De novo transcriptome and small RNA analysis of two Chinese willow cultivars reveals stress response genes in Salix matsudana.
Salix matsudana Koidz. is a deciduous, rapidly growing, and drought resistant tree and is one of the most widely distributed and commonly cultivated willow species in China. Currently little transcriptomic and small RNAomic data are available to reveal the genes involve in the stress resistant in S....
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2014-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4183547?pdf=render |
| _version_ | 1818566558086070272 |
|---|---|
| author | Guodong Rao Jinkai Sui Yanfei Zeng Caiyun He Aiguo Duan Jianguo Zhang |
| author_facet | Guodong Rao Jinkai Sui Yanfei Zeng Caiyun He Aiguo Duan Jianguo Zhang |
| author_sort | Guodong Rao |
| collection | DOAJ |
| description | Salix matsudana Koidz. is a deciduous, rapidly growing, and drought resistant tree and is one of the most widely distributed and commonly cultivated willow species in China. Currently little transcriptomic and small RNAomic data are available to reveal the genes involve in the stress resistant in S. matsudana. Here, we report the RNA-seq analysis results of both transcriptome and small RNAome data using Illumina deep sequencing of shoot tips from two willow variants(Salix. matsudana and Salix matsudana Koidz. cultivar 'Tortuosa'). De novo gene assembly was used to generate the consensus transcriptome and small RNAome, which contained 106,403 unique transcripts with an average length of 944 bp and a total length of 100.45 MB, and 166 known miRNAs representing 35 miRNA families. Comparison of transcriptomes and small RNAomes combined with quantitative real-time PCR from the two Salix libraries revealed a total of 292 different expressed genes(DEGs) and 36 different expressed miRNAs (DEMs). Among the DEGs and DEMs, 196 genes and 24 miRNAs were up regulated, 96 genes and 12 miRNA were down regulated in S. matsudana. Functional analysis of DEGs and miRNA targets showed that many genes were involved in stress resistance in S. matsudana. Our global gene expression profiling presents a comprehensive view of the transcriptome and small RNAome which provide valuable information and sequence resources for uncovering the stress response genes in S. matsudana. Moreover the transcriptome and small RNAome data provide a basis for future study of genetic resistance in Salix. |
| first_indexed | 2024-12-14T01:55:15Z |
| format | Article |
| id | doaj.art-00009c709bd4440aa6c7f7714b88f07d |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-14T01:55:15Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-00009c709bd4440aa6c7f7714b88f07d2022-12-21T23:21:12ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-01910e10912210.1371/journal.pone.0109122De novo transcriptome and small RNA analysis of two Chinese willow cultivars reveals stress response genes in Salix matsudana.Guodong RaoJinkai SuiYanfei ZengCaiyun HeAiguo DuanJianguo ZhangSalix matsudana Koidz. is a deciduous, rapidly growing, and drought resistant tree and is one of the most widely distributed and commonly cultivated willow species in China. Currently little transcriptomic and small RNAomic data are available to reveal the genes involve in the stress resistant in S. matsudana. Here, we report the RNA-seq analysis results of both transcriptome and small RNAome data using Illumina deep sequencing of shoot tips from two willow variants(Salix. matsudana and Salix matsudana Koidz. cultivar 'Tortuosa'). De novo gene assembly was used to generate the consensus transcriptome and small RNAome, which contained 106,403 unique transcripts with an average length of 944 bp and a total length of 100.45 MB, and 166 known miRNAs representing 35 miRNA families. Comparison of transcriptomes and small RNAomes combined with quantitative real-time PCR from the two Salix libraries revealed a total of 292 different expressed genes(DEGs) and 36 different expressed miRNAs (DEMs). Among the DEGs and DEMs, 196 genes and 24 miRNAs were up regulated, 96 genes and 12 miRNA were down regulated in S. matsudana. Functional analysis of DEGs and miRNA targets showed that many genes were involved in stress resistance in S. matsudana. Our global gene expression profiling presents a comprehensive view of the transcriptome and small RNAome which provide valuable information and sequence resources for uncovering the stress response genes in S. matsudana. Moreover the transcriptome and small RNAome data provide a basis for future study of genetic resistance in Salix.http://europepmc.org/articles/PMC4183547?pdf=render |
| spellingShingle | Guodong Rao Jinkai Sui Yanfei Zeng Caiyun He Aiguo Duan Jianguo Zhang De novo transcriptome and small RNA analysis of two Chinese willow cultivars reveals stress response genes in Salix matsudana. PLoS ONE |
| title | De novo transcriptome and small RNA analysis of two Chinese willow cultivars reveals stress response genes in Salix matsudana. |
| title_full | De novo transcriptome and small RNA analysis of two Chinese willow cultivars reveals stress response genes in Salix matsudana. |
| title_fullStr | De novo transcriptome and small RNA analysis of two Chinese willow cultivars reveals stress response genes in Salix matsudana. |
| title_full_unstemmed | De novo transcriptome and small RNA analysis of two Chinese willow cultivars reveals stress response genes in Salix matsudana. |
| title_short | De novo transcriptome and small RNA analysis of two Chinese willow cultivars reveals stress response genes in Salix matsudana. |
| title_sort | de novo transcriptome and small rna analysis of two chinese willow cultivars reveals stress response genes in salix matsudana |
| url | http://europepmc.org/articles/PMC4183547?pdf=render |
| work_keys_str_mv | AT guodongrao denovotranscriptomeandsmallrnaanalysisoftwochinesewillowcultivarsrevealsstressresponsegenesinsalixmatsudana AT jinkaisui denovotranscriptomeandsmallrnaanalysisoftwochinesewillowcultivarsrevealsstressresponsegenesinsalixmatsudana AT yanfeizeng denovotranscriptomeandsmallrnaanalysisoftwochinesewillowcultivarsrevealsstressresponsegenesinsalixmatsudana AT caiyunhe denovotranscriptomeandsmallrnaanalysisoftwochinesewillowcultivarsrevealsstressresponsegenesinsalixmatsudana AT aiguoduan denovotranscriptomeandsmallrnaanalysisoftwochinesewillowcultivarsrevealsstressresponsegenesinsalixmatsudana AT jianguozhang denovotranscriptomeandsmallrnaanalysisoftwochinesewillowcultivarsrevealsstressresponsegenesinsalixmatsudana |