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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....

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Tác giả chính: Guodong, Rao, Jinkai, Sui, Yanfei, Zeng, Caiyun, He, Aiguo, Duan, Jianguo, Zhang
Ngôn ngữ:English
Năm xuất bản: Public Library of Science (PLoS) 2018
Chủ đề:
De novo transcriptome
small RNA
chinese willow cultivars reveals stress
Salix matsudana
Truy cập Trực tuyến:http://lrc.quangbinhuni.edu.vn:8181/dspace/handle/DHQB_123456789/3834
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spelling oai:localhost:DHQB_123456789-38342018-10-22T08:43:08Z De novo transcriptome and small RNA analysis of two Chinese willow cultivars reveals stress response genes in Salix matsudana. Guodong, Rao Jinkai, Sui Yanfei, Zeng Caiyun, He Aiguo, Duan Jianguo, Zhang De novo transcriptome small RNA chinese willow cultivars reveals stress 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. 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. 2018-08-23T03:55:18Z 2018-08-23T03:55:18Z 2014-10 Rao G, Sui J, Zeng Y, He C, Duan A, et al. (2014) De Novo Transcriptome and Small RNA Analysis of Two Chinese Willow Cultivars Reveals Stress Response Genes in Salix matsudana. PLoS ONE 9(10): e109122. doi:10.1371/journal.pone.0109122 1932-6203 (Online) http://lrc.quangbinhuni.edu.vn:8181/dspace/handle/DHQB_123456789/3834 en Public Library of Science (PLoS)
institution Trung tâm Học liệu Đại học Quảng Bình (Dspace)
collection Trung tâm Học liệu Đại học Quảng Bình (Dspace)
language English
topic De novo transcriptome
small RNA
chinese willow cultivars reveals stress
Salix matsudana
spellingShingle De novo transcriptome
small RNA
chinese willow cultivars reveals stress
Salix matsudana
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.
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.
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
title 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_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_sort de novo transcriptome and small rna analysis of two chinese willow cultivars reveals stress response genes in salix matsudana.
publisher Public Library of Science (PLoS)
publishDate 2018
url http://lrc.quangbinhuni.edu.vn:8181/dspace/handle/DHQB_123456789/3834
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score 9,463379

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