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

Романова, Е. В.; Bukin, Yu. S.; Mikhailov, Kirill V.; Logacheva, Maria D.; Aleoshin, Vladimir V.; Sherbakov, D. Yu.

doi:10.3390/genes12122030

Cited by 10 publications

(6 citation statements)

References 145 publications

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“…Our study confirms for the first time with molecular data the phylogenetic position of this species, which is a glacial relict that has almost gone extinct in Central Europe due to climate warming and eutrophication [11,67]. The peculiar mitogenomic structure of Pallaseopsis is outstanding even among other Baikalian amphipods [66,[68][69][70], possibly reflecting intense periods of selection [71,72].…”

Section: Discussionsupporting

confidence: 79%

Comparative mitogenomics of native European and alien Ponto-Caspian amphipods

Macher

Šidagytė-Copilas

Copilaş‐Ciocianu

2023

Preprint

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European inland surface waters harbor an extensive diversity of native amphipod crustaceans with many species facing threats from invasive counterparts of Ponto-Caspian origin. Herein, we examine mitochondrial genomes to infer phylogenetic relationships and compare gene order and nucleotide composition between representative native European and invasive Ponto-Caspian taxa belonging to five families, ten genera, and 20 species (13 newly sequenced herein). We observe diverse gene rearrangement patterns in the phylogenetically disparate native species pool.Pallaseopsis quadrispinosaandSynurella ambulansshow significant departures from the typical organization, with extensive translocations of tRNAs and thenad1gene, as well as a tRNA-F polarity switch in the latter. The monophyletic alien Ponto-Caspian gammarids display a conserved gene order, mainly differing from the native species by a tRNA-E and tRNA-R translocation, which strengthens previous findings. However, extensive rearrangement is observed inChaetogammarus warpachowskyiwith translocations of six tRNAs. The alien corophiid,Chelicorophium curvispinum, displays a very conserved gene order despite its distant phylogenetic position. We also find that native species have a significantly higher GC and lower AT content than invasive ones. The observed mitogenomic differences between native and invasive amphipods need further investigation and could shed light on the mechanisms underlying invasion success.

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Section: Discussionsupporting

confidence: 79%

Comparative mitogenomics of native European and alien Ponto-Caspian amphipods

Macher

Šidagytė-Copilas

Copilaş‐Ciocianu

2023

Preprint

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“… 2016a ); MT047459 (Romanova et al. 2021 ); KP161875 (Romanova et al. 2016b ); KM287572 (Romanova et al.…”

Section: Resultsmentioning

confidence: 99%

The complete mitochondrial genome of freshwater gammarid Gammarus nipponensis (Crustacea: Amphipoda: Gammaridae)

de la Cruz-Huervana,

Miyamoto,

Kano

et al. 2024

Mitochondrial DNA Part B

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This study presents the complete mitochondrial genome sequence of Gammarus nipponensis , a freshwater crustacean found in the western regions of Honshu, Shikoku and Kyushu in Japan. The entire genome is 16,429 bp in length, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, as well as the putative control regions. The mitochondrial genome of G. nipponensis is characterized by a high concentration of A and T nucleotides (67.1%). Notably, the mitogenome contains long TATTTTA repeats in the control region 2 at 686 bp long. This newly available genome information will be useful for studying the evolutionary relationships within the genus Gammarus and for understanding diversification among G. nipponensis populations.

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“…These transcriptome assemblies are particularly valuable for proteomic studies (Bedulina et al, 2021;Zolotovskaya et al, 2021). Genome DNA sequenc ing data are available for seven species, which enabled the assembly of mitochondrial genomes and can be used to eva luate the diversity of repeated sequences in nuclear genomes (RivarolaDuarte et al, 2014;Romanova et al, 2016aRomanova et al, , 2021RivarolaDuarte, 2021;Yuxiang et al, 2023) (Supplementary Material 3).…”

Section: What Is Known About Genomes Of Lake Baikal Amphipods?mentioning

confidence: 99%

“…At the moment, eight complete and six partial mitochond rial genomes have been published for Baikal amphipods Lake Baikal amphipods and their genomes, great and small (Riva rola Duarte et al, 2014;Romanova et al, 2016aRomanova et al, -c, 2021Mamos et al, 2021) (Supplementary Material 4). Most of these assemblies are within 15-18 kb in length, but the mitochondrial genome of M. branickii is over 42 kblong, making it one of the largest known animal mitochondrial ge nomes (Romanova et al, 2021). Furthermore, mitochondrial genomes of some Baikal amphipods exhibit gene order rear rangements, gene duplications and the phenomenon of tRNA gene re molding, i. e. changes in tRNA specificity due to a mutation in the anticodon sequence.…”

Section: Mitochondrial Genomesmentioning

confidence: 99%

Lake Baikal amphipods and their genomes, great and small

Drozdova,

Madyarova,

Gurkov

et al. 2024

Vestn. VOGiS

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Endemic amphipods (Crustacea: Amphipoda) of Lake Baikal represent an outstanding example of large species flocks occupying a wide range of ecological niches and originating from a handful of ancestor species. Their development took place at a restricted territory and is thus open for comprehensive research. Such examples provide unique opportunities for studying behavioral, anatomic, or physiological adaptations in multiple combinations of environmental conditions and thus attract considerable attention. The existing taxonomies of this group list over 350 species and subspecies, which, according to the molecular phylogenetic studies of marker genes, full transcriptomes and mitochondrial genomes, originated from at least two introductions into the lake. The studies of allozymes and marker genes have revealed a significant cryptic diversity in Baikal amphipods, as well as a large variance in genetic diversity within some morphological species. Crossing experiments conducted so far for two morphological species suggest that the differences in the mitochondrial marker (cytochrome c oxidase subunit I gene) can potentially be applied for making predictions about reproductive isolation. For about onetenth of the Baikal amphipod species, nuclear genome sizes and chromosome numbers are known. While genome sizes vary within one order of magnitude, the karyotypes are relatively stable (2n = 52 for most species studied). Moreover, analysis of the diversity of repeated sequences in nuclear genomes showed significant betweenspecies differences. Studies of mitochondrial genomes revealed some unusual features, such as variation in length and gene order, as well as duplications of tRNA genes, some of which also underwent remolding (change in anticodon specificity due to point mutations). The next important steps should be (i) the assembly of whole genomes for different species of Baikal amphipods, which is at the moment hampered by complicated genome structures with high repeat content, and (ii) updating species taxonomy taking into account all the data.

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

Cited by 10 publications

References 145 publications

Comparative mitogenomics of native European and alien Ponto-Caspian amphipods

Comparative mitogenomics of native European and alien Ponto-Caspian amphipods

The complete mitochondrial genome of freshwater gammarid Gammarus nipponensis (Crustacea: Amphipoda: Gammaridae)

Lake Baikal amphipods and their genomes, great and small

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