eCite Digital Repository

Index-free de novo assembly and deconvolution of mixed mitochondrial genomes

Citation

McComish, BJ and Hills, SFK and Biggs, PJ and Penny, D, Index-free de novo assembly and deconvolution of mixed mitochondrial genomes, Genome Biology and Evolution, 2 pp. 410-424. ISSN 1759-6653 (2010) [Refereed Article]


Preview
PDF
2Mb
  

Copyright Statement

Copyright 2014 Oxford University Press

DOI: doi:10.1093/gbe/evq029

Abstract

Second-generation sequencing technology has allowed a very large increase in sequencing throughput. In order to make use of this high throughput, we have developed a pipeline for sequencing and de novo assembly of multiple mitochondrial genomes without the costs of indexing. Simulation studies on a mixture of diverse animal mitochondrial genomes showed that mitochondrial genomes could be reassembled from a high coverage of short (35 nt) reads, such as those generated by a second-generation Illumina Genome Analyzer. We then assessed this experimentally with long-range polymerase chain reaction products from mitochondria of a human, a rat, a bird, a frog, an insect, and a mollusc. Comparison with reference genomes was used for deconvolution of the assembled contigs rather than for mapping of sequence reads. As proof of concept, we report the complete mollusc mitochondrial genome of an olive shell (Amalda northlandica). It has a very unusual putative control region, which contains a structure that would probably only be detectable by next-generation sequencing. The general approach has considerable potential, especially when combined with indexed sequencing of different groups of genomes.

Item Details

Item Type:Refereed Article
Research Division:Biological Sciences
Research Group:Genetics
Research Field:Genomics
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Biological Sciences
Author:McComish, BJ (Mr Bennet McComish)
ID Code:96195
Year Published:2010
Web of Science® Times Cited:15
Deposited By:Mathematics and Physics
Deposited On:2014-10-22
Last Modified:2014-11-12
Downloads:168 View Download Statistics

Repository Staff Only: item control page