Besnard G. auteur aut IRD Juhling F. auteur aut IRD Chapuis Elodie auteur aut IRD Zedane L. auteur aut IRD Lhuillier E. auteur aut IRD Mateille Thierry auteur aut IRD Bellafiore Stéphane auteur aut IRD text journalArticle eng text/pdf born digital access 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. specialized Organellar genome assembly Genome skimming Meloidogyne Mitogenomics Nematode Next generation sequencing 076 020 337 5 295-301 2014 1631-0691 https://www.documentation.ird.fr/hor/fdi:010062237 10.1016/j.crvi.2014.03.003 1631-0691 [F B010062237] https://www.documentation.ird.fr/hor/fdi:010062237 https://www.documentation.ird.fr/intranet/publi/2014/07/010062237.pdf Accès réservé (Intranet de l'IRD) IRD - Base Horizon / Pleins textes 2014-07-24 2017-08-23 fdi:010062237 fre