The complete mitochondrial genome of Aphelenchoides besseyi (Nematoda: Aphelenchoididae), the first sequenced representative of the subfamily Aphelenchoidinae

Abstract

The complete mitochondrial genome (mitogenome) of Aphelenchoides besseyi is 16216 bp in size and has the typical organisation of nematode mitogenomes of Chromadorea, including 12 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and the AT-rich non-coding region. The nucleotide composition of the mitogenome of A. besseyi is AT-biased (80.0%) and the AT skew is -0.289. The most common start codon for A. besseyi is ATT. The nad3 and nad4L genes have an incomplete stop codon consisting of just a T and the other PCGs stop with the full stop codons. All the tRNA genes display a non-typical cloverleaf structure of mitochondrial tRNA. The AT-rich non-coding region contains ten tandem repeat units with four different regions. Phylogenetic analysis based on concatenated amino acid sequences of 12 protein-coding genes showed that three Tylenchomorpha species, including A. besseyi, Bursaphelenchus mucronatus and B. xylophilus from the superfamily Aphelenchoidea, are placed within a well-supported monophyletic clade, but far from the other six Tylenchomorpha species Meloidogyne chitwoodi, M. graminicola, M. incognita, Pratylenchus vulnus, Heterodera glycines and Radopholus similis of Tylenchoidea. This phytogeny suggests that Aphelenchoides has a close relative relationship with Bursaphelenchus and that the Tylenchomorpha is not monophyletic.

Complete Mitogenome of Cruznema tripartitum Confirms Highly Conserved Gene Arrangement within Family Rhabditidae

“…Indeed, a success primer design is often challenging for using few but high variable existing references. As a result, plenty of primer pairs were designed for a specific species ( Humphreys-Pereira and Elling, 2014 ; Sun et al, 2014 ; Kim et al, 2015 ). With the development of high-throughput sequencing techniques, assembly of mitogenome from whole genome sequencing data became a feasible alternative.…”

“…Complete mitogenome has shown promise as an additional independently evolving genome for developing phylogenetic hypotheses for nematodes (Hu and Gasser, 2006;Sultana et al, 2013;Humphreys-Pereira and Elling 2014;Sun et al, 2014;Kern et al, 2020). Regardless of their importance, the study of nematode mitogenome falls far behind those of other metazoans (Ye et al, 2014).…”

The Mitochondrial Genome of a Freshwater Pelagic Amphipod Macrohectopus branickii Is among the Longest in Metazoa

“…These non-coding regions often (but not always) contain repeat sequences ( Figure S12 ). Relatively long direct repeats were identified in the mt genomes of mollusks, nematodes, and annelid species ( Figure S12 ) [ 135 , 136 , 137 , 138 ]. Vestiges of different mt genes inside non-coding regions illuminate what parts of the genome were duplicated and degenerated, leading to mt genome length changes [ 46 , 139 , 140 ].…”