Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2021 May 24;376(1825):20200165.
doi: 10.1098/rstb.2020.0165. Epub 2021 Apr 5.

Digging into bivalve miRNAomes: between conservation and innovation

Umberto Rosani  1 , Enrico Bortoletto  1 , Chang-Ming Bai  2 , Beatriz Novoa  3 , Antonio Figueras  3 , Paola Venier  1 , Bastian Fromm  4
Affiliations
Review

Digging into bivalve miRNAomes: between conservation and innovation

Umberto Rosani et al. Philos Trans R Soc Lond B Biol Sci. .

Abstract

Bivalves are a diverse mollusc group of economic and ecological importance. An evident resilience to pollution, parasites and extreme environments makes some bivalve species important models for studying adaptation and immunity. Despite substantial progress in sequencing projects of bivalves, information on non-coding genes and gene-regulatory aspects is still lacking. Here, we review the current repertoire of bivalve microRNAs (miRNAs), important regulators of gene expression in Metazoa. We exploited available short non-coding RNA (sncRNA) data for Pinctada martensii, Crassostrea gigas, Corbicula fluminea, Tegillarca granosa and Ruditapes philippinarum, and we produced new sncRNA data for two additional bivalves, the Mediterranean mussel Mytilus galloprovincialis and the blood clam Scapharca broughtonii. We found substantial heterogeneity and incorrect annotations of miRNAs; hence, we reannotated conserved miRNA families using recently established criteria for bona fide microRNA annotation. We found 106 miRNA families missing in the previously published bivalve datasets and 89 and 87 miRNA complements were identified in the two additional species. The overall results provide a homogeneous and evolutionarily consistent picture of miRNAs in bivalves and enable future comparative studies. The identification of two bivalve-specific miRNA families sheds further light on the complexity of transcription and its regulation in bivalve molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

Keywords: Bivalvia; bivalves; blood clam; microRNA; mussel.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
miRNA families conserved in bivalves. For the analysed species, the presence of Eumetazoa (Eu.), Bilateria, Protosomia, Lophotrochozoa (Lop.), Neotrochozoa (Neo.) and Mollusca (Moll.) conserved miRNA families is reported with different colours, if already mentioned (white) or newly reported (green, orange or blue). For the species with a sequenced genome, the number of paralogs for each miRNA family is also indicated.
Figure 2.
Figure 2.
Conservation among bivalves of miRNA complements previously reported as oyster novelties. The conservation of the 23 novel oyster miRNAs retrieved from MirGeneDB was investigated in the genomes of 28 bivalve species. Four C. gigas genome assemblies have been considered, (1) oyster_v9, (2) ASM29789v2, (3) ASM1103280v1 and (4) cgigas_uk_roslin_v1.
Figure 3.
Figure 3.
Gene pathways regulated by miRNAs in bivalves. According to published data on validated miRNA-mRNA interactions, the gene pathways regulated by C. gigas miRNAs (Cgi-miR, in pink), P. fucata (Pma-miR, in green) and H. comingii (Hcu-miR, in blue) are depicted. The picture was drawn with BioRender.com.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. FAO. 2020. The state of world fisheries and aquaculture 2020: sustainability in action. Rome, Italy: FAO. See http://www.fao.org/documents/card/en/c/ca9229en.
    1. Morton B, Machado FM. 2019. Predatory marine bivalves: a review. Adv. Mar. Biol. 84, 1-98. (10.1016/bs.amb.2019.10.001) - DOI - PubMed
    1. Tan Y, Fang L, Qiu M, Huo Z, Yan X. 2020. Population genetics of the Manila clam (Ruditapes philippinarum) in East Asia. Sci. Rep. 10, 21890. (10.1038/s41598-020-78923-w) - DOI - PMC - PubMed
    1. Fernández Robledo JA, et al. 2019. From the raw bar to the bench: bivalves as models for human health. Dev. Comp. Immunol. 92, 260-282. (10.1016/j.dci.2018.11.020) - DOI - PMC - PubMed
    1. Takeuchi T, et al. 2016. Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle. Zool. Lett. 2, 3. (10.1186/s40851-016-0039-2) - DOI - PMC - PubMed

Publication types

LinkOut - more resources