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

Yi Wang,Jian Zeng,Lina Sha,Ruijiao Wang,Yulin Jiang,Fan Peng,Houyang Kang,Yonghong Zhou,Haiqin Zhang,Chao Wang,Xue Xiao,Xing Fan,Xiaolu Wang

doi:10.1155/2016/5781412

Abstract

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.

Highlights

Due to the high-thousand kernel weight, elongated and plump kernels, high Zn, Fe, and Cu concentrations in seeds [1], high amylose content in seeds [2], and alternatively dwarfing genes [3, 4], polish wheat (2n = 4x = 28, AABB, Triticum polonicum L.) attracts the interest of producers and breeders [1]
697.13 million (370.82 in roots, 115.51 in stems, and 210.80 in leaves) 100 bp paired-end raw reads were generated from dwarf polish wheat (DPW), after cleaning and quality checks, 671.49 million (361.96 in roots, 108.11 in stems, and 201.32 in leaves) 100 bp paired-end clean reads were used for assembly
76,014 unigenes with mean sizes of 872 bp (Table 1, all assembled unigenes have been deposited at GenBank under the accession GEDT00000000) were assembled

Summary

Introduction

It is inappropriate to reveal the genetic information of polish wheat using the genome or transcriptomes of T. turgidum and T. aestivum [9,10,11,12]. All unigenes were blasted against draft wheat genome [22] with e-value < 10−5, coverage > 90%, and alignment length > 200 bp. All unigenes were blasted against the transcriptome of T. turgidum [10] with e-value < 10−5.

Results

Conclusion