Mitogenome of a stink worm (Annelida: Travisiidae) includes degenerate group II intron that is also found in five congeneric species

Genki Kobayashi,Hajime Itoh,Shigeaki Kojima

doi:10.1038/s41598-022-08103-5

Genki Kobayashi, Hajime Itoh + Show 1 more

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https://doi.org/10.1038/s41598-022-08103-5

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Abstract

Mitogenomes are useful for inferring phylogenetic relationships between organisms. Although the mitogenomes of Annelida, one of the most morphologically and ecologically diverse metazoan groups have been well sequenced, those of several families remain unexamined. This study determined the first mitogenome from the family Travisiidae (Travisia sanrikuensis), analyzed its mitogenomic features, and reconstructed a phylogeny of Sedentaria. The monophyly of the Terebellida + Arenicolida + Travisiidae clade is supported by molecular phylogenetic analysis. The placement of Travisiidae is unclear because of the lack of mitogenomes from closely related lineages. An unexpected intron appeared within the cox1 gene of T. sanrikuensis and in the same positions of five undescribed Travisia spp. Although the introns are shorter (790–1386 bp) than other group II introns, they can be considered degenerate group II introns due to type II intron maturase open reading frames, found in two of the examined species, and motifs characteristic of group II introns. This is likely the first known case in metazoans where mitochondrial group II introns obtained by a common ancestor are conserved in several descendants. Insufficient evolutionary time for intron loss in Travisiidae, or undetermined mechanisms may have helped maintain the degenerate introns.

Highlights

IntroductionThe mitochondrial genome (mitogenome) has become commonly used for molecular phylogenetic analysis
The mitochondrial genome has become commonly used for molecular phylogenetic analysis
The circular mitogenome of T. sanrikuensis was recovered by concatenating the contig and 16S rRNA gene sequence (LC566242), a dubious control region (> 2000 bp) between the nad[5] and trnR genes, which includes tRNAs encoded on “−” strand and a long palindrome like sequence, was present

Summary

Introduction

The mitochondrial genome (mitogenome) has become commonly used for molecular phylogenetic analysis. The gene order in some marine invertebrates, including annelids, shows an intra-familial v ariation[2,5–9] and may shed light on the phylogenetic relationships of relatively closely related taxa. Known mitochondrial introns are mainly classified as groups I and II based on their structural features[11]. Group II introns are generally characterized by a secondary structure with six domains and intronic open reading frames (ORFs), encoding functions for splicing and mobility (e.g., reverse transcriptase and RNA maturase), and motifs beginning with 5′ GUGYG 3′ and ending with 5′ AY 3′11,19,20. Scalibregmatidae is clustered with Terebellida + Arenicolidae clade in recent phylogenomics based on t ranscriptomes[48]

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