Transcriptome library construction in whole plant of Erigeron breviscapus stressed by low nitrogen and its sequencing
10.7501/j.issn.0253-2670.2015.21.020
- Author:
Bao-Qiang TIAN
1
Author Information
1. School of Life Sciences, Yunnan Normal University
- Publication Type:Journal Article
- Keywords:
De nove assembling;
Erigeron breviacapus (Vant.) Hand.-Mazz.;
Low nitrogen stress;
Sequencing;
Tanscriptome library;
Unigene
- From:
Chinese Traditional and Herbal Drugs
2015;46(21):3235-3241
- CountryChina
- Language:Chinese
-
Abstract:
Objective: To explore the genetic background of Erigeron breviscapus, a very important herb, we used the plantlets under low nitrogen and normal condition cultured in vitro as material to construct the transcriptome library, and to sequence the library via next generation sequencing technique. Methods: Modified guanidinium isothiocyanate-CTAB method was used to isolate the total RNA from low nitrogen and normal condition cultured plantlets. The mRNA was enriched from the total RNA and broken into short fragments, and then the cDNA library was established for RNA-Seq. Results: In total, 35.87 million and 25.82 million raw reads were generated from LD and CK libraries via next generation sequencing, respectively. The overall sequencing outputs were over 6 Gb. Among all of the raw reads, more than 98.37% and 98.67% had Phred-like quality scores at Q20 level (an error probability of 1%), respectively. After filtered to remove low quality reads, the high quality sequencing sequence was used for de novo assembling. Unigenes of 101 and 156 pieces with the average length of 768 bp (N50 1 290 bp) were obtained, and the length of 44 908 pieces (about 44.39%) is more than 500 bp. Among 101 and 156 Unigenes, 59 538 (58.86%) showed the significant BLAST hits in the public databases. Many sequences concerning flavanoids bio-synthesis which included PAL, C4H, CHS, CHI, F3H, F3'H, and ANS were obtained from the experiment. Conclusion: Transcriptome information of E. breviscapus has been better preserved, which provides the foundation for the further analysis in genetic-environment interaction and molecular assistant breeding.
