Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line

Abstract

Background: Agropyron cristatum (L.) Gaertn. (2n = 4x = 28; genomes PPPP) is a wild relative of common wheat (Triticum aestivum L.) and provides many desirable genetic resources for wheat improvement. However, there is still a lack of reference genome and transcriptome information for A. cristatum, which severely impedes functional and molecular breeding studies.

Results: Single-molecule long-read sequencing technology from Pacific Biosciences (PacBio) was used to sequence full-length cDNA from a mixture of leaves, roots, stems and caryopses and constructed the first full-length transcriptome dataset of A. cristatum, which comprised 44,372 transcripts. As expected, the PacBio transcripts were generally longer and more complete than the transcripts assembled via the Illumina sequencing platform in previous studies. By analyzing RNA-Seq data, we identified tissue-enriched transcripts and assessed their GO term enrichment; the results indicated that tissue-enriched transcripts were enriched for particular molecular functions that varied by tissue. We identified 3398 novel and 1352 A. cristatum-specific transcripts compared with the wheat gene model set. To better apply this A. cristatum transcriptome, the A. cristatum transcripts were integrated with the wheat genome as a reference sequence to try to identify candidate A. cristatum transcripts associated with thousand-grain weight in a wheat-A. cristatum translocation line, Pubing 3035.

Conclusions: Full-length transcriptome sequences were used in our study. The present study not only provides comprehensive transcriptomic insights and information for A. cristatum but also proposes a new method for exploring the functional genes of wheat relatives under a wheat genetic background. The sequence data have been deposited in the NCBI under BioProject accession number PRJNA534411.

Keywords: Agropyron cristatum; Full-length transcriptome; Gene expression; Thousand-grain weight; Wheat; Wild relative.

Fig. 1

Pipeline for constructing the A. cristatum transcriptome and the application of this transcriptome in the identification of candidate alien genes in wheat-A. cristatum translocation line Pubing 3035

Fig. 2

Length distribution of transcripts obtained by different sequencing platforms. Illumina_1 and Illumina_2 represent the transcripts assembled by Zhang [20] and Zhou [21], respectively, using the Illumina sequencing platform

Fig. 3

Venn diagram showing the overlap of Pfam, SwissProt, eggNOG, GO and Kegg annotations of A. cristatum FLNC transcripts

Fig. 4

Tissue expression analysis of A. cristatum FLNC transcripts. a, Number of the protein-coding transcripts expressed in each sampled tissue. b, GO enrichment analysis for transcripts expressed in all sampled tissues. c, GO enrichment analysis for transcripts enriched in leaves. d, GO enrichment analysis for transcripts enriched in stems. e, GO enrichment analysis for transcripts enriched in roots. f, GO enrichment analysis for transcripts enriched in caryopses

Fig. 5

Distribution of orthologues of A. cristatum transcripts in the wheat genome. a, Karyotype of the wheat genome. The putative pericentromeric-centromeric regions are marked with black [51]. b, A. cristatum FLNC transcript density distribution; transcript density was calculated in a 10-Mb window. c, Loci density distribution; loci density was calculated in a 10-Mb window. d, Novel transcript density distribution; transcript density was calculated in a 10-Mb window. e, Distribution of FLNC transcripts in the wheat genome. f, Box plot of transcript density in the wheat genome. g, Distribution of loci in the wheat genome. h, Box plot of loci density in the wheat genome. i, Distribution of novel transcripts in the wheat genome. j, Box plot of novel transcript density in the wheat genome

Fig. 6

GO enrichment analysis for novel and A. cristatum-specific transcripts. a, GO enrichment analysis for novel transcripts. b, GO enrichment analysis for A. cristatum-specific transcripts

Fig. 7

Comparative genomics map between the 6P chromosome translocation fragment in Pubing 3035 and the 6A chromosome of wheat