In Silico Genome-Wide Analysis of the Pear (Pyrus bretschneideri) KNOX Family and the Functional Characterization of PbKNOX1, an Arabidopsis BREVIPEDICELLUS Orthologue Gene, Involved in Cell Wall and Lignin Biosynthesis

Cheng, Xi; Li, Manli; Abdullah, Muhammad; Li, Guohui; Zhang, Jingyun; Manzoor, Muhammad Aamir; Wang, Han; Jin, Qing; Jiang, Tao‐Shan; Cai, Yongping; Li, Dahui; Lin, Yi

doi:10.3389/fgene.2019.00632

Cited by 34 publications

(35 citation statements)

References 43 publications

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“…The members of the WOX class have a derived function of stem cell control besides embryonic patterning, stem cell maintenance, and organ formation, indicating that gene amplification followed by functional diversification is a major force in their evolution [19,20]. The TALE (three-amino acid loop extension) class (BEL and KNOX) is characterized by three extra residues between helix 1 and helix 2 [6,21], among which KNOX plays important roles in plant cell growth and development, including cell wall formation and lignification [22,23]. Moreover, studies in Arabidopsis and the peach have shown that AtBP and PpKNOPE1 can interact with the typical KNOX DNA-binding site (TGACAGC) in 4CL, COMT, and LAC to regulate their expression during lignification [24,25].…”

Section: Introductionmentioning

confidence: 99%

Identification of Homeobox Genes Associated with Lignification and Their Expression Patterns in Bamboo Shoots

Lou

Yang

et al. 2019

Biomolecules

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Homeobox (HB) genes play critical roles in regulating various aspects of plant growth and development. However, little is known about HB genes in bamboo. In this study, a total of 115 HB genes (PeHB001–PeHB115) were identified from moso bamboo (Phyllostachys edulis) and grouped into 13 distinct classes (BEL, DDT, HD-ZIP I–IV, KNOX, NDX, PHD, PINTOX, PLINC, SAWADEE, and WOX) based on the conserved domains and phylogenetic analysis. The number of members in the different classes ranged from 2 to 24, and they usually varied in terms of exon–intron distribution pattern and length. There were 20 conserved motifs found in 115 PeHBs, with motif 1 being the most common. Gene ontology (GO) analysis showed that PeHBs had diverse molecular functions, with 19 PeHBs being annotated as having xylem development, xylem, and phloem pattern formation functions. Co-expression network analysis showed that 10 of the 19 PeHBs had co-expression correlations, and three members of the KNOX class were hub proteins that interacted with other transcription factors (TFs) such as MYB, bHLH, and OVATE, which were associated with lignin synthesis. Yeast two-hybridization results further proved that PeHB037 (BEL class) interacted with PeHB057 (KNOX class). Transcriptome expression profiling indicated that all PeHBs except PeHB017 were expressed in at least one of the seven tissues of moso bamboo, and 90 PeHBs were expressed in all the tissues. The qRT-PCR results of the 19 PeHBs showed that most of them were upregulated in shoots as the height increased. Moreover, a KNOX binding site was found in the promoters of the key genes involved in lignin synthesis such as Pe4CL, PeC3H, PeCCR, and PeCOMT, which had positive expression correlations with five KNOX genes. Similar results were found in winter bamboo shoots with prolonged storage time, which was consistent with the degree of lignification. These results provide basic data on PeHBs in moso bamboo, which will be helpful for future functional research on PeHBs with positive regulatory roles in the process of lignification.

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Section: Introductionmentioning

confidence: 99%

Identification of Homeobox Genes Associated with Lignification and Their Expression Patterns in Bamboo Shoots

Lou

Yang

et al. 2019

Biomolecules

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“…Whether it is consistent with KNOX regulation of Arabidopsis meristem stems and buds are worth further investigation [59]. Xi Cheng found that in pear plants co-expressing KNOX and PbKNOX1 these factors are involved in cell wall thickening and lignin biosynthesis, with inhibition of key structural genes involved in lignin synthesis [60].…”

Section: Discussionmentioning

confidence: 94%

Revealing the full-length transcriptome of caucasian clover rhizome development

Yin

Zhao

et al. 2020

Preprint

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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 transcripts in five tissues taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) of 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), 6,821 alternative splicing (AS) sites, 24,29 long noncoding RNAs (lncRNAs) and 4,501 putative transcription factors (TFs) from 64 different families. Compared with other tissues, T5 exhibited more differentially expressed genes, 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) cluster analysis of transcription factors and physiological indicators were combined to reveal 11 candidate genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analysed 276 differential transcripts involved in hormone signaling and transduction, and the largest number of transcripts are associated with the IAA signaling pathway, with significant up-regulation in T2 and T5. Conclusions: Taken together, 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.

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“…Whether it is consistent with KNOX regulation of Arabidopsis meristem stems and buds is worth further investigation [53]. Xi Cheng found that in pear plants coexpressing KNOX and PbKNOX1, these factors are involved in cell wall thickening and lignin biosynthesis, with inhibition of key structural genes involved in lignin synthesis [54].…”

Section: Discussionmentioning

confidence: 95%

Revealing the full-length transcriptome of caucasian clover rhizome development

Yin

Zhao

et al. 2020

Preprint

View full text Add to dashboard Cite

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 transcripts in five tissues taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) of the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analyzed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6,821 alternative splicing (AS) sites, 24,29 long noncoding RNAs (lncRNAs) and 4,501 putative transcription factors (TFs)from 64 different families. Compared with other tissues, T5 exhibited more differentially expressed genes, 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. WGCNA cluster analysis of transcription factors and physiological indicators were combined to reveal 11 candidate genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analyzed 276 differential transcripts involved in hormone signaling and transduction, and the largest number of transcripts are associated with the IAA signaling pathway, with significant upregulation in T2 and T5. Conclusions: Taken together, 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.

show abstract

In Silico Genome-Wide Analysis of the Pear (Pyrus bretschneideri) KNOX Family and the Functional Characterization of PbKNOX1, an Arabidopsis BREVIPEDICELLUS Orthologue Gene, Involved in Cell Wall and Lignin Biosynthesis

Cited by 34 publications

References 43 publications

Identification of Homeobox Genes Associated with Lignification and Their Expression Patterns in Bamboo Shoots

Identification of Homeobox Genes Associated with Lignification and Their Expression Patterns in Bamboo Shoots

Revealing the full-length transcriptome of caucasian clover rhizome development

Revealing the full-length transcriptome of caucasian clover rhizome development

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