The complete mitochondrial genome of the Columbia lance nematode, Hoplolaimus columbus, a major agricultural pathogen in North America

Xinyuan Ma,Paula Agudelo,Vincent P Richards,J Antonio Baeza

doi:10.1186/s13071-020-04187-y

Xinyuan Ma, Paula Agudelo + Show 2 more

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https://doi.org/10.1186/s13071-020-04187-y

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Journal: Parasites & Vectors	Publication Date: Jun 22, 2020
Citations: 13	License type: open-access

Affiliation: Clemson University

Abstract

BackgroundThe plant-parasitic nematode Hoplolaimus columbus is a pathogen that uses a wide range of hosts and causes substantial yield loss in agricultural fields in North America. This study describes, for the first time, the complete mitochondrial genome of H. columbus from South Carolina, USA.MethodsThe mitogenome of H. columbus was assembled from Illumina 300 bp pair-end reads. It was annotated and compared to other published mitogenomes of plant-parasitic nematodes in the superfamily Tylenchoidea. The phylogenetic relationships between H. columbus and other 6 genera of plant-parasitic nematodes were examined using protein-coding genes (PCGs).ResultsThe mitogenome of H. columbus is a circular AT-rich DNA molecule 25,228 bp in length. The annotation result comprises 12 PCGs, 2 ribosomal RNA genes, and 19 transfer RNA genes. No atp8 gene was found in the mitogenome of H. columbus but long non-coding regions were observed in agreement to that reported for other plant-parasitic nematodes. The mitogenomic phylogeny of plant-parasitic nematodes in the superfamily Tylenchoidea agreed with previous molecular phylogenies. Mitochondrial gene synteny in H. columbus was unique but similar to that reported for other closely related species.ConclusionsThe mitogenome of H. columbus is unique within the superfamily Tylenchoidea but exhibits similarities in both gene content and synteny to other closely related nematodes. Among others, this new resource will facilitate population genomic studies in lance nematodes from North America and beyond.

Highlights

The plant-parasitic nematode Hoplolaimus columbus is a pathogen that uses a wide range of hosts and causes substantial yield loss in agricultural fields in North America
Hoplolaimus columbus belongs to the subgenus Basirolaimus together with 17 other nematode species [2]
The complete mitogenome of H. columbus was de novo assembled into a closed-circular DNA molecule of 25,228 bp in length (GenBank: MH657221; Fig. 1)

Summary

Introduction

The plant-parasitic nematode Hoplolaimus columbus is a pathogen that uses a wide range of hosts and causes substantial yield loss in agricultural fields in North America. According to the current taxonomical view that relies on a combination of molecular and morphological characters, lance nematodes belong to the class Chromadorea, infraorder Tylenchomorpha [2, 4,5,6] They exhibit a wide range of hosts, including, among others, turf grasses, cereals, soybean, corn, cotton, sugar cane, and some trees [1, 4, 7]. Hoplolaimus columbus, known as the ‘Columbia lance nematode’, is considered among the most economically important species in the world [1] This nematode was described as a new species from samples collected in Columbia, South Carolina, USA. Considering its wide distribution and damage to crops, a better genomic understanding of H. columbus would prove helpful to understand its population genetic structure and effects, or the lack thereof, on commercially relevant crops

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