Discovery and functional understanding of MiRNAs in molluscs: a genome-wide profiling approach

Huang, Songqian; Yoshitake, Kazutoshi; Asaduzzaman, Md.; Kinoshita, Shigeharu; Watabe, Shugo; Asakawa, Shuichi

doi:10.1080/15476286.2020.1867798

Cited by 8 publications

(5 citation statements)

References 112 publications

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“…The comparison of the miRNAs copy number shows differences within a species between the different approaches used for their annotation limiting the ability to make reliable comparisons. In C. gigas , 8 copies of miRNA-184 are identified by Huang et al, (2021) versus 44 by Rosani et al, (2021). More, differences are evidenced when comparing predicted miRNA and miRNA identified in small-RNAseq sequencing which do not confirm that the predicted miRNAs are actually expressed.…”

Section: Discussionmentioning

confidence: 91%

Chromosomal assembly of the flat oyster (Ostrea edulisL.) genome as a new genetic ressource for aquaculture

Boutet

Monteiro

Takeuchi

et al. 2022

Preprint

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The European flat oyster (Ostrea edulis L.) is the endemic species of the European coasts. Its exploitation has been reduced during the last decades, because of the appearance of two parasites that have led to the collapse of the stocks and the strong decline of the natural oyster beds. O. edulis has been the subject of numerous studies and programs in population genetics and on the presence of the parasites Bonamia ostreae and Marteilia refringens. These studies investigated the effects of these parasites mainly on immunity at the molecular and cellular levels. Several genetic selection programs especially related to resistance to the parasite have been initiated. Within the framework of a European project (PERLE 2) which aims to produce genetic lines of O. edulis with hardiness traits (growth, survival, resistance) for the purpose of repopulating natural oyster beds in Brittany and reviving the culture of this species on the foreshore, obtaining a reference genome has proved to be essential as done recently in many bivalve species of aquaculture interest. Here, we present a chromosome-level genome assembly and annotation for the European flat oyster, generated by combining PacBio technology, Illumina, 10X linked and Hi-C sequencing. The finished assembly is 887.2 Mb with a scaffold-N50 of 97.1 Mb scaffolded on the expected 10 pseudo-chromosomes. Annotation of the genome revealed the presence of 35962 protein-coding genes. We analyzed in details the transposable elements (TE) diversity in the flat oyster genome, highlight some specificities in tRNA and miRNA composition and provide first insights in the molecular response of O. edulis to M. refringens. This genome will serve as a reference for genomic studies on O. edulis to better understand its basic physiology or developing genetic markers in breeding projects for aquaculture or natural reef restoration.

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Section: Discussionmentioning

confidence: 91%

Chromosomal assembly of the flat oyster (Ostrea edulisL.) genome as a new genetic ressource for aquaculture

Boutet

Monteiro

Takeuchi

et al. 2022

Preprint

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show abstract

“…The comparison of the miRNAs copy number shows differences within a species between the different approaches used for their annotation limiting the ability to make reliable comparisons. In C. gigas , eight copies of miRNA‐184 are identified by Huang et al ( 2021 ) versus 44 by Rosani et al ( 2021 ). Further, differences are observed when comparing predicted miRNA and miRNA identified in small‐RNAseq sequencing, which do not confirm that the predicted miRNAs are actually expressed.…”

Section: Discussionmentioning

confidence: 99%

Chromosomal assembly of the flat oyster (Ostrea edulis L.) genome as a new genetic resource for aquaculture

