Transcriptome analysis of Neocaridina denticulate sinensis challenged by Vibrio parahemolyticus

Liu, Yujie; Xing, Kefan; Yan, Congcong; Zhou, Yongzhao; Xu, Xuemei; Sun, Yuying; Zhang, Jiquan

doi:10.1016/j.fsi.2021.10.004

Cited by 15 publications

(5 citation statements)

References 47 publications

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“…90.5% of the transcripts were novel, highlighting the potential of long-read sequencing to identify new isoforms. Regarding Illumina sequencing results, the N50 of unigenes ranged from 1513 bp to 2079 bp, and the mean length of unigenes was about 1000 bp 20,21 . Based on SMRT sequencing results, the N50 and mean length of transcripts were 3697 bp and 3167 bp, respectively, which is signi cantly longer than the second-generation sequencing data.…”

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

Self Cite

View full text Add to dashboard Cite

show abstract

“…A total of 90.5% of the transcripts were novel, highlighting the potential of long-read sequencing to identify new isoforms. Regarding the Illumina sequencing results, the N50 value of the unigenes ranged from 1513 bp to 2079 bp, and the mean length of the unigenes was about 1000 bp [ 32 , 33 ]. Based on the SMRT sequencing results, the N50 value and mean length of transcripts were 3697 bp and 3167 bp, respectively, which are significantly longer than the second-generation sequencing data [ 32 ].…”

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

Self Cite

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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“…Compared with other shrimp such as Litopenaeus vannamei and Exopalaemon carinicauda [7,8], there are few reports related to embryonic development. Besides, some studies were focused on the effects of heavy metal stimulation and pathogenic bacteria stimulation on innate immune of adult shrimp [9]. Nevertheless, the molecular mechanisms and functional genes about early embryonic development of the shrimp are rarely reported.…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptomic analysis primarily explores the molecular mechanism of compound eye formation in Neocaridina denticulata sinensis

Yan,

Wu,

Liu

et al. 2024

Preprint

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Compound eyes formation in decapod crustaceans occurs after the nauplius stage. However, the key genes and regulatory mechanisms of compound eye development during crustacean embryonic development have not yet been clarified. In this study, RNA-seq was used to investigate the gene expression profiles of Neocaridina denticulata sinensis from nauplius to zoea stage. Based on RNA-seq data analysis, the phototransduction and insect hormone biosynthesis pathways were enriched, and molting-related neuropeptides were highly expressed. There was strong cell proliferation in the embryo prior to compound eye development. The formation of the visual system and the hormonal regulation of hatching were the dominant biological events during compound eye development. The functional analysis of DEGs across all four developmental stages showed that cuticle formation, muscle growth and the establishment of immune system occurred from nauplius to zoea stage. Key genes related to eye development were discovered, including those involved in the determination and differentiation of the eye field, eye-color formation, and visual signal transduction. In conclusion, the results increase the understanding of the molecular mechanism of eye formation in crustacean embryonic stage.

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Transcriptome analysis of Neocaridina denticulate sinensis challenged by Vibrio parahemolyticus

Cited by 15 publications

References 47 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

Comparative transcriptomic analysis primarily explores the molecular mechanism of compound eye formation in Neocaridina denticulata sinensis

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