The complete mitogenome of clam <i>Corbicula fluminea</i> determined usingnext-generation and PacBio sequencing

Zhang, Tongqing; Yin, Jiawen; Tang, Shengkai; Li, Daming; Liu, Xiaowei; Gu, Xiankun; Liu, Yan-Shan

doi:10.1080/23802359.2019.1607577

Cited by 6 publications

(7 citation statements)

References 16 publications

(13 reference statements)

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“…Mitochondrial genes have been used for animal, particularly aquatic animal, population genetics for decades ( 94 – 99 ), whereas full mitogenome sequencing has become common only in the past 5 years ( 100 ). We developed a high-throughput two-fragment, mitochondrial amplicon workflow for the Oxford Nanopore Technologies long-read sequencer, which to our knowledge is the first demonstration of using ONT for this application with fish.…”

Section: Methodsmentioning

confidence: 99%

Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus

Minich

Petrus

Michael

et al. 2020

mSphere

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Changing ocean conditions driven by anthropogenic activities may have a negative impact on fisheries by increasing stress and disease. To understand how environment and host biology drives mucosal microbiomes in a marine fish, we surveyed five body sites (gill, skin, digesta, gastrointestinal tract [GI], and pyloric ceca) from 229 Pacific chub mackerel, Scomber japonicus, collected across 38 time points spanning 1 year from the Scripps Institution of Oceanography Pier (La Jolla, CA). Mucosal sites had unique microbial communities significantly different from the surrounding seawater and sediment communities with over 10 times more total diversity than seawater. The external surfaces of skin and gill were more similar to seawater, while digesta was more similar to sediment. Alpha and beta diversity of the skin and gill was explained by environmental and biological factors, specifically, sea surface temperature, chlorophyll a, and fish age, consistent with an exposure gradient relationship. We verified that seasonal microbial changes were not confounded by regional migration of chub mackerel subpopulations by nanopore sequencing a 14,769-bp region of the 16,568-bp mitochondria across all temporal fish specimens. A cosmopolitan pathogen, Photobacterium damselae, was prevalent across multiple body sites all year but highest in the skin, GI, and digesta between June and September, when the ocean is warmest. The longitudinal fish microbiome study evaluates the extent to which the environment and host biology drives mucosal microbial ecology and establishes a baseline for long-term surveys linking environment stressors to mucosal health of wild marine fish. IMPORTANCE Pacific chub mackerel, Scomber japonicus, are one of the largest and most economically important fisheries in the world. The fish is harvested for both human consumption and fish meal. Changing ocean conditions driven by anthropogenic stressors like climate change may negatively impact fisheries. One mechanism for this is through disease. As waters warm and chemistry changes, the microbial communities associated with fish may change. In this study, we performed a holistic analysis of all mucosal sites on the fish over a 1-year time series to explore seasonal variation and to understand the environmental drivers of the microbiome. Understanding seasonality in the fish microbiome is also applicable to aquaculture production for producers to better understand and predict when disease outbreaks may occur based on changing environmental conditions in the ocean.

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Section: Methodsmentioning

confidence: 99%

Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus

Minich

Petrus

Michael

et al. 2020

mSphere

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“…Most of the PCGs employ ATN (ATG, ATA and ATT) as an initiation codon. In addition to the classical metazoan start codon, GTG (Valine) initiated translation 38 – 40 of ATP6 and nad2 gene in Cyrenid clams 41 including V. cyprinoides . Ten PCGs were terminated by TAG, and TAA codons whilst remaining were terminated by truncated codons T– and TA- which presumably functions as complete termination codon after post-transcriptional polyadenylation 42 , 43 (Table 2 ).…”

Section: Resultsmentioning

confidence: 99%

Mitogenomic architecture of the multivalent endemic black clam (Villorita cyprinoides) and its phylogenetic implications

Rahuman

Jeena

Asokan

et al. 2020

Sci Rep

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The Indian black clam Villorita cyprinoides (Family: Cyrenidae), an extractive commercially exploited species with aquaculture importance contributing more than 70% of clam fishery in India, is endemic to the Indian peninsula. Currently, there is very sparse information, especially on the molecular data of Villorita. The present study aims to provide a comprehensive knowledge of mitogenome architecture and assess the phylogenetic status of Cyrenidae. This has resulted in reporting the first complete mitogenome of V. cyprinoides using next-generation sequencing technology. The A+T circular mitogenome was 15,880 bp long, exhibiting 13 protein-coding genes (PCGs) including ATP8 (absent in several bivalves), 22 transfer RNA, and two ribosomal RNA genes residing in the heavy strand in a clockwise orientation and a gene order akin to Corbicula fluminea. The molecular phylogeny inferred from a concatenated multi-gene sequence [14 mitochondrial (12 PCGs, rrnS and rrnL) and two nuclear genes (Histone H3, 18S rRNA)] from 47 representative species of superorder Imparidentia, clustered V. cyprinoides and Cyrenid clams to a single clade supporting the monophyly of Cyrenidae. The subsequent mitochondrial gene order analysis substantiates the close relationship of V. cyprinoides and C. fluminea, analogous to phylogenetic output. The multilocus tree topology calibrated with verified fossil data deciphered the origin and diversification of Cyrenid clams during late Triassic-early Jurassic. The data derived from this study shall contribute remarkably for further insights on cryptic species identification, molecular characterization of bivalve mitogenomes and mitochondrial evolutionary history of genus Villorita. Moreover, complete mitogenome can aid in potential marker development for assessing the genetic health of black clam populations.

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“…The methods of mtDNA extraction and sequencing were described in our previous work (Zhang et al. 2019 ).…”

Section: Methodsmentioning

confidence: 99%

The complete mitogenome of freshwater gammarid Grandidierella taihuensis (Crustacea: Amphipoda)

Yin

Zhao

Zeng

et al. 2021

Mitochondrial DNA Part B

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The freshwater gammarid Grandidierella taihuensis is an important composition of benthic community. In this study, the complete mitogenome sequences of G. taihuensis are determined using next-generation and PacBio long-read sequencing. The mitogenome of G. taihuensis is 15,099 bp in size, and consisted of 13 protein-coding genes, two ribosomal RNA genes, 22 tRNA genes, and a putative control region. Gene arrangement is as same as that of G. rubroantennata . The base composition of the entire mitogenome showed a conspicuous A + T bias of 69.4%. The mitogenome data produced in this study provides a useful resource for future evolutionary and ecological studies.

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The complete mitogenome of clam Corbicula fluminea determined usingnext-generation and PacBio sequencing

Cited by 6 publications

References 16 publications

Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus

Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus

Mitogenomic architecture of the multivalent endemic black clam (Villorita cyprinoides) and its phylogenetic implications

The complete mitogenome of freshwater gammarid Grandidierella taihuensis (Crustacea: Amphipoda)

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