Complete mitochondrial genome of Ark shell
            <i>Scapharca subcrenata</i>

Hou, Ya Ming; Wu, Biao; Liu, Zhihong; Yang, Aiguo; Ren, Jianfeng; Zhou, Liqing; Dong, Chunguang; Tian, Jing

doi:10.3109/19401736.2014.926495

Cited by 10 publications

(9 citation statements)

References 3 publications

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“…Though proportions of unassigned regions may potentially be the discerning feature for some taxonomic groups 129 , this notion should also be treated with caution as the sizes of these regions may be influenced by the assembly or annotation methods used to predict genes, exemplified by the identification of three trnL genes by Segawa and Aotsuka 127 as opposed to only two copies reported following re-annotations by MITOS in this study 10 . But generally, decapod mitogenome sizes are relatively stable compared to those of other metazoan groups such as bivalves, nematodes and sponges that exhibit strong heterogeneity in size 88 , with some larger molecules spanning lengths of over 20 kbp and even up to 48 kbp 130 .…”

Section: Discussionmentioning

confidence: 99%

Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition

Tan

Gan

Lee

et al. 2019

Sci Rep

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The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.

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Section: Discussionmentioning

confidence: 99%

Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition

Tan

Gan

Lee

et al. 2019

Sci Rep

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“…Unlike vertebrates with a highly conserved mitochondrial genome, the available mollusk mitochondrial genomes have shown exceptional features, including doubly uniparental inheritance, gene rearrangements, large sizes, gene duplications, different gene distribution between DNA strands, and a high degree of mtDNA variability [ 1 , 9 – 11 ]. The mtDNA as a molecular marker has been widely used throughout animal groups for the study of phylogenetic relationships among taxa, resolution of taxonomic controversies, and population genetics [ 12 – 15 ].…”

Section: Introductionmentioning

confidence: 99%

The mitochondrial genome of the semi-slug Omalonyx unguis (Gastropoda: Succineidae) and the phylogenetic relationships within Stylommatophora

2021

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Here we report the first complete mitochondrial genome of the semi-slug Omalonyx unguis (d’Orbigny, 1836) (Gastropoda: Succineidae). Sequencing was performed on a specimen from Argentina. Assembly was performed using Sanger data and Illumina next generation sequencing (NGS). The mitogenome was 13,984 bp in length and encoded the 37 typical Metazoan genes. A potential origin for mitochondrial DNA replication was found in a non-coding intergenic spacer (49 bp) located between cox3 and tRNA-Ile genes, and its secondary structure was characterized. Secondary structure models of the tRNA genes of O. unguis largely agreed with those proposed for other mollusks. Secondary structure models for the two rRNA genes were also obtained. To our knowledge, the 12S-rRNA model derived here is the first complete one available for mollusks. Phylogenetic analyses based on the mitogenomes of O. unguis and 37 other species of Stylommatophora were performed using amino acid sequences from the 13 protein-coding genes. Our results located Succineoidea as a sister group of Helicoidea + Urocoptoidea, similar to previous studies based on mitochondrial genomes. The gene arrangement of O. unguis was identical to that reported for another species of Succineoidea. The unique rearrangements observed for this group within Stylommatophora, may constitute synapomorphies for the superfamily.

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“…For example, Malagasy poison frogs (Mantella spp.) commonly have > 22 kbp mt genomes enlarged by the duplication of genes and CR regions [20,25], and two Scapharca ark shells exhibit > 46 kbp mt genomes, mainly caused by elongations (> 30 kbp) of non-coding sequences [4,57]. However, there has been no similar example to that of Breviceps where the mt genome enlargement occurs in independent congeneric lineages, from distinct causes.…”

Section: Phylogeny Timing and Distinct Causes Of Mt Genome Enlargement In These Congeneric Rain Frogsmentioning

confidence: 99%

Sequencing of Mitochondrial DNA with Long Repetitive Regions and Detection of the Frog Lineages of Large mt Genome Showing Reduction of Purifying Selection

Kakehashi¹,

Hemmi²,

Kambayashi³

et al. 2021

Prime Archives in Genetics

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The mitochondrial (mt) genome of the bushveld rain frog (Breviceps adspersus, family Brevicipitidae, Afrobatrachia) is the largest (28.8 kbp) among the vertebrates investigated to date. The major cause of genome size enlargement in this species is the duplication of multiple genomic regions. To investigate the evolutionary lineage, timing, and process of mt genome enlargement, we sequenced the complete mtDNAs of two congeneric rain frogs, B. mossambicus and B. poweri. The mt genomic organization, gene content, and gene arrangements of these two rain frogs are very similar to each other but differ from that of B. adspersus. The B. mossambicus mt genome (22.5 kbp) does not differ significantly from that of most other afrobatrachians. In contrast, the B. poweri mtDNA (28.1 kbp) is considerably larger: currently the second largest among vertebrates, after B. adspersus. The main causes of genome enlargement differ among Breviceps species. Unusual elongation (12.5 kbp) of the control region (CR), a single major non-coding region of the vertebrate mt genome, is responsible for the extremely large mt genome in B. poweri. Based on the current Breviceps phylogeny and estimated divergence age, it can be concluded that the genome enlargements occurred independently in each species lineage within relatively short periods. Furthermore, a high nucleotide substitution rate and relaxation of selective pressures, which are considered to be involved in changes in genome size, were also detected in afrobatrachian lineages. Our results suggest that these factors were not direct causes but may have indirectly affected mt genome enlargements in Breviceps.

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Complete mitochondrial genome of Ark shell Scapharca subcrenata

Cited by 10 publications

References 3 publications

Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition

Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition

The mitochondrial genome of the semi-slug Omalonyx unguis (Gastropoda: Succineidae) and the phylogenetic relationships within Stylommatophora

Sequencing of Mitochondrial DNA with Long Repetitive Regions and Detection of the Frog Lineages of Large mt Genome Showing Reduction of Purifying Selection

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