Boutet

Monteiro

Baudry

et al. 2022

Evolutionary Applications

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The European flat oyster (Ostrea edulis L.) is a native bivalve of the European coasts. Harvest of this species has declined during the last decades because of the appearance of two parasites that have led to the collapse of the stocks and the loss of the natural oyster beds. O. edulis has been the subject of numerous studies in population genetics and on the detection of the parasites Bonamia ostreae and Marteilia refringens. These studies investigated immune responses to these parasites at the molecular and cellular levels. Several genetic improvement programs have been initiated especially for parasite resistance. Within the framework of a European project (PERLE 2) that aims to produce genetic lines of O. edulis with hardiness traits (growth, survival, resistance) for the purpose of repopulating natural oyster beds in Brittany and reviving the culture of this species in the foreshore, obtaining a reference genome becomes essential as done recently in many bivalve species of aquaculture interest. Here, we present a chromosome‐level genome assembly and annotation for the European flat oyster, generated by combining PacBio, Illumina, 10X linked, and Hi‐C sequencing. The finished assembly is 887.2 Mb with a scaffold‐N50 of 97.1 Mb scaffolded on the expected 10 pseudochromosomes. Annotation of the genome revealed the presence of 35,962 protein‐coding genes. We analyzed in detail the transposable element (TE) diversity in the flat oyster genome, highlighted some specificities in tRNA and miRNA composition, and provided the first insight into the molecular response of O. edulis to M. refringens. This genome provides a reference for genomic studies on O. edulis to better understand its basic physiology and as a useful resource for genetic breeding in support of aquaculture and natural reef restoration.

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“…Small RNA molecules were isolated and sequenced using sRNA-seq from P. fucata exosomes. A total of 38 miRNA species were identified in the examined samples during grafting transplantation, which was fewer than those identified from sRNA-seq from somatic and gonadal tissues and genome-wide prediction [ 41 , 48 ]. Furthermore, the expression levels of most miRNAs were very low in the exosomes.…”

Section: Discussionmentioning

confidence: 99%

“…In fact, miR-2, an invertebrate-specific family member, plays a vital role in the immune response [ 52 ], and miR-29 is involved in the immune response by regulating neuropeptide Y receptor 2 (Y2R) in Pinctada martensii [ 53 ]. In addition, several miRNAs, namely miR-750, miR-1175, miR-1990 and miR-1991, were also observed in P. fucata exosomes, which were specifically discovered in molluscs by genome-wide prediction [ 48 ]. Specifically, miR-1990 showed a mantle-specific expression pattern in P. fucata [ 41 ], and miR-1991 was specifically expressed in the adductor muscle of C. gigas [ 54 ] and exosome-derived miR-15b negatively regulated hcApo to mediate shell colour formation in H. cumingii [ 11 ].…”

Section: Discussionmentioning

confidence: 99%

Exosome-derived small non-coding RNAs reveal immune response upon grafting transplantation in Pinctada fucata (Mollusca)

et al. 2022

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Exosomes, a subset of small extracellular vesicles, carry various nucleic acids, proteins, lipids, amino acids and metabolites. They function as a mode of intercellular communication and molecular transfer. Exosome cargo molecules, including small non-coding RNAs (sncRNAs), are involved in the immune response in various organisms. However, the role of exosome-derived sncRNAs in immune responses in molluscs remains unclear. Here, we aimed to reveal the sncRNAs involved in the immune response during grafting transplantation by the pearl oyster Pinctada fucata . Exosomes were successfully extracted from the P. fucata haemolymph during graft transplantation. Abundant microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) were simultaneously discovered in P. fucata exosomes by small RNA sequencing. The expression patterns of the miRNAs and piRNAs at the grafting and initial stages were not substantially different, but varied significantly between the initial and later stages. Target prediction and functional analysis indicate that these miRNAs and piRNAs are related to immune response upon grafting transplantation, whereas piRNAs may also be associated with transposon silencing by targeting with genome transposon elements. This work provides the basis for a functional understanding of exosome-derived sncRNAs and helps to gain further insight into the PIWI/piRNA pathway function outside of germline cells in molluscs.

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Discovery and functional understanding of MiRNAs in molluscs: a genome-wide profiling approach

Cited by 8 publications

References 112 publications

Chromosomal assembly of the flat oyster (Ostrea edulisL.) genome as a new genetic ressource for aquaculture

Chromosomal assembly of the flat oyster (Ostrea edulisL.) genome as a new genetic ressource for aquaculture

Chromosomal assembly of the flat oyster (Ostrea edulis L.) genome as a new genetic resource for aquaculture

Exosome-derived small non-coding RNAs reveal immune response upon grafting transplantation in Pinctada fucata (Mollusca)

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