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

Elena V Romanova,Maria D Logacheva,Dmitry Y Sherbakov,Kirill V Mikhailov,Vladimir V Aleoshin,Yurij S Bukin

doi:10.3390/genes12122030

Abstract

There are more than 350 species of amphipods (Crustacea) in Lake Baikal, which have emerged predominantly through the course of endemic radiation. This group represents a remarkable model for studying various aspects of evolution, one of which is the evolution of mitochondrial (mt) genome architectures. We sequenced and assembled the mt genome of a pelagic Baikalian amphipod species Macrohectopus branickii. The mt genome is revealed to have an extraordinary length (42,256 bp), deviating significantly from the genomes of other amphipod species and the majority of animals. The mt genome of M. branickii has a unique gene order within amphipods, duplications of the four tRNA genes and Cox2, and a long non-coding region, that makes up about two thirds of the genome’s size. The extension of the mt genome was most likely caused by multiple duplications and inversions of regions harboring ribosomal RNA genes. In this study, we analyzed the patterns of mt genome length changes in amphipods and other animal phyla. Through a statistical analysis, we demonstrated that the variability in the mt genome length may be a characteristic of certain phyla and is primarily conferred by expansions of non-coding regions.

Highlights

Mitochondrial genome sequencing is a powerful tool used in many areas of modern biology, such as phylogenetics and phylogenomics; population genetics and molecular evolution; and studies of biodiversity, conservation, aging, and genetic diseases.At the same time, a mitochondrial genome is itself used for the investigation of fundamental molecular mechanisms governing its functionality and evolution [1,2].Previous studies have demonstrated that most animal phyla have a relatively uniform mt genome length and gene content, establishing the concept of a “typical mt genome”in animals [3]
Similarity searches with BLAST identified six mitochondrial contigs in the SPAdes assembly with the genomic sequencing data and another six contigs in the assembly with the transcriptomic data, ranging in size from 242 bp to 22 Kbp
The new sequencing data led to slight correction of the assembly, which turned into a final version of the M. branickii mt genome, spanning a total of 42,256 bp (GenBank accession MT047459)

Summary

Introduction

Mitochondrial (mt) genome sequencing is a powerful tool used in many areas of modern biology, such as phylogenetics and phylogenomics; population genetics and molecular evolution; and studies of biodiversity, conservation, aging, and genetic diseases.At the same time, a mitochondrial genome is itself used for the investigation of fundamental molecular mechanisms governing its functionality and evolution [1,2].Previous studies have demonstrated that most animal phyla have a relatively uniform mt genome length and gene content, establishing the concept of a “typical mt genome”in animals [3]. Mitochondrial (mt) genome sequencing is a powerful tool used in many areas of modern biology, such as phylogenetics and phylogenomics; population genetics and molecular evolution; and studies of biodiversity, conservation, aging, and genetic diseases. A mitochondrial genome is itself used for the investigation of fundamental molecular mechanisms governing its functionality and evolution [1,2]. Previous studies have demonstrated that most animal phyla have a relatively uniform mt genome length and gene content, establishing the concept of a “typical mt genome”. The majority of animal mt genomes are single circular molecules of about 16 Kbp, with 13 protein-coding genes (PCG), that encode components of the electron transport chain and ATP synthesis, 22 tRNA genes, 2 ribosomal RNA genes, that provide a basis for the in-house protein synthesis machinery, and a control region, that maintain regulatory elements for replication and transcription [4]. Deeper exploration of animal diversity, facilitated by advances in sequencing technologies, have shown that the mt genomes of many species deviate in terms of structure, length, gene content, and gene order from the archetypical animal mt genome [3,5,6].

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Discussion

Conclusion