The complete mitochondrial genome of Chionodraco hamatus (Notothenioidei: Channichthyidae) with phylogenetic consideration

Complete mitochondrial genome of Trematomus newnesi (Perciformes, Nototheniidae)

The complete mitochondrial genome of Trematomus newnesi was sequenced using an Illumina platform. The 18,602 bp mitogenome contains 13 protein-coding genes, two rRNAs, and 23 tRNAs (tRNAMet is duplicated). The eight stop codons are TAA, TAG, CTT, GTA, AAT, ACT, AGG, and TTA. Two start codons ATG and GTG are present. The GC content is 44.4% and AT content is 55.6%. A phylogenetic tree was generated using 13 species from three families. The results showed that T. newnesi is closely related to Pagothenia borchgrevinki in Nototheniidae. This study provides fundamental data for further genetic evolutionary studies on T. newnesi.

Population genomics of an icefish reveals mechanisms of glacier-driven adaptive radiation in Antarctic notothenioids

Background

Antarctica harbors the bulk of the species diversity of the dominant teleost fish suborder—Notothenioidei. However, the forces that shape their evolution are still under debate.

Results

We sequenced the genome of an icefish, Chionodraco hamatus, and used population genomics and demographic modelling of sequenced genomes of 52 C. hamatus individuals collected mainly from two East Antarctic regions to investigate the factors driving speciation. Results revealed four icefish populations with clear reproduction separation were established 15 to 50 kya (kilo years ago) during the last glacial maxima (LGM). Selection sweeps in genes involving immune responses, cardiovascular development, and photoperception occurred differentially among the populations and were correlated with population-specific microbial communities and acquisition of distinct morphological features in the icefish taxa. Population and species-specific antifreeze glycoprotein gene expansion and glacial cycle-paced duplication/degeneration of the zona pellucida protein gene families indicated fluctuating thermal environments and periodic influence of glacial cycles on notothenioid divergence.

Conclusions

We revealed a series of genomic evidence indicating differential adaptation of C. hamatus populations and notothenioid species divergence in the extreme and unique marine environment. We conclude that geographic separation and adaptation to heterogeneous pathogen, oxygen, and light conditions of local habitats, periodically shaped by the glacial cycles, were the key drivers propelling species diversity in Antarctica.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01432-x.

Not Frozen in the Ice: Large and Dynamic Rearrangements in the Mitochondrial Genomes of the Antarctic Fish

The vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In this first systematic study of 28 species, we analyzed known and undescribed mitochondrial genome rearrangements for a total of eight different gene orders within the notothenioid fish. Our reconstructions suggest that transpositions, duplications, and inversion of multiple genes are the most likely mechanisms of rearrangement in notothenioid mitochondrial genomes. In Trematominae, we documented an extremely rare inversion of a large genomic segment of 5,300 bp that partially affected the gene compositional bias but not the phylogenetic output. The genomic region delimited by nad5 and trnF, close to the area of the Control Region, was identified as the hot spot of variation in Antarctic fish mitochondrial genomes. Analyzing the sequence of several intergenic spacers and mapping the arrangements on a newly generated phylogeny showed that the entire history of the Antarctic notothenioids is characterized by multiple, relatively rapid, events of disruption of the gene order. We hypothesized that a pre-existing genomic flexibility of the ancestor of the Antarctic notothenioids may have generated a precondition for gene order rearrangement, and the pressure of purifying selection could have worked for a rapid restoration of the mitochondrial functionality and compactness after each event of rearrangement.

The complete mitochondrial genome sequence and gene organization of Cryodraco antarcticus (Perciformes, Channichthyidae) with phylogenetic consideration

The complete mitochondrial genome DNA sequence of Cryodraco antarcticus was 17,857 bp in size. It consists of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and one control region. Among 22 tRNA genes, 8 tRNAs were encoded on the L-strand. The overall base composition of the genome is 26.45% for A, 25.96% for T, 29.78% for C, and 17.81% for G. The phylogenetic tree suggested C. antarcticus was genetically closest to some species in family Channichthyidae. This study could provide valuable information for further studies on population structure, conservation genetics and molecular evolution of C. antarcticus.

The complete mitochondrial genome sequence and gene organization of Lepidotrigla Kanagashira (Scorpaeniformes, Triglidae) with phylogenetic consideration

The complete mitochondrial genome DNA sequence of Lepidotrigla kanagashira was 16,504 bp in length. It consists of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and one control region. Among 22 tRNA genes, 8 tRNAs were encoded on the L-strand. The overall base composition of the genome is 26.65% for A, 25.42% for T, 30.89% for C and17.04% for G. The phylogenetic tree suggested that L. kanagashira was genetically closest to L. microptera and Chelidonichthys kumu among 13 related species. This study could provide some valuable information for further studies on L. kanagashira.

