2014
Output statusPublished
File
Permalink -

https://repository.canterbury.ac.uk/item/87317/reconstruction-of-gross-avian-genome-structure-organization-and-evolution-suggests-that-the-chicken-lineage-most-closely-resembles-the-dinosaur-avian-ancestor

Download files

File
Fowler_Chicken_Lineage.pdf

  • 90
    total views
  • 117
    total downloads
  • 3
    views this month
  • 0
    downloads this month

Export as

Related outputs

Supplementation of porcin in vitro maturation medium with FGF2, LIF, and IGF1 enhances cytoplasmic maturation in prepubertal gilts oocytes and improves embryo quality
Serrano Albal, M., Silvestri, G., Kiazim, Lucas G., Vining, Lucy M., Zak, Louisa J., Walling, Grant A., Haigh, Alexandra M., Harvey, Simon C., Harvey, Katie E. and Griffin, Darren K. 2022. Supplementation of porcin in vitro maturation medium with FGF2, LIF, and IGF1 enhances cytoplasmic maturation in prepubertal gilts oocytes and improves embryo quality. Zygote (Cambridge, England). https://doi.org/10.1017/S0967199422000284
The role of apoptosis in cryopreserved animal oocytes and embryos
Vining, Lucy May, Zak, Louisa J, Harvey, Simon Crawford and Harvey, K. 2021. The role of apoptosis in cryopreserved animal oocytes and embryos. Theriogenology. 173, pp. 93-101. https://doi.org/S0093-691X(21)00242-9
Identification of optimal assisted aspiration conditions of oocytes for use in porcine in vitro maturation: a re-evaluation of the relationship between the cumulus oocyte complex and oocyte quality
Silvestri, S., Rathje, C.C., Harvey, S.C., Gould, R.L., Walling, G.A., Ellis, P.J.I., Harvey, K.E. and Griffin D.K. 2020. Identification of optimal assisted aspiration conditions of oocytes for use in porcine in vitro maturation: a re-evaluation of the relationship between the cumulus oocyte complex and oocyte quality. Veterinary Medicine and Science.
Eukaryotic response to hypothermia in relation to integrated stress responses
Adjirackor, N. A., Harvey, K. E. and Harvey, S. C. 2020. Eukaryotic response to hypothermia in relation to integrated stress responses. Cell Stress & Chaperones.
Cryopreservation produces limited long-term effects on the nematode Caenorhabditis elegans
Stastna, J., Yiapanas, A., Mandawala, D., Fowler, K. and Harvey, S. 2019. Cryopreservation produces limited long-term effects on the nematode Caenorhabditis elegans . Cryobiology . https://doi.org/0.​1016/​j.​cryobiol.​2019.​11.​039
The role of chromosome segregation and nuclear organisation in human subfertility
Fowler, K., Mandawala, A. and Griffin, D. 2019. The role of chromosome segregation and nuclear organisation in human subfertility. Biochemical Society Transactions. 47 (1), pp. 425-432. https://doi.org/10.1042/BST20180231
The production of pig preimplantation embryos in vitro: current progress and future prospects
Fowler, K., Mandawala, A., Griffin, D., Walling, G. and Harvey, S. 2018. The production of pig preimplantation embryos in vitro: current progress and future prospects. Reproductive Biology. 18 (3), pp. 203-211. https://doi.org/10.1016/j.repbio.2018.07.001
Canine recommended breed weight ranges are not a good predictor of an ideal body condition score
Smith, E., Davis, K., Sulsh, L., Harvey, S., Fowler, K., Canterbury Christ Church University and Portland Road Veterinary Surgery 2018. Canine recommended breed weight ranges are not a good predictor of an ideal body condition score. Journal Of Animal Physiology And Nutrition. 102 (4), pp. 1088-1090. https://doi.org/10.1111/jpn.12919
Time-lapse embryo imaging and morphokinetic profiling: towards a general characterisation of embryogenesis
Mandawala, A., Harvey, S., Roy, T. and Fowler, K. 2016. Time-lapse embryo imaging and morphokinetic profiling: towards a general characterisation of embryogenesis. Animal Reproduction Science. 174, pp. 2-10. https://doi.org/10.1016/j.anireprosci.2016.09.015
Cryopreservation of animal oocytes and embryos: current progress and future prospects
Mandawala, A., Harvey, S., Roy, T. and Fowler, K. 2016. Cryopreservation of animal oocytes and embryos: current progress and future prospects. Theriogenology. 86 (7), pp. 1637-1644. https://doi.org/10.1016/j.theriogenology.2016.07.018
Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
Damas, J., O'Connor, R., Farré, M., Lenis, V., Martell, H., Mandawala, A., Fowler, K., Joseph, S., Swain, M., Griffin, D. and Larkin, D. 2016. Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Research.
Multicolour detection of every chromosome as a means of detecting mosaicism and nuclear organisation in human embryonic nuclei
Turner, K., Fowler, K., Fonseka, G., Griffin, D. and Ioannou, D. 2016. Multicolour detection of every chromosome as a means of detecting mosaicism and nuclear organisation in human embryonic nuclei. Panminerva Medica.
[Avian cytogenetics goes functional] Third report on chicken genes and chromosomes 2015
Grffin, D., Romanov, M., O'Connor, R., Fowler, K. and Larkin, D. 2015. [Avian cytogenetics goes functional] Third report on chicken genes and chromosomes 2015. Cytogenetic and Genome Research. 145 (2), pp. 78-179. https://doi.org/10.1159/000430927
20th International Chromosome Conference (ICCXX)
Griffin, D., Fowler, K., Ellis, P. and Jackson, D. 2015. 20th International Chromosome Conference (ICCXX). Chromosome Research. https://doi.org/10.1007/s10577-014-9447-3
Novel approach for deriving genome wide SNP analysis data from archived blood spots
Fowler, K., Reitter, C., Walling, G. and Griffin, D. 2012. Novel approach for deriving genome wide SNP analysis data from archived blood spots. BMC Research Notes. 5 (1), p. 503. https://doi.org/10.1186/1756-0500-5-503
Analyses of pig genomes provide insight into porcine demography and evolution
Groenen, M., Archibald, A., Uenishi, H., Tuggle, C., Takeuchi, Y., Rothschild, M., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H., Li, S., Larkin, D., Kim, H., Frantz, L., Caccamo, M., Ahn, H., Aken, B., Anselmo, A., Anthon, C., Auvil, L., Badaoui, B., Beattie, C., Bendixen, C., Berman, D., Blecha, F., Blomberg, J., Bolund, L., Bosse, M., Botti, S., Bujie, Z., Bystrom, M., Capitanu, B., Carvalho-Silva, D., Chardon, P., Chen, C., Cheng, R., Choi, S., Chow, W., Clark, R., Clee, C., Crooijmans, R., Dawson, H., Dehais, P., De Sapio, F., Dibbits, B., Drou, N., Du, Z., Eversole, K., Fadista, J., Fairley, S., Faraut, T., Faulkner, G., Fowler, K., Fredholm, M., Fritz, E., Gilbert, J., Giuffra, E., Gorodkin, J., Griffin, D., Harrow, J., Hayward, A., Howe, K., Hu, Z., Humphray, S., Hunt, T., Hornshøj, H., Jeon, J., Jern, P., Jones, M., Jurka, J., Kanamori, H., Kapetanovic, R., Kim, J., Kim, J., Kim, K., Kim, T., Larson, G., Lee, K., Lee, K., Leggett, R., Lewin, H., Li, Y., Liu, W., Loveland, J., Lu, Y., Lunney, J., Ma, J., Madsen, O., Mann, K., Matthews, L., McLaren, S., Morozumi, T., Murtaugh, M., Narayan, J., Truong Nguyen, D., Ni, P., Oh, S., Onteru, S., Panitz, F., Park, E., Park, H., Pascal, G., Paudel, Y., Perez-Enciso, M., Ramirez-Gonzalez, R., Reecy, J., Rodriguez-Zas, S., Rohrer, G., Rund, L., Sang, Y., Schachtschneider, K., Schraiber, J., Schwartz, J., Scobie, L., Scott, C., Searle, S., Servin, B., Southey, B., Sperber, G., Stadler, P., Sweedler, J., Tafer, H., Thomsen, B., Wali, R., Wang, J., Wang, J., White, S., Xu, X., Yerle, M., Zhang, G., Zhang, J., Zhang, J., Zhao, S., Rogers, J., Churcher, C. and Schook, L. 2012. Analyses of pig genomes provide insight into porcine demography and evolution. Nature. 491 (7424), pp. 393-398. https://doi.org/10.1038/nature11622
Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis
Skinner, B., Robertson, L., Tempest, H., Langley, E., Ioannou, D., Fowler, K., Crooijmans, R., Hall, A., Griffin, D. and Völker, M. 2009. Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis. BMC Genomics. 10 (1), p. 357. https://doi.org/10.1186/1471-2164-10-357
Genome wide analysis reveals single nucleotide polymorphisms associated with fatness and putative novel copy number variants in three pig breeds
Fowler, K., Pong-Wong, R., Bauer, J., Clemente, E., Reitter, C., Affara, N., Waite, S., Walling, G. and Griffin, D. 2013. Genome wide analysis reveals single nucleotide polymorphisms associated with fatness and putative novel copy number variants in three pig breeds. BMC Genomics. 14 (1), p. 784. https://doi.org/10.1186/1471-2164-14-784