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

ABSTRACT: Caucasian clover is the only perennial herb of the genus Leguminous clover with underground rhizomes. However, we know very little about its development process and mechanism. Transcriptome studies were conducted on the roots of Caucasian clover without a rhizome (NR) at the young seedling stage and the fully developed rhizome, including the root neck (R1), main root (R2), horizontal root (R3), and rhizome bud (R4), of the tissues in the mature phase. Compared with the rhizome in the mature phase, NR had 893 upregulated differentially expressed genes (DEGs), most of which were enriched in 'phenylpropanoid biosynthesis', 'phenylalanine metabolism', 'DNA replication' and 'biosynthesis of amino acids'. A higher number of transcription factors (AP2/ERF, C2H2 and FAR1) were found in NR. There were highly expressed genes for R4, such as auxin response factor SAUR, galacturonosyltransferase (GAUT), and sucrose synthase (SUS). Phenylpropanoids are very important for the entire process of rhizome development. We drew a cluster heat map of genes related to the phenylpropanoid biosynthesis pathway, in which the largest number of genes belonged to COMT, and most of them were upregulated in R4.

SUBMITTER: Meng L

PROVIDER: S-EPMC8277049 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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

Meng Lingdong L Zhang Xiaomeng X Wang Lina L Liu Haoyue H Zhao Yihang Y Yi Kun K Cui Guowen G Yin Xiujie X

PloS one 20210713 7

Caucasian clover is the only perennial herb of the genus Leguminous clover with underground rhizomes. However, we know very little about its development process and mechanism. Transcriptome studies were conducted on the roots of Caucasian clover without a rhizome (NR) at the young seedling stage and the fully developed rhizome, including the root neck (R1), main root (R2), horizontal root (R3), and rhizome bud (R4), of the tissues in the mature phase. Compared with the rhizome in the mature phas ...[more]

PMID: 34255805

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Project description:BackgroundCaucasian 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.ResultWe 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.ConclusionsThis study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.

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

Publications

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

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