Revealing the full-length transcriptome of caucasian clover rhizome development

Abstract

Background Caucasian clover (Trifolium ambiguum M. Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. Result We adopted PacBio sequencing and Illumina sequencing to identify differentially expressed genes (DEGs) in five tissues, including taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) tissues, in the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analysed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6821 alternative splicing (AS) events, 2429 long noncoding RNAs (lncRNAs) and 4501 putative transcription factors (TFs) from 64 different families. Compared with other tissues, T5 exhibited more DEGs, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase (BADH) as a highly expressed gene-specific to T5. A weighted gene co-expression network analysis (WGCNA) of transcription factors and physiological indicators were combined to reveal 11 hub genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analysed 276 DEGs involved in hormone signalling and transduction, and the largest number of genes are associated with the auxin (IAA) signalling pathway, with significant up-regulation in T2 and T5. Conclusions This study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.

Screening and identification of multiple abiotic stress responsive candidate genes based on hybrid-sequencing in Vicia sativa

“…With the development of current state-of-the-art sequencing technologies, hybrid-sequencing transcriptome analysis followed by identification of candidate genes will help to better understand the molecular mechanism of plant organ formation and development, as well as the stress response. FL transcriptome studies of species based on SMRT sequencing data, supplemented by NGS, have been widely reported, such as Trifolium ambiguum [ 37 ], Cassia obtusifolia [ 38 ], and Linum usitatissimum [ 15 ]. However, the deficiency of information about common vetch in this regard may be one of the factors accounting for the research tends to move along at a particularly slow pace compared with that on other major forage crops.…”

“…TFs are key regulatory proteins necessary for regulating gene expression. TFs can activate or inhibit the transcription of multiple target genes by combining with specific motifs in target genes in living organisms [ 37 ], so as to guide the growth, development, and metabolic processes of multifarious plants and also fulfill a vital role in signal transduction and promote the tolerance or adaptation of plants to adverse environments [ 50 , 51 ]. In the present study, among the 64 TF families identified, C3H, WRKY, and bHLH were listed as the top three TF families in common vetch.…”

Transcriptome profiling unveils the mechanism of phenylpropane biosynthesis in rhizome development of Caucasian clover

“…We also explored the role of hormones, especially IAA, in rhizomes. However, there are few studies on the role of the phenylpropane biosynthesis pathway in different tissues of the Caucasian clover rhizome [ 29 ]. RNA-seq transcriptome data have accelerated our understanding of the complex system of gene transcription patterns, gene structural differences and gene regulatory networks.…”

Identification and Evolutionary Analysis of the Auxin Response Factor (ARF) Family Based on Transcriptome Data from Caucasian Clover and Analysis of Expression Responses to Hormones

“…The transcriptomic data generated from different organs and for different developmental stages of Caucasian clover have been described previously [70]. Based on the sequencing data, the differential expression of the ARF gene family at different sites was analyzed.…”