Mitochondrial genome diversity in dagger and needle nematodes (Nematoda: Longidoridae)

J E Palomares-Rius,C Cantalapiedra-Navarrete,A Archidona-Yuste,V C Blok,P Castillo

doi:10.1038/srep41813

J E Palomares-Rius, C Cantalapiedra-Navarrete + Show 3 more

Open Access

https://doi.org/10.1038/srep41813

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Abstract

Dagger and needle nematodes included in the family Longidoridae (viz. Longidorus, Paralongidorus, and Xiphinema) are highly polyphagous plant-parasitic nematodes in wild and cultivated plants and some of them are plant-virus vectors (nepovirus). The mitochondrial (mt) genomes of the dagger and needle nematodes, Xiphinema rivesi, Xiphinema pachtaicum, Longidorus vineacola and Paralongidorus litoralis were sequenced in this study. The four circular mt genomes have an estimated size of 12.6, 12.5, 13.5 and 12.7 kb, respectively. Up to date, the mt genome of X. pachtaicum is the smallest genome found in Nematoda. The four mt genomes contain 12 protein-coding genes (viz. cox1-3, nad1-6, nad4L, atp6 and cob) and two ribosomal RNA genes (rrnL and rrnS), but the atp8 gene was not detected. These mt genomes showed a gene arrangement very different within the Longidoridae species sequenced, with the exception of very closely related species (X. americanum and X. rivesi). The sizes of non-coding regions in the Longidoridae nematodes were very small and were present in a few places in the mt genome. Phylogenetic analysis of all coding genes showed a closer relationship between Longidorus and Paralongidorus and different phylogenetic possibilities for the three Xiphinema species.

Highlights

The phylum Nematoda is one of the largest and most diverse groups of animal organisms, with a global distribution
The main objectives of this research were: (i) to determine the mitochondrial genomes in three different genera within important Plant-parasitic nematodes (PPNs) from Longidoridae (Xiphinema, Longidorus and Paralongidorus); and (ii) to associate their gene structures and protein-coding gene sequences with their phylogeny
The four new mt genomes showed a similar size and gene number complement to X. americanum (NC_005928) (12,626 bp). They are smaller in size than other Enopleans species such as Romanomermis culicivorax (26,194 bp) or Hexamermis agrotis (24,606 bp)

Summary

Introduction

The phylum Nematoda is one of the largest and most diverse groups of animal organisms, with a global distribution. There are fourteen mt genomes of PPNs sequenced to date, and only one of them was included in the class Enoplea (Xiphinema americanum) and fourteen in the class Chromadorea (Aphelenchoides besseyi, Bursaphelenchus mucronatus, B. xylophilus, Globodera ellingtonae, G. pallida, G. rostochiensis, Heterodera glycines, Pratylenchus vulnus, Meloidogyne chitwoodi, M. floridensis, M. graminicola, M. hapla, M. incognita, Radopholus similis) and some of them display some unusual features[9,10,11,12,13,14,15,16,17,18,19,20,21]. The main objectives of this research were: (i) to determine the mitochondrial genomes in three different genera within important PPNs from Longidoridae (Xiphinema, Longidorus and Paralongidorus); and (ii) to associate their gene structures and protein-coding gene sequences with their phylogeny

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