Journal
COMPTES RENDUS BIOLOGIES
Volume 337, Issue 5, Pages 295-301Publisher
centre Mersenne pour ldition scientifique ouverte
DOI: 10.1016/j.crvi.2014.03.003
Keywords
Organellar genome assembly; Genome skimming; Meloidogyne; Mitogenomics; Nematode; Next generation sequencing
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Funding
- Plateforme Genomique and Bioinformatics platform of Genopole Toulouse Midi-Pyrenees
- Agence nationale de la recherch [ANR-10-LABX-0041]
- Rice Science Partnership (GRiSP) Grant (Menergep Project)
- [ANR-12-AGRI-0002 (ARIMNET 2011-PESTOLIVE)]
- Agence Nationale de la Recherche (ANR) [ANR-10-LABX-0041] Funding Source: Agence Nationale de la Recherche (ANR)
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Little is known about the variations of nematode mitogenomes (mtDNA). Sequencing a complete mtDNA using a PCR approach remains a challenge due to frequent genome reorganizations and low sequence similarities between divergent nematode lineages. Here, a genome skimming approach based on HiSeq sequencing (shotgun) was used to assemble de novo the first complete mtDNA sequence of a root-knot nematode (Meloidogyne graminicola). An AT-rich genome (84.3%) of 20,030 bp was obtained with a mean sequencing depth superior to 300. Thirty-six genes were identified with a semi-automated approach. A comparison with a gene map of the M. javanica mitochondrial genome indicates that the gene order is conserved within this nematode lineage. However, deep genome rearrangements were observed when comparing with other species of the superfamily Hoplolaimoidea. Repeat elements of 111 bp and 94 bp were found in a long non-coding region of 7.5 kb, as similarly reported in M. javanica and M. hapla. This study points out the power of next generation sequencing to produce complete mitochondrial genomes, even without a reference sequence, and possibly opening new avenues for species/race identification, phylogenetics and population genetics of nematodes. (C) 2014 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.
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