Revealing the full-length transcriptome of caucasian clover rhizome development

• Published in: BMC plant biology Vol. 20; no. 1; p. 429
• Main Authors: Yin, Xiujie, Yi, Kun, Zhao, Yihang, Hu, Yao, Li, Xu, He, Taotao, Liu, Jiaxue, Cui, Guowen
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 16.09.2020; BioMed Central; BMC
• Subjects: Aldehyde dehydrogenase; Aldehydes; Alternative splicing; Amino acids; Analysis; Aquatic plants; Aridity; Betaine; Biological activity; Biosynthesis; Caucasian clover (Trifolium ambiguum M. Bieb.); Clover; DNA binding proteins; DNA sequencing; Endoplasmic reticulum; Full-length transcriptome; Gene expression; Gene Expression Regulation, Plant - genetics; Genes; Genes, Plant - genetics; Genomes; Genomics; Ground cover; Indoleacetic acid; Legumes; Low temperature resistance; Metabolism; Microsatellite Repeats - genetics; Network analysis; Ontology; Open reading frames; Open Reading Frames - genetics; Ornamental plants; Physiological effects; Plant hormone; Post-transcription; Proteins; Rhizome; Rhizome - genetics; Rhizome - growth & development; Rhizome - metabolism; Rhizomes; RNA; RNA, Long Noncoding - genetics; RNA, Plant - genetics; RNA-seq; Sequence Analysis, DNA; Signal transduction; Signaling; Simple sequence repeats; Sorghum; Splicing; TFs; Tissues; Transcription (Genetics); Transcription factors; Transcriptome; Trifolium - genetics; Trifolium - growth & development; Trifolium - metabolism; TFs; Plant hormone; Caucasian clover (Trifolium ambiguum M. Bieb.); RNA-seq; Full-length transcriptome; Rhizome
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-020-02637-4

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. 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. 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.