The Mitochondrial Genome of the Sea Anemone Stichodactyla haddoni Reveals Catalytic Introns, Insertion-Like Element, and Unexpected Phylogeny

Steinar Daae Johansen,Tor Erik Jørgensen,Sylvia I Chi,Arseny Dubin

doi:10.3390/life11050402

Steinar Daae Johansen, Tor Erik Jørgensen + Show 2 more

Open Access

https://doi.org/10.3390/life11050402

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Journal: Life	Publication Date: Apr 28, 2021
Citations: 5	License type: CC BY 4.0

Affiliation: Nord University, UiT The Arctic University of Norway

Abstract

A hallmark of sea anemone mitochondrial genomes (mitogenomes) is the presence of complex catalytic group I introns. Here, we report the complete mitogenome and corresponding transcriptome of the carpet sea anemone Stichodactyla haddoni (family Stichodactylidae). The mitogenome is vertebrate-like in size, organization, and gene content. Two mitochondrial genes encoding NADH dehydrogenase subunit 5 (ND5) and cytochrome c oxidase subunit I (COI) are interrupted with complex group I introns, and one of the introns (ND5-717) harbors two conventional mitochondrial genes (ND1 and ND3) within its sequence. All the mitochondrial genes, including the group I introns, are expressed at the RNA level. Nonconventional and optional mitochondrial genes are present in the mitogenome of S. haddoni. One of these gene codes for a COI-884 intron homing endonuclease and is organized in-frame with the upstream COI exon. The insertion-like orfA is expressed as RNA and translocated in the mitogenome as compared with other sea anemones. Phylogenetic analyses based on complete nucleotide and derived protein sequences indicate that S. haddoni is embedded within the family Actiniidae, a finding that challenges current taxonomy.

Highlights

Hexacoral mitochondria harbor economically organized and vertebrate-like mitochondrial genomes ranging in size from 16 to 22 kb [1]
Most mitogenomes consist of a single circular DNA coding for the same set of two ribosomal RNAs and 13 hydrophobic oxidative phosphorylation (OxPhos) proteins as compared with that of vertebrates [2]
The NADH dehydrogenase subunit 5 (ND5)-717 and CO-884 introns are schematically indicated below the gene map as paired segment (P1 to P9) catalytic RNA core folds

Summary

Introduction

Hexacoral mitochondria harbor economically organized and vertebrate-like mitochondrial genomes (mitogenomes) ranging in size from 16 to 22 kb [1]. Most mitogenomes consist of a single circular DNA coding for the same set of two ribosomal RNAs (rRNAs) and 13 hydrophobic oxidative phosphorylation (OxPhos) proteins as compared with that of vertebrates [2]. More than 200 complete hexacoral mitogenome sequences are available representing all five extant orders, i.e., Actiniaria (sea anemones), Zoantharia (colonial anemones), Corallimorpharia (mushroom corals), Antipatharia (black corals), and Scleractinia (stony corals) [1]. Insertion-like orfA is a representative of a widespread nonconventional mitochondrial gene in sea anemones, but its RNA transcript or derived protein has, so far, not been linked to a cellular function [5,8]. The most unusual feature, is the presence of complex group I introns [1,9]

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