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

Abstract

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.