Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi

BMC Evolutionary Biology

Research Article

Craig D Millar¹  Leon Huynen²  Sankar Subramanian²  David M Lambert² 

[1] Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand;Griffith School of Environment and the School of Biomolecular and Physical Sciences, Griffith University, 170 Kessels Road, 4111, Nathan, Qld, Australia;Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand;

关键词: Zebra Finch;    Synonymous Site;    Nonsynonymous Divergence;    Synonymous Divergence;    Nonsynonymous Site;   

DOI  :  10.1186/1471-2148-10-387

 received in 2010-07-13, accepted in 2010-12-15,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundKiwi is a highly distinctive, flightless and endangered ratite bird endemic to New Zealand. To understand the patterns of molecular evolution of the nuclear protein-coding genes in brown kiwi (Apteryx australis mantelli) and to determine the timescale of avian history we sequenced a transcriptome obtained from a kiwi embryo using next generation sequencing methods. We then assembled the conserved protein-coding regions using the chicken proteome as a scaffold.ResultsUsing 1,543 conserved protein coding genes we estimated the neutral evolutionary divergence between the kiwi and chicken to be ~45%, which is approximately equal to the divergence computed for the human-mouse pair using the same set of genes. A large fraction of genes was found to be under high selective constraint, as most of the expressed genes appeared to be involved in developmental gene regulation. Our study suggests a significant relationship between gene expression levels and protein evolution. Using sequences from over 700 nuclear genes we estimated the divergence between the two basal avian groups, Palaeognathae and Neognathae to be 132 million years, which is consistent with previous studies using mitochondrial genes.ConclusionsThe results of this investigation revealed patterns of mutation and purifying selection in conserved protein coding regions in birds. Furthermore this study suggests a relatively cost-effective way of obtaining a glimpse into the fundamental molecular evolutionary attributes of a genome, particularly when no closely related genomic sequence is available.

【 授权许可】

Unknown   
© Subramanian et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.