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

Abstract

Background 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. This study describes, for the first time, the complete mitochondrial genome of H. columbus from South Carolina, USA. Methods The 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). Results The 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. Conclusions The 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.

Yes, we can use it: a formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics and barcoding research using the Caribbean spiny lobster Panulirus argus

“…Furthermore, with the advent of second-(i.e., Illumina short-reads) and third-generation (long-read) sequencing technologies, whole mitochondrial genomes have been used for phylogeographic and phylogenomic analyses ( [10][11][12] and references therein) instead of only a few fragments (i.e., cox1, cob, 12S, 16S). An ever increasing number of studies reporting the structural and functional organization of animal mitochondrial genomes is available in NCBI's Genbank (https://www.ncbi.nlm.nih.gov/genbank/) permitting the integration of mtDNA topological features (i.e., deletions, insertions, translocations, and overall gene synteny) concomitantly with sequence similarity to inform phylogenetic relationships among species at multiple taxonomic levels (e.g., [11,[13][14][15]).…”

“…During the last decade, however, second generation sequencing technologies have been used for low-coverage (= lowpass) whole genome sequencing (i.e., genome skimming) with or without prior mitochondrial enrichment to assemble mitochondrial chromosomes (e.g., [13]). This strategy often results in the assembly of complete and totally accurate mitochondrial genomes but it is time consuming, with projects often lasting from weeks to months from initial DNA purification to genome assembly and annotation [11,[13][14][15]. Rapid and simple library preparation, sequencing, and assembly of any DNA marker, including complete mitochondrial genomes, are desirable to solve a plethora of problems in conservation biology, including resource management.…”

Genome survey sequencing of the phyto-parasitic nematode Hoplolaimus galeatus

“…Turf grass soil samples with specimens of Hoplolaimus galeatus were collected from Brightview Landscape, The Villages, Florida (28°58′01.9″N 82°00′02.7″W) and transported to Clemson University Nematode Assay Laboratory for further study. In the laboratory, the sugar centrifugal flotation method was used to extract nematodes from soil samples as previously described ( Jenkins, 1964 ; Handoo & Golden, 1992 ; Ma et al, 2020 ). Specifically, a few fixed specimens were identified morphologically referring to diagnostic key characters under the microscope ( Handoo & Golden, 1992 ).…”

“…Specifically, a few fixed specimens were identified morphologically referring to diagnostic key characters under the microscope ( Handoo & Golden, 1992 ). For DNA extraction, live nematodes ( n = 9) were cleaned using distilled water, 3% hydrogen peroxide solution (Aaron Industry, Clinton, SC, USA), DNA Away solution (Aaron Industry, Clinton, SC, USA) and PCR-grade water as described in Ma et al (2020) . DNA extraction followed Ma et al (2011) .…”

“…Library preparation and sequencing was conducted as previously described in Ma et al (2020) . Specifically, the Nextera XT kit (Illumina, San Diego, CA, USA) was used for library preparation using the manufacturer’s instructions.…”