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The complete mitochondrial DNA of the tropical oyster Crassostrea belcheri from the Can Gio' mangrove in Vietnam.

ABSTRACT: The complete mitochondrial genome of the oyster Crassostrea belcheri from the C?n Giò' mangrove in Vietnam has been sequenced. It consists of a circular DNA molecule of 21020 base pairs (bp), coding for 12 proteins, 20 transfer RNAs, and two ribosomal RNAs. Like the mitogenomes of Crassostrea iredalei and Crassostrea sp. DB1, it contains a non-coding region and two ORFs. The C. belcheri mitogenome provides information that could improve the molecular phylogeny of Asian oysters and be useful to the development of oyster aquaculture in South East Asia.

SUBMITTER: Gastineau R

PROVIDER: S-EPMC7800500 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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The complete mitochondrial DNA of the tropical oyster Crassostrea belcheri from the Cần Giò' mangrove in Vietnam.

Gastineau Romain R Nguyễn Đŭc-Hùng ĐH Lemieux Claude C Turmel Monique M Tremblay Réjean R Nguyễn Văn Duy VD Widowati Ita I Witkowski Andrzej A Mouget Jean-Luc JL

Mitochondrial DNA. Part B, Resources 20180412 1

The complete mitochondrial genome of the oyster Crassostrea belcheri from the Cần Giò' mangrove in Vietnam has been sequenced. It consists of a circular DNA molecule of 21020 base pairs (bp), coding for 12 proteins, 20 transfer RNAs, and two ribosomal RNAs. Like the mitogenomes of Crassostrea iredalei and Crassostrea sp. DB1, it contains a non-coding region and two ORFs. The C. belcheri mitogenome provides information that could improve the molecular phylogeny of Asia ...[more]

PMID: 33474205

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Project description:BACKGROUND:Many types of shellfish including oysters are sometime cooked before ingestion and it has been demonstrated that cooking may affect the allergenicity of food. Therefore, the aim of our present study is to identify major and minor allergens of tropical oyster (Crassostrea belcheri) and to investigate the effect of different cooking processing on the allergenicity of this oyster. METHODS:Raw, boiled, fried and roasted extracts of oyster were prepared. Protein profiles were analysed using sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). Major and minor allergens and allergenicity patterns of all extracts were then determined by immunoblotting with sera from patients with positive skin prick tests (SPT) to the raw oyster extract. Mass-spectrometry was used to identify the major allergenic proteins of this oyster. RESULTS:SDS-PAGE of the raw extract showed 15 protein bands (20-180 kDa). In contrast, smaller numbers of protein bands were demonstrated in the boiled extract, those ranging between 40-42 and 55-150 kDa were denatured, whereas the protein profiles were altered to a similar degree by frying or roasting. The 37 kDa proteins had the highest frequency of IgE-binding (95 %), thus identified as the major allergen of this tropical oyster. Other minor IgE-binding proteins were observed at various molecular weights. Immunoblot of raw extract yielded 11 IgE-binding proteins. The cooked extracts showed only a single IgE-binding protein at 37 kDa. Mass spectrometry analysis of the 37 kDa major allergen identified this spot as tropomyosin. CONCLUSIONS:Cooked extracts produce lower IgE-binding than raw extract, which suggest that thermal treatment can be used as a tool in attempting to reduce oyster allergenicity by reducing the number of IgE-reactive bands. The degree of allergenicity of this oyster was demonstrated in the order raw > boiled > fried ? roasted. A heat-resistent 37 kDa protein, corresponding to tropomyosin, was identified as the major allergen of this tropical oyster.

