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PMID: 17307883 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 104 ·No. 8 ·2007-02-20 ·Pages 2767-72

Shedlock AM, Botka CW, Zhao S, Shetty J, Zhang T, Liu JS, Deschavanne PJ, Edwards SV

Abstract

We report results of a megabase-scale phylogenomic analysis of the Reptilia, the sister group of mammals. Large-scale end-sequence scanning of genomic clones of a turtle, alligator, and lizard reveals diverse, mammal-like landscapes of retroelements and simple sequence repeats (SSRs) not found in the chicken. Several global genomic traits, including distinctive phylogenetic lineages of CR1-like long interspersed elements (LINEs) and a paucity of A-T rich SSRs, characterize turtles and archosaur genomes, whereas higher frequencies of tandem repeats and a lower global GC content reveal mammal-like features in Anolis. Nonavian reptile genomes also possess a high frequency of diverse and novel 50-bp unit tandem duplications not found in chicken or mammals. The frequency distributions of approximately 65,000 8-mer oligonucleotides suggest that rates of DNA-word frequency change are an order of magnitude slower in reptiles than in mammals. These results suggest a diverse array of interspersed and SSRs in the common ancestor of amniotes and a genomic conservatism and gradual loss of retroelements in reptiles that culminated in the minimalist chicken genome. The sequences reported in this paper have been deposited in the GenBank database (accession nos. CZ 250707-CZ 257443 and DX 390731-DX 389174).

MeSH Terms
Animals Base Composition/genetics Birds/genetics Genetic Variation Genome/genetics Genomics Mammals/genetics Molecular Sequence Data Phylogeny Reptiles/genetics Retroelements/genetics Tandem Repeat Sequences/genetics
Chemicals
Retroelements
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Shedlock Andrew M
Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA. [email protected]
Botka Christopher W
Zhao Shaying
Shetty Jyoti
Zhang Tingting
Liu Jun S
Deschavanne Patrick J
Edwards Scott V
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.0606204104
Email
[email protected]
Published
2007-02-20
Epub
2007-00-16
Pages
2767-72
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC1815256
Subset
IM
Databases
GENBANK
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PubMed source DOI: 10.1073/pnas.0606204104 PMC Full Text View journal details
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