CLE peptide-mediated signaling in shoot and vascular meristem development

Dao, Thai Q.; Fletcher, Jennifer

doi:10.1007/s11515-017-1468-9

Cited by 5 publications

(3 citation statements)

References 129 publications

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“…The analysis of ortholog cluster expansion and contraction, however, did not include all gene families of interest. The CLE (CLAVATA3/EMBRYO SURROUNDING REGION-RELATED) family of short (∼21 amino acids) signaling peptides are known to regulate both primary and secondary tissue differentiation in flowering plants (43), but low sequence conservation among members of this gene family precludes many types of analysis. We therefore used CLANS clustering to assess patterns of relatedness between all putative CLE homologs (10) from Phytozome v12 (44) genomes, genomes of N. thermarum and Nelumbo nucifera (45), available angiosperm transcriptomes from the OneKP initiative (46), and N. thermarum transcriptomes (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.

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show abstract

“…The ortholog cluster expansion/contraction analysis, however, did not include all gene families of interest. The CLE (CLAVATA3/EMBRYO SURROUNDING REGION-RELATED) family of short (~21 amino acids) signaling peptides are known to regulate both primary and secondary tissue differentiation in flowering plants (45), but low sequence conservation among this gene family precludes many types of analysis. We therefore used CLANS clustering to assess patterns of relatedness between all putative CLE homologs (13) from Phytozome v12 (46) genomes, genomes of N. thermarum and Nelumbo nucifera (47), available angiosperm transcriptomes from the OneKP initiative (48), and N. thermarum transcriptomes [ Figure 3A] [SI Appendix, Figure S7].…”

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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“…Another foreseeable application is for plant defense compounds that may not be desirable (or even toxic) if produced in fruits or other edible parts of a plant, but could be very useful if controllable expressed in other tissues/organs for plant protection. CRE editing also presents the possibility to activate gene expression because CREs may bind transcriptional repressors, prominent examples include jasmonate signaling [ 75 ] and the CLV3–WUS stem cell homeostasis network [ 76 ], or to generate novel transcriptional output combinations. Lastly, as already demonstrated by the work in tomato and maize, CRE variants provide an opportunity to fine-tune gene expression to generate quantitative variation, particularly for dose-dependent genes like TFs.…”

Section: Epigenome Guided Improvementmentioning

confidence: 99%

Epigenome guided crop improvement: current progress and future opportunities

Zhang

Andrews

Eglitis-Sexton

et al. 2022

Emerging Topics in Life Sciences

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Epigenomics encompasses a broad field of study, including the investigation of chromatin states, chromatin modifications and their impact on gene regulation; as well as the phenomena of epigenetic inheritance. The epigenome is a multi-modal layer of information superimposed on DNA sequences, instructing their usage in gene expression. As such, it is an emerging focus of efforts to improve crop performance. Broadly, this might be divided into avenues that leverage chromatin information to better annotate and decode plant genomes, and into complementary strategies that aim to identify and select for heritable epialleles that control crop traits independent of underlying genotype. In this review, we focus on the first approach, which we term ‘epigenome guided’ improvement. This encompasses the use of chromatin profiles to enhance our understanding of the composition and structure of complex crop genomes. We discuss the current progress and future prospects towards integrating this epigenomic information into crop improvement strategies; in particular for CRISPR/Cas9 gene editing and precision genome engineering. We also highlight some specific opportunities and challenges for grain and horticultural crops.

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CLE peptide-mediated signaling in shoot and vascular meristem development

Cited by 5 publications

References 129 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

Epigenome guided crop improvement: current progress and future opportunities

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