Project description:BackgroundMitochondrial DNA sequences are extensively used as genetic markers not only for studies of population or ecological genetics, but also for phylogenetic and evolutionary analyses. Complete mt-sequences can reveal information about gene order and its variation, as well as gene and genome evolution when sequences from multiple phyla are compared. Mitochondrial gene order is highly variable among mollusks, with bivalves exhibiting the most variability. Of the 41 complete mt genomes sequenced so far, 12 are from bivalves. We determined, in the current study, the complete mitochondrial DNA sequence of Crassostrea hongkongensis. We present here an analysis of features of its gene content and genome organization in comparison with two other Crassostrea species to assess the variation within bivalves and among main groups of mollusks.ResultsThe complete mitochondrial genome of C. hongkongensis was determined using long PCR and a primer walking sequencing strategy with genus-specific primers. The genome is 16,475 bp in length and contains 12 protein-coding genes (the atp8 gene is missing, as in most bivalves), 22 transfer tRNA genes (including a suppressor tRNA gene), and 2 ribosomal RNA genes, all of which appear to be transcribed from the same strand. A striking finding of this study is that a DNA segment containing four tRNA genes (trnk1, trnC, trnQ1 and trnN) and two duplicated or split rRNA gene (rrnL5' and rrnS) are absent from the genome, when compared with that of two other extant Crassostrea species, which is very likely a consequence of loss of a single genomic region present in ancestor of C. hongkongensis. It indicates this region seem to be a "hot spot" of genomic rearrangements over the Crassostrea mt-genomes. The arrangement of protein-coding genes in C. hongkongensis is identical to that of Crassostrea gigas and Crassostrea virginica, but higher amino acid sequence identities are shared between C. hongkongensis and C. gigas than between other pairs. There exists significant codon bias, favoring codons ending in A or T and against those ending with C. Pair analysis of genome rearrangements showed that the rearrangement distance is great between C. gigas-C. hongkongensis and C. virginica, indicating a high degree of rearrangements within Crassostrea. The determination of complete mt-genome of C. hongkongensis has yielded useful insight into features of gene order, variation, and evolution of Crassostrea and bivalve mt-genomes.ConclusionThe mt-genome of C. hongkongensis shares some similarity with, and interesting differences to, other Crassostrea species and bivalves. The absence of trnC and trnN genes and duplicated or split rRNA genes from the C. hongkongensis genome is a completely novel feature not previously reported in Crassostrea species. The phenomenon is likely due to the loss of a segment that is present in other Crassostrea species and was present in ancestor of C. hongkongensis, thus a case of "tandem duplication-random loss (TDRL)". The mt-genome and new feature presented here reveal and underline the high level variation of gene order and gene content in Crassostrea and bivalves, inspiring more research to gain understanding to mechanisms underlying gene and genome evolution in bivalves and mollusks.

Project description:BackgroundBecause of its typical architecture, inheritance and small size, mitochondrial (mt) DNA is widely used for phylogenetic studies. Gene order is generally conserved in most taxa although some groups show considerable variation. This is particularly true in the phylum Mollusca, especially in the Bivalvia. During the last few years, there have been significant increases in the number of complete mitochondrial sequences available. For bivalves, 35 complete mitochondrial genomes are now available in GenBank, a number that has more than doubled in the last three years, representing 6 families and 23 genera. In the current study, we determined the complete mtDNA sequence of O. edulis, the European flat oyster. We present an analysis of features of its gene content and genome organization in comparison with other Ostrea, Saccostrea and Crassostrea species.ResultsThe Ostrea edulis mt genome is 16 320 bp in length and codes for 37 genes (12 protein-coding genes, 2 rRNAs and 23 tRNAs) on the same strand. As in other Ostreidae, O. edulis mt genome contains a split of the rrnL gene and a duplication of trnM. The tRNA gene set of O. edulis, Ostrea denselamellosa and Crassostrea virginica are identical in having 23 tRNA genes, in contrast to Asian oysters, which have 25 tRNA genes (except for C. ariakensis with 24). O. edulis and O. denselamellosa share the same gene order, but differ from other Ostreidae and are closer to Crassostrea than to Saccostrea. Phylogenetic analyses reinforce the taxonomic classification of the 3 families Ostreidae, Mytilidae and Pectinidae. Within the Ostreidae family the results also reveal a closer relationship between Ostrea and Saccostrea than between Ostrea and Crassostrea.ConclusionsOstrea edulis mitogenomic analyses show a high level of conservation within the genus Ostrea, whereas they show a high level of variation within the Ostreidae family. These features provide useful information for further evolutionary analysis of oyster mitogenomes.

Dataset Information

The complete mitochondrial DNA of the tropical oyster Crassostrea belcheri from the Can Gio' mangrove in Vietnam.

Publications

The complete mitochondrial DNA of the tropical oyster <i>Crassostrea belcheri</i> from the Cần Giò' mangrove in Vietnam.

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