Comprehensive transcriptome characterization of Grus japonensis using PacBio SMRT and Illumina sequencing

Wentao Ye,Rong Chen,Hongyi Liu,Nan Xu,Wei Xu,Changhu Lu

doi:10.1038/s41598-021-03474-7

Wentao Ye, Rong Chen + Show 4 more

Open Access

https://doi.org/10.1038/s41598-021-03474-7

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Abstract

The red-crowned crane (Grus japonensis) is an endangered species distributed across southeast Russia, northeast China, Korea, and Japan. Here, we sequenced for the first time the full-length unreferenced transcriptome of red-crowned crane mixed samples using a PacBio Sequel platform. A total of 359,136 circular consensus sequences (CCS) were obtained via clustering to remove redundancy. A total of 303,544 full-length non-chimeric sequences were identified by judging whether CCS contained 5′ and 3′ adapters, and the poly(A) tail. Eight samples were sequenced using Illumina, and PacBio sequencing data were corrected according to the collected Illumina data to obtain more accurate full-length transcripts. A total of 4,100 long non-coding RNAs, 13,115 simple sequences repeat loci and 29 transcription factor families were identified. The expression of lncRNAs and TFs in pancreas was lowest comparing with other tissues. Many enriched immune-related transmission pathways (MHC and IL receptors) were identified in the spleen. This study will contribute to a better understanding of the gene structure and post-transcriptional regulatory network, and provide references for future studies on red-crowned cranes.

Highlights

The red-crowned crane (Grus japonensis) is an endangered species distributed across southeast Russia, northeast China, Korea, and Japan
It has been reported that Single Molecule Real-Time (SMRT) Sequel has the advantage of ultra-long reading length, including the 5’- and 3’-untranslated regions (UTRs) and poly(A) tail of the transcript, which provides important information for the stability and translation of mRNA40
The hierarchical n*log(n) algorithm was used to cluster the full-length non-chimeric sequences of the same transcript to obtain the consensus sequence, which was further polished by arrow software to obtain 23,452 polished consensus

Summary

Introduction

The red-crowned crane (Grus japonensis) is an endangered species distributed across southeast Russia, northeast China, Korea, and Japan. SMRT sequencing technology provides an important method for understanding gene structure and transcription network of endangered a nimals[34,35] This is of great significance for studying the regulatory mechanism of endangered animals and the differential expression of environmental impact genes. The full-length transcripts of red-crowned crane were obtained for the first time through PacBio SMRT sequencing and the expression landscapes of eight different tissues (brain, muscle, pancreas, heart, kidney, liver, lung, and spleen) were further evaluated using Illumina NovaSeq 6000 sequencing. The collected data provides a reference for understanding the gene structure and post-transcriptional regulatory network of red-crowned crane, and may lay the foundation for future molecular research related to red-crowned crane, and contribute to the protection of this endangered species

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