PMID- 29396453
OWN - NLM
STAT- MEDLINE
DCOM- 20181217
LR  - 20181217
IS  - 2045-2322 (Electronic)
IS  - 2045-2322 (Linking)
VI  - 8
IP  - 1
DP  - 2018 Feb 2
TI  - SMRT sequencing of full-length transcriptome of flea beetle Agasicles hygrophila 
      (Selman and Vogt).
PG  - 2197
LID - 10.1038/s41598-018-20181-y [doi]
LID - 2197
AB  - This study was aimed at generating the full-length transcriptome of flea beetle 
      Agasicles hygrophila (Selman and Vogt) using single-molecule real-time (SMRT) 
      sequencing. Four developmental stages of A. hygrophila, including eggs, larvae, 
      pupae, and adults were harvested for isolating total RNA. The mixed samples were 
      used for SMRT sequencing to generate the full-length transcriptome. Based on the 
      obtained transcriptome data, alternative splicing event, simple sequence repeat 
      (SSR) analysis, coding sequence prediction, transcript functional annotation, and 
      lncRNA prediction were performed. Total 9.45 Gb of clean reads were generated, 
      including 335,045 reads of insert (ROI) and 158,085 full-length non-chimeric 
      (FLNC) reads. Transcript clustering analysis of FLNC reads identified 40,004 
      consensus isoforms, including 31,015 high-quality ones. After removing redundant 
      reads, 28,982 transcripts were obtained. Total 145 alternative splicing events 
      were predicted. Additionally, 12,753 SSRs and 16,205 coding sequences were 
      identified based on SSR analysis. Furthermore, 24,031 transcripts were annotated 
      in eight functional databases, and 4,198 lncRNAs were predicted. This is the 
      first study to perform SMRT sequencing of the full-length transcriptome of A. 
      hygrophila. The obtained transcriptome may facilitate further exploration of the 
      genetic data of A. hygrophila and uncover the interactions between this insect 
      and the ecosystem.
FAU - Jia, Dong
AU  - Jia D
AD  - College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China.
FAU - Wang, Yuanxin
AU  - Wang Y
AD  - College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China.
FAU - Liu, Yanhong
AU  - Liu Y
AD  - College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China.
FAU - Hu, Jun
AU  - Hu J
AD  - College of Life Science, Shanxi Agricultural University, Taigu, 030801, China.
FAU - Guo, Yanqiong
AU  - Guo Y
AD  - College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China.
FAU - Gao, Lingling
AU  - Gao L
AD  - College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China.
AD  - CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, 
      Western Australia, 6014, Australia.
FAU - Ma, Ruiyan
AU  - Ma R
AD  - College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China. 
      maruiyan2004@163.com.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20180202
PL  - England
TA  - Sci Rep
JT  - Scientific reports
JID - 101563288
SB  - IM
MH  - Animals
MH  - Coleoptera/*genetics/growth & development
MH  - Data Curation
MH  - *Gene Expression Profiling
MH  - Larva/genetics/growth & development
MH  - Pupa/genetics/growth & development
MH  - RNA Splicing
MH  - *Sequence Analysis, RNA
MH  - Zygote/growth & development
PMC - PMC5797098
COIS- The authors declare that they have no competing interests.
EDAT- 2018/02/06 06:00
MHDA- 2018/12/18 06:00
PMCR- 2018/02/02
CRDT- 2018/02/04 06:00
PHST- 2017/09/14 00:00 [received]
PHST- 2018/01/03 00:00 [accepted]
PHST- 2018/02/04 06:00 [entrez]
PHST- 2018/02/06 06:00 [pubmed]
PHST- 2018/12/18 06:00 [medline]
PHST- 2018/02/02 00:00 [pmc-release]
AID - 10.1038/s41598-018-20181-y [pii]
AID - 20181 [pii]
AID - 10.1038/s41598-018-20181-y [doi]
PST - epublish
SO  - Sci Rep. 2018 Feb 2;8(1):2197. doi: 10.1038/s41598-018-20181-y.