Tandem amino acid repeats in the green anole Anolis carolinensis and other squamates may have a role in increasing genetic variabilityReport as inadecuate

Tandem amino acid repeats in the green anole Anolis carolinensis and other squamates may have a role in increasing genetic variability - Download this document for free, or read online. Document in PDF available to download.

BMC Genomics

, 17:109

Comparative and evolutionary genomics


BackgroundTandem amino acid repeats are characterised by the consecutive recurrence of a single amino acid. They exhibit high rates of length mutations in addition to point mutations and have been proposed to be involved in genetic plasticity. Squamate reptiles lizards and snakes diversify in both morphology and physiology. The underlying mechanism is yet to be understood. In a previous phylogenomic analysis of reptiles, the density of tandem repeats in an anole lizard diverged heavily from that of the other reptiles. To gain further insight into the tandem amino acid repeats in squamates, we analysed the repeat content in the green anole Anolis carolinensis proteome and compared the amino acid repeats in a large orthologous protein data set from six vertebrates the Western clawed frog, the green anole, the Chinese softshell turtle, the zebra finch, mouse and human.

ResultsOur results revealed that the number of amino acid repeats in the green anole exceeded those found in the other five species studied. Species-only repeats were found in high proportion in the green anole but not in the other five species, suggesting that the green anole had gained many amino acid repeats in either the Anolis or the squamate lineage. Since the amino acid repeat containing genes in the green anole were highly enriched in genes related to transcription and development, an important family of developmental genes, i.e., the Hox family, was further studied in a wide collection of squamates. Abundant amino acid repeats were also observed, implying the general high tolerance of amino acid repeats in squamates. A particular enrichment of amino acid repeats was observed in the central class Hox genes that are known to be responsible for defining cervical to lumbar regions.

ConclusionsOur study suggests that the abundant amino acid repeats in the green anole, and possibly in other squamates, may play a role in increasing the genetic variability, and contribute to the evolutionary diversity of this clade.

KeywordsHomopolymeric tract Homopeptide Squamates Lepidosauria Comparative genomics AbbreviationsAAamino acid

BLASTBasic Local Alignment Search Tool

cDNAcomplementary DNA

GOGene Ontology

PGparalogous groups

PLPproportion of the longest consecutive pure codon to the complete repeat size

PRANKThe Probabilistic Alignment Kit

RCPrepeat-containing proteins

UCSCUniversity of California, Santa Cruz

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-016-2430-y contains supplementary material, which is available to authorized users.

Download fulltext PDF

Author: Riga Wu - Qingfeng Liu - Peng Zhang - Dan Liang

Source: https://link.springer.com/

Related documents