|
|
Cite this paper: |
|
|
Fangrui LOU, Zhiqiang HAN. Full-length transcripts facilitates Portunus trituberculatus genome structure annotation*[J]. Journal of Oceanology and Limnology, 2022, 40(5): 2042-2051 |
|
|
|
|
|
|
|
Full-length transcripts facilitates Portunus trituberculatus genome structure annotation* |
|
| Fangrui LOU1, Zhiqiang HAN2 |
|
1 School of Ocean, Yantai University, Yantai 264005, China;
2 Fishery College, Zhejiang Ocean University, Zhoushan 316022, China |
|
| Abstract: |
| Portunus trituberculatus is an ideal model for elucidating crustacean genetic networks. Here we combined single molecule real-time (SMRT) sequencing and Illumina RNA-seq to characterize the coding genes, non-coding RNAs and pseudogenes and further to improve the genome annotation information of P. trituberculatus. In this study, we assembled 9 694 non-redundancy full-length transcripts, and 658 737 307- bp repetitive sequences were identified in the P. trituberculatus full-length transcriptome. We also predicted the P. trituberculatus genome structure based on full-length transcripts, including 18 602 genes, 28 686 non-coding RNAs, 1 407 pseudogenes, 740 motif, and 26 434 domain. Meanwhile, 14 460, 10 211, 5 412, 7 314, and 14 448 genes had significant matches with sequences in the NR, KOG, GO, KEGG, and TrEMBL database, respectively. Overall, our work firstly provided the long-read transcriptome and we believed that these data are very necessary to improve the annotation information of P. trituberculatus genome structure, and useful information for the future studies on evolution and physiological regulation of P. trituberculatus. |
|
| Key words:
Portunus trituberculatus
full-length transcripts
single molecule real-time (SMRT) sequencing
|
|
| Received: 2021-07-27 Revised: 2021-10-28 |
|
|
|
|
References:
|
|
|
|