The complete mitochondrial genome sequence and gene organization of Istigobius campbelli (Perciformes, Gobiidae) with phylogenetic consideration

The complete mitochondrial genome DNA sequence of Istigobius campbelli was 16,527 bp in length. It consists of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and 1 control region. 28 of the 37 genes were encoded on the heavy strand, and 9 of them were encoded on the light strand. The overall base composition of the genome is 27.84% A, 25.81% T, 29.68% C, and 16.67% G. The phylogenetic tree suggested I. campbelli was genetically closest to Acentrogobius pflaumii and Oxyurichthys formosanus. This study could provide valuable information for further studies on I. campbelli.

The full-length mitochondrial genome of the crocodile icefish, Chionobathyscus dewitti (Teleostei: Perciformes: Channichthyidae)

The full-length mitochondrial genome of the crocodile icefish, Chionobathyscus dewitti (Teleostei: Perciformes: Channichthyidae) was analyzed by the primer walking method. The mitogenome was 17,451 bp in total length, comprising 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Its gene order was congruent with those of the other crocodile icefish but different with those of typical vertebrates. In the phylogenetic tree, C. dewitti showed the closest relationship to Chaenocephalus aceratus in the same family.

The complete mitochondrial genome of Neopagetopsis ionah (Channichthyidae, neopagetopsis) with phylogenetic consideration

In this study, the complete mitochondrial genome of Neopagetopsis ionah was obtained, which was 17,634 bp including two ribosomal RNAs, 13 protein-coding genes, 22 transfer RNAs, and a non-coding control region. In 13 protein-coding genes, there types of initiation codon (ATC, ATG, and GTG) and four types of stop codons (TAA, TAG, TA, and T) were identified. Among the 22 transfer RNAs, eight tRNAs were encoded by L-strand. The length of D-loop was 1519 bp and its contents of A, T, C, and G were 26.9%, 27.6%, 17.5%, and 30%, respectively. The complete mtDNA sequences of N. ionah and other 13 species were used to reconstruct the phylogenetic tree suggested that N. ionah was closest to some species of Channichthyidae. The study would provide a basic data for further research on population structure, conservation genetics and molecular evolution of N. ionah.

The complete mitochondrial genome of Chionodraco rastrospinosus (Notothenioidei: Channichthyidae) with phylogenetic consideration

In this study, the complete mitochondrial genome of Chionodraco rastrospinosus was obtained, which was 17598 bp including 2 ribosomal RNAs, 13 protein-coding genes, 22 transfer RNAs, and a non-coding control region. The length of D-loop was 1332 bp and its contents of A, T, C, and G were 30.3%, 27.6%, 26.8%, and 15.3%. The complete mtDNA sequences of C. rastrospinosus and other 14 species were used to reconstruct the phylogenetic tree, suggested that C. rastrospinosus was closest to two species of Chionodraco. The study would provide a basic data for further research on population structure, conservation genetics and molecular evolution of C. rastrospinosus.

The complete mitochondrial genome of Electrona carlsbergi (Myctophiformes, Myctophidae) with phylogenetic consideration

The complete mitochondrial genome of Electrona carlsbergi was obtained, which was 18,282 bp in size and including 13 protein-coding genes, 2 ribosomal RNAs, 23 transfer RNAs and 1 control region. The overall nucleotide composition is 27.92% for A, 24.66% for T, 30.90% for C and 16.52% for G. Among 23 tRNA genes, 8 tRNAs were encoded on the L-strand. Further, the phylogenetic tree, which based on complete mtDNA sequences, revealed that the E. carlsbergi was genetically closest to species E. antarctica and Krefftichthys anderssoni. This study could provide a basic data for the studies on evolution for low temperature adaptability, stock evaluation and conservation genetics.

Isolation and characterization of the mitochondrial genome of Gymnodraco acuticeps (Perciformes: Bathydraconidae) with phylogenetic consideration

Gymnodraco acuticepsis is an Antarctic fish living in the Southern Ocean. Until now, studies on G. acuticeps are still limited. As an Antarctic fish, obtaining and characterization of the mitochondrial genome of G. acuticeps will be important for elucidation of the mechanism of cold-adapting evolution in mitochondrion. In this study, we first isolated and characterized the mitochondrial genome sequence of G. acuticeps with 15,987 bp in length. It contained of 34 genes (12 protein-coding genes, 20 transfer RNA genes, 2 ribosomal RNA genes) and a partial putative control region. Gene organization and nucleotide composition of obtained mito-genome were similar to those of other Antarctic fish. Twenty-eight genes were encoded by heavy strand, while six genes were encoded by light strand. Further, the phylogenetic tree, which based on 12 protein-coding genes, revealed that the G. acuticeps was genetically closest to species Parachaenichthys charcoti among 18 species. We hope this work would be helpful for the population genetics and molecular evolution studies.