Regulatory function of homeodomain‐leucine zipper (<scp>HD</scp>‐<scp>ZIP)</scp> family proteins during embryogenesis

Roodbarkelari, Farshad; Groot, Edwin P.

doi:10.1111/nph.14132

Cited by 35 publications

(24 citation statements)

References 131 publications

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“…The contracted cluster associated with the meristem initiation GO term comprises class III HD-ZIP genes, a gene family known to regulate differentiation of both primary and secondary vascular tissues (34,35). Specifically, N. thermarum lacks a copy that belongs to the REVOLUTA (REV) subgroup ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Water lily ( Nymphaea thermarum ) genome reveals variable genomic signatures of ancient vascular cambium losses

Povilus

DaCosta

Grassa

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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For more than 225 million y, all seed plants were woody trees, shrubs, or vines. Shortly after the origin of angiosperms ∼140 million y ago (MYA), the Nymphaeales (water lilies) became one of the first lineages to deviate from their ancestral, woody habit by losing the vascular cambium, the meristematic population of cells that produces secondary xylem (wood) and phloem. Many of the genes and gene families that regulate differentiation of secondary tissues also regulate the differentiation of primary xylem and phloem, which are produced by apical meristems and retained in nearly all seed plants. Here, we sequenced and assembled a draft genome of the water lily Nymphaea thermarum, an emerging system for the study of early flowering plant evolution, and compared it to genomes from other cambium-bearing and cambium-less lineages (e.g., monocots and Nelumbo). This revealed lineage-specific patterns of gene loss and divergence. Nymphaea is characterized by a significant contraction of the HD-ZIP III transcription factors, specifically loss of REVOLUTA, which influences cambial activity in other angiosperms. We also found the Nymphaea and monocot copies of cambium-associated CLE signaling peptides display unique substitutions at otherwise highly conserved amino acids. Nelumbo displays no obvious divergence in cambium-associated genes. The divergent genomic signatures of convergent loss of vascular cambium reveals that even pleiotropic genes can exhibit unique divergence patterns in association with independent events of trait loss. Our results shed light on the evolution of herbaceousness—one of the key biological innovations associated with the earliest phases of angiosperm evolution.

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Section: Resultsmentioning

confidence: 99%

Water lily ( Nymphaea thermarum ) genome reveals variable genomic signatures of ancient vascular cambium losses

Povilus

DaCosta

Grassa

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…The contracted cluster associated with the meristem initiation GO term comprises Class III HD-ZIP genes, a gene family known to regulate differentiation of both primary and secondary vascular tissues (36,37). Specifically, N. thermarum lacks a copy that belongs to the REVOLUTA (REV) subgroup [ Figure 2C, SI Appendix, Figure S6].…”

Section: Resultsmentioning

confidence: 99%

Water lily (Nymphaea thermarum) draft genome reveals variable genomic signatures of ancient vascular cambium losses

Povilus

DaCosta

Grassa

et al. 2019

Preprint

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For more than 225 million years, all seed plants were woody trees, shrubs, or vines (1)(2)(3)(4). Shortly after the origin of angiosperms ~135 million years ago (MYA) (5), the Nymphaeales (water lilies) became one of the first lineages to deviate from their ancestral, woody habit by losing the vascular cambium (6), the meristematic population of cells that produces secondary xylem (wood) and phloem. Many of the genes and gene families that regulate differentiation of secondary tissues also regulate the differentiation of primary xylem and phloem (7-9), which are produced by apical meristems and retained in nearly all seed plants. Here we sequence and assemble a draft genome of the water lily Nymphaea thermarum, an emerging system for the study of early flowering plant evolution, and compare it to genomes from other cambium-bearing and cambium-less lineages (like monocots and Nelumbo). This reveals lineage-specific patterns of gene loss and divergence. Nymphaea is characterized by a significant contraction of the HD-ZIP III transcription factors, specifically loss of REVOLUTA, which influences cambial activity in other angiosperms. We also find the Nymphaea and monocot copies of cambium-associated CLE signaling peptides display unique substitutions at otherwise highly conserved amino acids. Nelumbo displays no obvious divergence in cambium-associated genes. The divergent genomic signatures of convergent vascular cambium loss reveals that even pleiotropic genes can exhibit unique divergence patterns in association with independent trait loss events. Our results shed light on the evolution of herbaceousness -one of the key biological innovations associated with the earliest phases of angiosperm evolution.

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“…In addition, the transcription factor ATHB-15 and other HD-ZIP transcription factor family members were positively correlated with the DEGs related to IAA signal transduction. HD-ZIP transcription factors regulate several genes in the auxin signaling pathway, including the ARF gene, to regulate plant embryonic development [54]. Moreover, the auxin response factors BDL and MP/ARF5 are coexpressed with HD-ZIP transcription factors during vascular development in A. thaliana embryos [55].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of lncRNA and mRNA expression and endogenous hormone regulation during tension wood formation in Catalpa bungei

Xiao

Ling

et al. 2020

BMC Genomics

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Background: Phytohormones are the key factors regulating vascular development in plants, and they are also involved in tension wood (TW) formation. Although the theory of hormone distribution in TW formation is widely supported, the effects of endogenous hormones on TW formation have not yet been assessed. In this study, TW formation was induced in Catalpa bungei by artificial bending. The phytohormone content of TW, opposite wood (OW) and normal wood (NW) was determined using liquid chromatography-mass spectrometry (LC-MS), and transcriptome sequencing was performed. The hormone content and related gene expression data were comprehensively analyzed. Results: The results of analyses of the plant hormone contents indicated significantly higher levels of cis-zeatin (cZ), indoleacetic acid (IAA) and abscisic acid (ABA) in TW than in OW. Genes involved in the IAA and ABA synthesis pathways, such as ALDH (evm.model.group5.1511) and UGT (evm.model.scaffold36.20), were significantly upregulated in TW. and the expression levels of ARF (evm.model.group5.1332), A-ARR (evm.model.group0.1600), and TCH4 (evm.model.group2.745), which participate in IAA, cZ and Brassinolide (BR) signal transduction, were significantly increased in TW. In particular, ARF expression may be regulated by long noncoding RNAs (lncRNAs) and the HD-ZIP transcription factor ATHB-15. Conclusions: We constructed a multiple hormone-mediated network of C. bungei TW formation based on hormone levels and transcriptional expression profiles were identified during TW formation.

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Regulatory function of homeodomain‐leucine zipper (HD‐ZIP) family proteins during embryogenesis

Cited by 35 publications

References 131 publications

Water lily ( Nymphaea thermarum ) genome reveals variable genomic signatures of ancient vascular cambium losses

Water lily ( Nymphaea thermarum ) genome reveals variable genomic signatures of ancient vascular cambium losses

Water lily (Nymphaea thermarum) draft genome reveals variable genomic signatures of ancient vascular cambium losses

Genome-wide analysis of lncRNA and mRNA expression and endogenous hormone regulation during tension wood formation in Catalpa bungei

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