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

Sankar Subramanian; L Huynen; C D Millar; D M Lambert

doi:10.1186/1471-2148-10-387

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

Journal article

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

Sankar Subramanian, L Huynen, C D Millar and D M Lambert

BMC Evolutionary Biology, Vol.10(1), 387

2010

DOI: https://doi.org/10.1186/1471-2148-10-387

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Abstract

kiwi

transcriptome

Background: Kiwi 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. Results. Using 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. Conclusions. The 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. © 2010 Subramanian et al; licensee BioMed Central Ltd.

Details

Title: Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi
Authors: Sankar Subramanian (Author) - Griffith University
L Huynen (Author) - Griffith University
C D Millar (Author) - University of Auckland, New Zealand
D M Lambert (Author) - Griffith University
Publication details: BMC Evolutionary Biology, Vol.10(1), 387; 10
Publisher: BioMed Central Ltd.
Date published: 2010
DOI: 10.1186/1471-2148-10-387
ISSN: 1471-2148
Copyright note: Copyright © 2010 Subramanian et al; licensee 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.
Organisation Unit: School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; School of Science, Technology and Engineering; Centre for Bioinnovation
Language: English
Record Identifier: 99450526102621
Output Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Web Of Science research areas: Evolutionary Biology; Genetics & Heredity

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