Anchoring genome sequence to chromosomes of the central bearded dragon (Pogona vitticeps) enables reconstruction of ancestral squamate macrochromosomes and identifies sequence content of the Z chromosome

BMC Genomics

Research Article

Jinmin Lian¹  Qiye Li²  Clare E. Holleley³  Alexandra M. Livernois³  Denis O’Meally³  Sam Ryan³  Janine E. Deakin³  Melanie J. Edwards³  Rachael Stenhouse³  Arthur Georges³  Bhumika Azad⁴  Hardip Patel⁵ 

[1] China National GeneBank, BGI-Shenzhen, 518083, Shenzhen, China;China National GeneBank, BGI-Shenzhen, 518083, Shenzhen, China;Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark;Institute for Applied Ecology, University of Canberra, ACT 2601, Canberra, Australia;Institute for Applied Ecology, University of Canberra, ACT 2601, Canberra, Australia;John Curtin School of Medical Research, Australian National University, ACT 2601, Canberra, Australia;John Curtin School of Medical Research, Australian National University, ACT 2601, Canberra, Australia;

关键词: Cytogenetic map;    Genome evolution;    Ancestral karyotype;    Reptile;    Macrochromosome;    Microchromosome;    Sex chromosome;    Sex determination;   

DOI  :  10.1186/s12864-016-2774-3

 received in 2016-02-22, accepted in 2016-05-25,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundSquamates (lizards and snakes) are a speciose lineage of reptiles displaying considerable karyotypic diversity, particularly among lizards. Understanding the evolution of this diversity requires comparison of genome organisation between species. Although the genomes of several squamate species have now been sequenced, only the green anole lizard has any sequence anchored to chromosomes. There is only limited gene mapping data available for five other squamates. This makes it difficult to reconstruct the events that have led to extant squamate karyotypic diversity. The purpose of this study was to anchor the recently sequenced central bearded dragon (Pogona vitticeps) genome to chromosomes to trace the evolution of squamate chromosomes. Assigning sequence to sex chromosomes was of particular interest for identifying candidate sex determining genes.ResultsBy using two different approaches to map conserved blocks of genes, we were able to anchor approximately 42 % of the dragon genome sequence to chromosomes. We constructed detailed comparative maps between dragon, anole and chicken genomes, and where possible, made broader comparisons across Squamata using cytogenetic mapping information for five other species. We show that squamate macrochromosomes are relatively well conserved between species, supporting findings from previous molecular cytogenetic studies. Macrochromosome diversity between members of the Toxicofera clade has been generated by intrachromosomal, and a small number of interchromosomal, rearrangements. We reconstructed the ancestral squamate macrochromosomes by drawing upon comparative cytogenetic mapping data from seven squamate species and propose the events leading to the arrangements observed in representative species. In addition, we assigned over 8 Mbp of sequence containing 219 genes to the Z chromosome, providing a list of genes to begin testing as candidate sex determining genes.ConclusionsAnchoring of the dragon genome has provided substantial insight into the evolution of squamate genomes, enabling us to reconstruct ancestral macrochromosome arrangements at key positions in the squamate phylogeny, demonstrating that fusions between macrochromosomes or fusions of macrochromosomes and microchromosomes, have played an important role during the evolution of squamate genomes. Assigning sequence to the sex chromosomes has identified NR5A1 as a promising candidate sex determining gene in the dragon.

【 授权许可】

CC BY   
© The Author(s). 2016