| Title |
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
|
|---|---|
| Published in |
BMC Genomics, June 2016
|
| DOI | 10.1186/s12864-016-2774-3 |
| Pubmed ID | |
| Authors |
Janine E. Deakin, Melanie J. Edwards, Hardip Patel, Denis O’Meally, Jinmin Lian, Rachael Stenhouse, Sam Ryan, Alexandra M. Livernois, Bhumika Azad, Clare E. Holleley, Qiye Li, Arthur Georges |
| Abstract |
Squamates (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. By 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. Anchoring 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. |
X Demographics
The data shown below were collected from the profiles of 21 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Australia | 2 | 10% |
| United States | 2 | 10% |
| Finland | 1 | 5% |
| Georgia | 1 | 5% |
| United Kingdom | 1 | 5% |
| Unknown | 14 | 67% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 14 | 67% |
| Scientists | 6 | 29% |
| Science communicators (journalists, bloggers, editors) | 1 | 5% |
Mendeley readers
The data shown below were compiled from readership statistics for 59 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Japan | 1 | 2% |
| Sweden | 1 | 2% |
| Unknown | 57 | 97% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 15 | 25% |
| Student > Ph. D. Student | 10 | 17% |
| Student > Master | 8 | 14% |
| Professor > Associate Professor | 4 | 7% |
| Student > Doctoral Student | 4 | 7% |
| Other | 8 | 14% |
| Unknown | 10 | 17% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 19 | 32% |
| Agricultural and Biological Sciences | 16 | 27% |
| Environmental Science | 2 | 3% |
| Computer Science | 2 | 3% |
| Business, Management and Accounting | 1 | 2% |
| Other | 5 | 8% |
| Unknown | 14 | 24% |
Attention Score in Context
This research output has an Altmetric Attention Score of 18. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 17 February 2019.
All research outputs
#1,772,393
of 23,342,092 outputs
Outputs from BMC Genomics
#428
of 10,745 outputs
Outputs of similar age
#33,799
of 346,815 outputs
Outputs of similar age from BMC Genomics
#11
of 181 outputs
Altmetric has tracked 23,342,092 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 92nd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 10,745 research outputs from this source. They receive a mean Attention Score of 4.7. This one has done particularly well, scoring higher than 96% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 346,815 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 90% of its contemporaries.
We're also able to compare this research output to 181 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 94% of its contemporaries.