Full-length transcripts facilitates<italic style="font-style: italic">Portunus trituberculatus</italic>genome structure annotation

Fangrui LOU; Zhiqiang HAN

doi:10.1007/s00343-021-1248-x

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Full-length transcripts facilitatesPortunus trituberculatusgenome structure annotation

Biology | Updated：2023-05-19

- Full-length transcripts facilitatesPortunus trituberculatusgenome structure annotation
- Journal of Oceanology and Limnology Vol. 40, Issue 5, Pages: 2042-2051(2022)
- Affiliations：
  
  1.School of Ocean, Yantai University, Yantai 264005, China
  2.Fishery College, Zhejiang Ocean University, Zhoushan 316022, China
- Author bio：
  
  Zhiqiang HAN,d6339124@163.com
- Funds：
- DOI：10.1007/s00343-021-1248-x
  CLC：
- Received：27 July 2021，
  
  Accepted：28 October 2021，
  
  Online First：28 November 2021，
  
  Published：2022-09
- Accepted：
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Fangrui LOU, Zhiqiang HAN. Full-length transcripts facilitatesPortunus trituberculatusgenome structure annotation[J]. Journal of Oceanology and Limnology, 2022, 40(5): 2042-2051.
DOI：

Fangrui LOU, Zhiqiang HAN. Full-length transcripts facilitatesPortunus trituberculatusgenome structure annotation[J]. Journal of Oceanology and Limnology, 2022, 40(5): 2042-2051. DOI： 10.1007/s00343-021-1248-x.

摘要

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

trituberculatus

. In this study

we assembled 9 694 non-redundancy full-length transcripts

and 658 737 307-bp repetitive sequences were identified in the

trituberculatus

full-length transcriptome. We also predicted the

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

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

trituberculatus

genome structure

and useful information for the future studies on evolution and physiological regulation of

trituberculatus

关键词

Keywords

references

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Full-length transcripts facilitatesPortunus trituberculatusgenome structure annotation

DOI：10.1007/s00343-021-1248-x

摘要

Abstract

关键词

Keywords

references