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De Novo Sequencing and Characterization of the Transcriptome of Dwarf Polish Wheat (Triticum polonicum L.)

Construction as well as characterization of a polish wheat transcriptome is a crucial step to study useful traits of polish wheat. In this study, a transcriptome, including 76,014 unigenes, was assembled from dwarf polish wheat (DPW) roots, stems, and leaves using the software of Trinity. Among thes...

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Autores principales: Wang, Yi, Wang, Chao, Wang, Xiaolu, Peng, Fan, Wang, Ruijiao, Jiang, Yulin, Zeng, Jian, Fan, Xing, Kang, Houyang, Sha, Lina, Zhang, Haiqin, Xiao, Xue, Zhou, Yonghong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4939322/
https://www.ncbi.nlm.nih.gov/pubmed/27429972
http://dx.doi.org/10.1155/2016/5781412
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author Wang, Yi
Wang, Chao
Wang, Xiaolu
Peng, Fan
Wang, Ruijiao
Jiang, Yulin
Zeng, Jian
Fan, Xing
Kang, Houyang
Sha, Lina
Zhang, Haiqin
Xiao, Xue
Zhou, Yonghong
author_facet Wang, Yi
Wang, Chao
Wang, Xiaolu
Peng, Fan
Wang, Ruijiao
Jiang, Yulin
Zeng, Jian
Fan, Xing
Kang, Houyang
Sha, Lina
Zhang, Haiqin
Xiao, Xue
Zhou, Yonghong
author_sort Wang, Yi
collection PubMed
description Construction as well as characterization of a polish wheat transcriptome is a crucial step to study useful traits of polish wheat. In this study, a transcriptome, including 76,014 unigenes, was assembled from dwarf polish wheat (DPW) roots, stems, and leaves using the software of Trinity. Among these unigenes, 61,748 (81.23%) unigenes were functionally annotated in public databases and classified into differentially functional types. Aligning this transcriptome against draft wheat genome released by the International Wheat Genome Sequencing Consortium (IWGSC), 57,331 (75.42%) unigenes, including 26,122 AB-specific and 2,622 D-specific unigenes, were mapped on A, B, and/or D genomes. Compared with the transcriptome of T. turgidum, 56,343 unigenes were matched with 103,327 unigenes of T. turgidum. Compared with the genomes of rice and barley, 14,404 and 7,007 unigenes were matched with 14,608 genes of barley and 7,708 genes of rice, respectively. On the other hand, 2,148, 1,611, and 2,707 unigenes were expressed specifically in roots, stems, and leaves, respectively. Finally, 5,531 SSR sequences were observed from 4,531 unigenes, and 518 primer pairs were designed.
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spelling pubmed-49393222016-07-17 De Novo Sequencing and Characterization of the Transcriptome of Dwarf Polish Wheat (Triticum polonicum L.) Wang, Yi Wang, Chao Wang, Xiaolu Peng, Fan Wang, Ruijiao Jiang, Yulin Zeng, Jian Fan, Xing Kang, Houyang Sha, Lina Zhang, Haiqin Xiao, Xue Zhou, Yonghong Int J Genomics Research Article Construction as well as characterization of a polish wheat transcriptome is a crucial step to study useful traits of polish wheat. In this study, a transcriptome, including 76,014 unigenes, was assembled from dwarf polish wheat (DPW) roots, stems, and leaves using the software of Trinity. Among these unigenes, 61,748 (81.23%) unigenes were functionally annotated in public databases and classified into differentially functional types. Aligning this transcriptome against draft wheat genome released by the International Wheat Genome Sequencing Consortium (IWGSC), 57,331 (75.42%) unigenes, including 26,122 AB-specific and 2,622 D-specific unigenes, were mapped on A, B, and/or D genomes. Compared with the transcriptome of T. turgidum, 56,343 unigenes were matched with 103,327 unigenes of T. turgidum. Compared with the genomes of rice and barley, 14,404 and 7,007 unigenes were matched with 14,608 genes of barley and 7,708 genes of rice, respectively. On the other hand, 2,148, 1,611, and 2,707 unigenes were expressed specifically in roots, stems, and leaves, respectively. Finally, 5,531 SSR sequences were observed from 4,531 unigenes, and 518 primer pairs were designed. Hindawi Publishing Corporation 2016 2016-06-27 /pmc/articles/PMC4939322/ /pubmed/27429972 http://dx.doi.org/10.1155/2016/5781412 Text en Copyright © 2016 Yi Wang et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Wang, Yi
Wang, Chao
Wang, Xiaolu
Peng, Fan
Wang, Ruijiao
Jiang, Yulin
Zeng, Jian
Fan, Xing
Kang, Houyang
Sha, Lina
Zhang, Haiqin
Xiao, Xue
Zhou, Yonghong
De Novo Sequencing and Characterization of the Transcriptome of Dwarf Polish Wheat (Triticum polonicum L.)
title De Novo Sequencing and Characterization of the Transcriptome of Dwarf Polish Wheat (Triticum polonicum L.)
title_full De Novo Sequencing and Characterization of the Transcriptome of Dwarf Polish Wheat (Triticum polonicum L.)
title_fullStr De Novo Sequencing and Characterization of the Transcriptome of Dwarf Polish Wheat (Triticum polonicum L.)
title_full_unstemmed De Novo Sequencing and Characterization of the Transcriptome of Dwarf Polish Wheat (Triticum polonicum L.)
title_short De Novo Sequencing and Characterization of the Transcriptome of Dwarf Polish Wheat (Triticum polonicum L.)
title_sort de novo sequencing and characterization of the transcriptome of dwarf polish wheat (triticum polonicum l.)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4939322/
https://www.ncbi.nlm.nih.gov/pubmed/27429972
http://dx.doi.org/10.1155/2016/5781412
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