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

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.

Automated summary

In this study, the researchers sequenced the full-length unreferenced transcriptome of red-crowned cranes for the first time using a PacBio Sequel platform. After correcting the PacBio sequencing data with Illumina data, they identified important genetic information and discovered differences in the expression of lncRNAs and TFs in various tissues of the cranes, as well as enriched immune-related pathways in the spleen.