Full-length transcriptome analysis of Misgurnus anguillicaudatus

Luo, Wei; Wu, Qing; Wang, Tianzhu; Xu, Zhou; Wang, Dongjie; Wang, Yan; Yang, Song; Long, Yuejin; Du, Zongjun

doi:10.1016/j.margen.2020.100785

Cited by 4 publications

(3 citation statements)

References 17 publications

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Section: Discussionmentioning

confidence: 99%

“…PacBio RNA-seq has fast sequencing speed, high accuracy, and long readings. Because of the advantages of PacBio RNA-seq, it has been widely used in various species research ( Ma et al, 2019 ; Xue et al, 2019 ; Luo et al, 2020 ; Zheng et al, 2020 ; Chen et al, 2021 ). Because C. antiquata is an important economic shellfish with high medicinal potential, there are many studies now.…”

Section: Discussionmentioning

confidence: 99%

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SMRT Sequencing of the Full-Length Transcriptome of the Coelomactra antiquata

Deng

Yao

et al. 2021

Front. Genet.

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Coelomactra antiquata is an important aquatic economic shellfish with high medicinal value. However, because C. antiquata has no reference genome, a lot of molecular biology research cannot be carried out, so the analysis of its transcripts is an important step to study the regulatory genes of various substances in C. antiquata. In the present study, we conducted the first full-length transcriptome analysis of C. antiquata by using PacBio single-molecule real-time (SMRT) sequencing technology. The results identified a total of 39,209 unigenes with an average length of 2,732 bp, 23,338 CDSs, 251 AS events, 9,881 lncRNAs, 20,106 SSRs, and 2,316 TFs. Subsequently, 59.22% (23,220) of the unigenes were successfully annotated, of which 23,164, 18,711, 15,840, 13,534, and 13,474 unigenes could be annotated using NR, Swiss-prot, KOG, GO, and KEGG databases, respectively. This study lays the foundation for the follow-up research of molecular biology and provides a reference for studying the more medicinal value of C. antiquata.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

SMRT Sequencing of the Full-Length Transcriptome of the Coelomactra antiquata

Deng

Yao

et al. 2021

Front. Genet.

View full text Add to dashboard Cite

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“…With the continuous development of nucleic acid sequencing technology, the Pacific BioSciences (PacBio) single-molecule real-time (SMRT) sequencing, as the third-generation sequencing technology, has been utilized to generate full-length transcripts without assembly. Furthermore, the combined analysis of second-and third-generation sequencing could overcome the shortages of both technologies and is widely used currently (Grabherr et al, 2011;Cao et al, 2020;Luo et al, 2020;Liao et al, 2022). In bivalves, Zeng et al (2022) published the first report of full-length transcriptome regarding bivalve gonads in freshwater pearl mussels (Hyriopsis schlegelii), and Liao et al (2022) used a full-length transcriptome to reveal the tissue-specific gene expression profile of mangrove clam (Geloina erosa).…”

Section: Introductionmentioning

confidence: 99%

Full-length transcriptome analysis provides insights into larval shell formation in Mulinia lateralis

Guo

Zhao

et al. 2023

Front. Mar. Sci.

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Mollusca is the second largest animal phylum and represents one of the most evolutionarily successful animal groups. Mulinia lateralis, a small bivalve, is a promising model organism to facilitate studies of mollusc development. However, because of the lack of published genomic and transcriptomic resources, integrated research on the formation of larval shells in this species, which is a representative developmental process of molluscs and of great importance for larva survival, is hindered. In this study, the blastula, gastrula, trochophore larva, and D-shaped larva of M. lateralis were utilized for generating a comprehensive full-length transcriptome through Pacific BioSciences (PacBio) isoform sequencing (Iso-seq) and Illumina RNA-Seq. A total of 238,919 full-length transcripts with an average length of 3,267 bp and 121,424 annotated genes were obtained. Illumina RNA-Seq data analysis showed that 4,512, 10,637, and 17,829 differentially expressed genes (DEGs) were obtained between the two adjacent developmental stages. Functional annotation and enrichment analysis revealed the specific function of genes in shell biomineralization during different developmental stages. Twelve genes that may be involved in the formation of the larval shell of M. lateralis were identified, including insoluble shell matrix protein-encoding gene 1 (ISMP1), ISMP2, ISMP5, chitin synthase, tyrosinase, chitin-binding protein, collagen and pu14 involved in shell matrix deposition, and carbonic anhydrase, solute carrier family 4 member 8 (slc4a8), EF-hand, and a calmodulin coding gene C-2442 participated in ion transportation. In addition, calcium ion binding function, calcium signaling pathway, and endocrine and other factor-regulated calcium reabsorption pathways were significantly enriched. Weighted gene correlation network analysis (WGCNA) identified two modules related to biomineralization and larval shell formation, and slc4a8 and ring finger protein 41 (rnf41) were key hub genes that may be involved in this process. Moreover, it could be implied that the process of ion transport occurs earlier than the deposition of the shell matrix. This work provided a clear view of the transcriptome for M. lateralis and will be valuable in elucidating the mechanisms of larval shell formation as well as other developmental processes in molluscs.

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The dynamic immune responses of Mandarin fish (Siniperca chuatsi) to ISKNV in early infection based on full-length transcriptome analysis and weighted gene co-expression network analysis

Zhou

Wang

et al. 2022

Fish & Shellfish Immunology

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Full-length transcriptome analysis of Misgurnus anguillicaudatus

Cited by 4 publications

References 17 publications

SMRT Sequencing of the Full-Length Transcriptome of the Coelomactra antiquata

SMRT Sequencing of the Full-Length Transcriptome of the Coelomactra antiquata

Full-length transcriptome analysis provides insights into larval shell formation in Mulinia lateralis

The dynamic immune responses of Mandarin fish (Siniperca chuatsi) to ISKNV in early infection based on full-length transcriptome analysis and weighted gene co-expression network analysis

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