Fast assembly of the mitochondrial genome of a plant parasitic nematode (Meloidogyne graminicola) using next generation sequencing.
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.
CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Évolution & Diversité biologique), 118, route de Narbonne, 31062 Toulouse, France. Electronic address: guillaume.besnard@univ-tlse3.fr.
Guillaume
G
Besnard
University of Leipzig, Interdisciplinary Center for Bioinformatics, Härtelstraße 16-18, 04107 Leipzig, Germany.
Frank
F
Jühling
IRD, UMR186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France.
Élodie
É
Chapuis
CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Évolution & Diversité biologique), 118, route de Narbonne, 31062 Toulouse, France.
Loubab
L
Zedane
INRA, GeT-PlaGe, UAR 1209 Département de génétique animale, INRA Auzeville, 31326 Castanet-Tolosan, France.
Émeline
É
Lhuillier
IRD, UMR 022 Centre de biologie pour la gestion des populations, campus de Baillarguet, CS30016, 34988 Montferrier-sur-Lez cedex, France.
Thierry
T
Mateille
IRD, UMR186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France.
Stéphane
S
Bellafiore
D000818:Animals; D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification; D054629:Genome, Mitochondrial; D008969:Molecular Sequence Data; D012343:RNA, Transfer / Q000096:biosynthesis / Q000235:genetics; D017422:Sequence Analysis, DNA; D014431:Tylenchoidea / Q000235:genetics*
D004272:DNA, Mitochondrial; D012343:RNA, Transfer
Assemblage de génome d’organelles; Genome skimming; Meloidogyne; Mitogenomics; Mitogénome; Nematode; Next generation sequencing; Nématode; Organellar genome assembly; Séquençage de nouvelle génération; Écrémage de génome