The Complete Mitochondrial Genome of Meloidogyne graminicola (Tylenchina): A Unique Gene Arrangement and Its Phylogenetic Implications

Abstract

Meloidogyne graminicola is one of the most economically important plant parasitic-nematodes (PPNs). In the present study, we determined the complete mitochondrial (mt) DNA genome sequence of this plant pathogen. Compared with other PPNs genera, this genome (19,589 bp) is only slightly smaller than that of Pratylenchus vulnus (21,656 bp). The nucleotide composition of the whole mtDNA sequence of M. graminicola is significantly biased toward A and T, with T being the most favored nucleotide and C being the least favored. The A+T content of the entire genome is 83.51%. The mt genome of M. graminicola contains 36 genes (lacking atp8) that are transcribed in the same direction. The gene arrangement of the mt genome of M. graminicola is unique. A total of 21 out of 22 tRNAs possess a DHU loop only, while tRNASer(AGN) lacks a DHU loop. The two large noncoding regions (2,031 bp and 5,063 bp) are disrupted by tRNASer(UCN). Phylogenetic analysis based on concatenated amino acid sequences of 12 protein-coding genes support the monophylies of the three orders Rhabditida, Mermithida and Trichinellida, the suborder Rhabditina and the three infraorders Spiruromorpha, Oxyuridomorpha and Ascaridomorpha, but do not support the monophylies of the two suborders Spirurina and Tylenchina, and the three infraorders Rhabditomorpha, Panagrolaimomorpha and Tylenchomorpha. The four Tylenchomorpha species including M. graminicola, P. vulnus, H. glycines and R. similis from the superfamily Tylenchoidea are placed within a well-supported monophyletic clade, but far from the other two Tylenchomorpha species B. xylophilus and B. mucronatus of Aphelenchoidea. In the clade of Tylenchoidea, M. graminicola is sister to P. vulnus, and H. glycines is sister to R. similis, which suggests root-knot nematodes has a closer relationship to Pratylenchidae nematodes than to cyst nematodes.

Morphological, Morphometric, and Molecular Characterization of Intraspecific Variations within Indian Populations of Meloidogyne graminicola

“…It has been suggested that mitochondrial phylogenetic markers including variable number tandem repeats could help resolve the population diversity better than nuclear markers (Lunt et al, 1998;Besnard et al, 2014;Sun et al, 2014;Humphreys-Pereira and Elling, 2015). Testing additional phylogenetic markers would resolve if our populations belong to M. graminicola or to other cryptic species.…”

Mitochondrial genome plasticity among species of the nematode genus Meloidogyne (Nematoda: Tylenchina)

“…Transfer RNA (trn) genes were identified using tRNAscan-SE 1.21 (Schattner et al, 2005) with the settings described by Humphreys-Pereira and , and by using the MITOS pipeline (Bernt et al, 2013). The secondary structures of trn genes from M. graminicola predicted by Besnard et al (2014) and Sun et al (2014) were re-analyzed in this study using tRNAscan-SE 1.21 and MITOS, and manually annotated by searching for anticodons. The ribosomal RNA genes rrnL and rrnS were identified through comparisons with other Meloidogyne spp.…”

“…Tandem Repeats Finder software was used to identify tandem repetitive elements (Benson, 1999). The gene architecture of the three mt genomes described in this study was compared with the mt genomes of M. chitwoodi, M. incognita and M. graminicola reported previously (Sun et al, 2014;Besnard et al, 2014).…”

“…The locations of the trn genes were similar among the three mt genomes, except that trnH in M. enterolobii was located between the cox2 gene and a NCR, whereas trnH in M. arenaria and M. javanica was located between a NCR and the rrnL gene. Two mt genomes of M. graminicola (Sun et al, 2014;Besnard et al, 2014) available in GenBank were re-analyzed to compare the secondary structures of the trn genes between them and with other Meloidogyne spp. The secondary structures of M. graminicola trnV and trnS2 observed by Besnard et al (2014) were not the same as those predicted by Sun et al (2014).…”

“…At the time of this study (October 2014), there are 11 mt genomes of PPNs published, i.e., M. chitwoodi, M. incognita, Meloidogyne graminicola, Heterodera glycines, Globodera pallida, Globodera rostochiensis, Pratylenchus vulnus, R. similis, B. xylophilus, Bursaphelenchus mucronatus and Xiphinema americanum (Armstrong et al, 2000;He et al, 2005;Gibson et al, 2007Gibson et al, , 2011Jacob et al, 2009;Sultana et al, 2013aSultana et al, , 2013bSun et al, 2014;Besnard et al, 2014). It is likely that the development of new sequencing technologies will accelerate and improve the sequencing of more nematode mt genomes, e.g., Zasada et al (2014) describe the use of Illumina HTS for sequencing the mt genome of single individuals of X. americanum from 12 populations.…”