First mitochondrial genome of a lugworm (Annelida: Arenicolidae) and its phylogenetic position

Abstract

The annelid mitochondrial genomes (mitogenomes) have been well documented, and phylogenetic analyses based on the mitogenomes provide insightful implications for annelid evolution. However, the mitogenomes of some families remain unknown. Herein, we determined the complete mitogenome of the lugworm Abarenicola claparedi oceanica (15,524 bp), representing the first mitogenome from the family Arenicolidae. The gene order of this species is the same as the various lineages in Sedentaria. The maximum likelihood phylogenetic analyses were performed based on six different datasets, including 43 ingroups (oligochaetes, hirudineans, echiurans and closely related polychaetes) and two outgroups (Siboglinidae), namely, aligned and trimmed datasets consisting of the nucleotide sequences of protein-coding genes (PCGs) and rRNAs, and amino acid sequences of PCGs. Phylogenetic analyses based on the nucleotide sequences yielded trees with better support values than those based on the amino acid sequences. Arenicolidae is clustered with Maldanidae in all analyses. Analyses based on nucleotide sequences confirm the monophyly of Terebellidae, which was paraphyletic in recent mitogenomic phylogenetic studies. We also performed the phylogenetic analysis based on the RY-coding of the nucleotide sequences of PCGs only to yield phylogeny with generally low support values. Additional mitogenome sequences of related ingroup species would be needed to comprehensively understand the phylogenetic relationship, which was not present in this study.

Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA)

“…Although the Acanthobdellida and Hirudinida clade was sister to Branchiobdellida in Phillips et al (2019) with full support, the relationship among Acanthobdellida, Branchiobdellida, and Hirudinida was not resolved in the present study. Also, the phylogenetic positions of Capitellidae, Thalassematidae, and Opheliidae, which were contentious in the recent phylogenetic studies focusing on the mitogenomes of Sedentaria ( Kobayashi, Itoh & Nakajima, 2022b ; Kobayashi, Itoh & Nakajima, 2022a ) despite well-resolved phylogenetic relationships based on transcriptomes, were not revolved in the present study. Mitogenomic phylogeny can be conducted with a more dense taxon sampling than phylogeny based on transcriptomes, it should be noted that support values in mitogenomic phylogeny of the higher classifications ( Sun et al, 2021 ; Fig.…”

“…Mitogenomic phylogeny can be conducted with a more dense taxon sampling than phylogeny based on transcriptomes, it should be noted that support values in mitogenomic phylogeny of the higher classifications ( Sun et al, 2021 ; Fig. 1 in Kobayashi, Itoh & Nakajima, 2022a ) are likely to be lower than phylogeny based on transcriptomes with similar taxon sampling ( Struck et al, 2015 ; Martín-Durán et al, 2021 ) (although it is apparent considering the difference in the total number of loci).…”