Alternative splicing derived invertebrate variable lymphocyte receptor displays diversity and specificity in immune system of crab Eriocheir sinensis

Xu, Yuanfeng; Yang, Yanan; Zheng, Jinbin; Cui, Zhaoxia

doi:10.3389/fimmu.2022.1105318

Cited by 6 publications

(3 citation statements)

References 35 publications

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“…AS generates multiple transcripts from a single gene, enriching the diversity of proteins and phenotypic traits, it can facilitate adaptation as well as contribute to species divergence 35 . In invertebrates, AS has proved to be involved in various processes, for instance, neuronal development, immune speci city, and sex determination [36][37][38][39] . 1236 AS events from 806 genes were predicted in this study, occupying 22% of total genes identi ed.…”

Section: Discussionmentioning

confidence: 99%

Analysis of NHL-1 gene family based on full-length transcriptome in Neocaridina denticulata sinensis

Xing,

Li,

Wang

et al. 2024

Preprint

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Neocaridina denticulata sinensis has emerged as a promising model organism for basic studies in Decapod. However, the current transcriptome information in this species is based on next generation sequencing (NGS) technologies, which is limited by the short read length. Therefore, the present study aims to generate a full-length transcriptome assembly of N. denticulata sinensis utilizing the PacBio Sequel Ⅱ platform. The resulting transcriptome assembly comprised 5831 transcripts, with an N50 of 3697 bp. Remarkably, 90.5% of these transcripts represented novel isoforms of known genes. The transcripts were further searched against NR, SwissProt, KEGG, KOG, GO, NT and Pfam databases. 24.8% of the transcripts can be annotated across all seven databases. Additionally, 1236 alternative splicing (AS) events, 344 transcription factors (TFs), and 124 long non-coding RNAs (lncRNAs) were predicted. Based on the AS annotation results, a RING finger protein NHL-1 gene from N. denticulata sinensis (NdNHL-1) was identified. There are 15 transcripts in NdNHL-1. The longest transcript is 4995 bp in length and encodes a putative protein of 1665 amino acids. Phylogenetic analysis showed its close relationship with NHL-1 from other crustacean species. This report represents the full-length transcriptome of N. denticulata sinensis, and will facilitate the research of functional genomics and environmental adaptation in this species.

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Section: Discussionmentioning

confidence: 99%

Analysis of NHL-1 gene family based on full-length transcriptome in Neocaridina denticulata sinensis

Xing,

Li,

Wang

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…Alternative splicing generates multiple transcripts from a single gene, enriching the diversity of proteins and phenotypic traits; it can facilitate adaptation as well as contribute to species divergence [ 47 ]. In invertebrates, alternative splicing has proven to be involved in various processes, for instance, neuronal development, immune specificity, and sex determination [ 48 , 49 , 50 , 51 ]. A total of 1236 alternative splicing events from 806 genes were predicted in this study, occupying 22% of the total genes identified.…”

Section: Discussionmentioning

confidence: 99%

A Full-Length Transcriptome and Analysis of the NHL-1 Gene Family in Neocaridina denticulata sinensis

Xing,

Li,

Wang

et al. 2024

Biology

View full text Add to dashboard Cite

Neocaridina denticulata sinensis has emerged as a promising model organism for basic studies in Decapod. However, the current transcriptome information on this species is based on next-generation sequencing technologies, which are limited by a short read length. Therefore, the present study aimed to generate a full-length transcriptome assembly of N. denticulata sinensis utilizing the PacBio Sequel Ⅱ platform. The resulting transcriptome assembly comprised 5831 transcripts with an N50 value of 3697 bp. Remarkably, 90.5% of these transcripts represented novel isoforms of known genes. The transcripts were further searched against the NR, SwissProt, KEGG, KOG, GO, NT, and Pfam databases. A total of 24.8% of the transcripts can be annotated across all seven databases. Additionally, 1236 alternative splicing events, 344 transcription factors, and 124 long non-coding RNAs (LncRNAs) were predicted. Based on the alternative splicing annotation results, a RING finger protein NHL-1 gene from N. denticulata sinensis (NdNHL-1) was identified. There are 15 transcripts in NdNHL-1. The longest transcript is 4995 bp in length and encodes a putative protein of 1665 amino acids. A phylogenetic analysis showed its close relationship with NHL-1 from other crustacean species. This report represents the full-length transcriptome of N. denticulata sinensis and will facilitate research on functional genomics and environmental adaptation in this species.

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“…However, the current understanding of transcriptomic responses to stress primarily revolves around the transcriptional level, leaving the posttranscriptional regulation aspect largely unexplored and poorly understood. In fact, the dynamic changes in the AS profile have been extensively elucidated under various stress conditions in shrimp and other crustacean species [10,16,30,31], providing valuable insights into the significant role of AS in the adaptive evolution of animals. However, the extent to which AS contributes to heat stress resistance in shrimp remains uncertain.…”

Section: Discussionmentioning

confidence: 99%

The Responses of Alternative Splicing during Heat Stress in the Pacific White Shrimp Litopenaeus vannamei

Zhang

Yuan

et al. 2023

Genes

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Heat tolerance is increasingly becoming a crucial trait for aquaculture species in the face of rapidly changing climate conditions. Alternative splicing (AS) is a vital mechanism within cells that modulates gene abundance and functional diversity, enabling organisms to effectively respond to diverse stressful conditions, including thermal stress. However, it is still uncertain whether AS contributes to heat tolerance in shrimp. In this study, we conducted an extensive transcriptome analysis on the Pacific white shrimp, Litopenaeus vannamei, revealing a total of 1267, 987, and 130 differential AS events (DAS) in the gill, hepatopancreas, and muscle, respectively, following exposure to heat stress. Among all of the DAS events, exon skipping (ES) was the predominant form of splicing modification observed. Interestingly, a minor portion of DAS genes exhibited overlap across the three tissues, implying that heat stress exerts unique effects on various tissue types. Moreover, the functional enrichment analysis demonstrated that commonly identified DAS genes were primarily associated with the “spliceosome” pathway, indicating that the AS of splicing-related genes played a crucial role in the response to heat stress. Our findings also revealed that heat stress tended to induce longer mRNA isoforms through differential alternative 3′ splice site (A3SS) events. Notably, A3SS events exhibited the highest proportion of maintained open reading frames (ORFs) under heat stress. Interestingly, we observed a limited overlap between the genes exhibiting DAS and those showing differential gene expression (DEG), indicating that AS may function as a distinct regulatory mechanism independent of transcriptional regulation in response to heat stress. This is the first comprehensive study on AS in crustacea species under heat stress, which broadens our understanding of the regulatory mechanisms governing the crustaceans’ response to environmental stress, providing valuable insights for the aquaculture breeding of shrimp and other aquatic animals.

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Alternative splicing derived invertebrate variable lymphocyte receptor displays diversity and specificity in immune system of crab Eriocheir sinensis

Cited by 6 publications

References 35 publications

Analysis of NHL-1 gene family based on full-length transcriptome in Neocaridina denticulata sinensis

Analysis of NHL-1 gene family based on full-length transcriptome in Neocaridina denticulata sinensis

A Full-Length Transcriptome and Analysis of the NHL-1 Gene Family in Neocaridina denticulata sinensis

The Responses of Alternative Splicing during Heat Stress in the Pacific White Shrimp Litopenaeus vannamei

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