Genomic Architecture and Evolution of the Cellulose synthase Gene Superfamily as Revealed by Phylogenomic Analysis

Pancaldi, Francesco; Loo, E.N. van; Schranz, M. Eric; Trindade, Luisa M.

doi:10.3389/fpls.2022.870818

Cited by 12 publications

(16 citation statements)

References 70 publications

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“…1 ) reveals that the CLSD family diversified independently in mosses, lycophytes, liverworts, and seed plants. As shown previously ( Hunter et al, 2012 ; Pancaldi et al, 2022 ), seed plant CSLDs cluster in three clades that correspond to distinct mutant phenotypes related to pollen tube development ( Bernal et al, 2008 ; Doblin et al, 2001 ; Moon et al, 2018 ; Wang et al, 2011 ), root hair development ( Bernal et al, 2008 ; Favery et al, 2001 ; Galway et al, 2011 ; Hu et al, 2018 ; Kim et al, 2007 ; Li et al, 2016 ; Park et al, 2011 ; Peng et al, 2019 ; Penning et al, 2009 ; Qi et al, 2013 ; Wang et al, 2001 ; Yoo et al, 2012 ), and general growth effects, in some cases attributed to defects in cytokinesis ( Bernal et al, 2007 ; Gu et al, 2016 ; Hu et al, 2010 ; Hunter et al, 2012 ; Luan et al, 2011 ; Samuga and Joshi, 2004 ; Wu et al, 2010 ; Yang et al, 2016 ; Yoshikawa et al, 2013 ; Zhu et al, 2010 ). The divergence of P. patens CSLDs into two clades, one containing CSLD2 and CSLD6 and the other containing the six remaining P. patens CSLDs ( Fig.…”

Section: Resultssupporting

confidence: 79%

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Cellulose synthase-like D movement in the plasma membrane requires enzymatic activity

Chaves

et al. 2023

Journal of Cell Biology

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Cellulose Synthase-Like D (CSLD) proteins, important for tip growth and cell division, are known to generate β-1,4-glucan. However, whether they are propelled in the membrane as the glucan chains they produce assemble into microfibrils is unknown. To address this, we endogenously tagged all eight CSLDs in Physcomitrium patens and discovered that they all localize to the apex of tip-growing cells and to the cell plate during cytokinesis. Actin is required to target CSLD to cell tips concomitant with cell expansion, but not to cell plates, which depend on actin and CSLD for structural support. Like Cellulose Synthase (CESA), CSLD requires catalytic activity to move in the plasma membrane. We discovered that CSLD moves significantly faster, with shorter duration and less linear trajectories than CESA. In contrast to CESA, CSLD movement was insensitive to the cellulose synthesis inhibitor isoxaben, suggesting that CSLD and CESA function within different complexes possibly producing structurally distinct cellulose microfibrils.

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Section: Resultssupporting

confidence: 79%

“…Phylogenetic analysis confirms that the CSLD families of mosses and seed plants diversified independently from a single ancestral gene ( Fig. 1 ; Pancaldi et al, 2022 ). CSLD families from both lineages include members that function in tip growth and cytokinesis, suggesting that both functions are ancestral.…”

Section: Discussionsupporting

confidence: 56%

Cellulose synthase-like D movement in the plasma membrane requires enzymatic activity

Chaves

et al. 2023

Journal of Cell Biology

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“…A group of 178 genomes from different plant species ( Supplementary Table S1 ) ( Pancaldi et al, 2022 ), with a range from Chlorophyta to flowering plants, was collected for genome-wide identification of CHS gene family. A total of 2,011 CHS homologous genes was detected in 162 genomes ( Figure 1 ; Supplementary Tables S2-S4 ), with 12.4 members per genome on average.…”

Section: Resultsmentioning

confidence: 99%

“…A set of 178 plant genomes, basically from Pancaldi et al (2022) , was used for analysis in this study ( Supplementary Table S1 ). Information of species taxonomic classification was obtained from Angiosperm Phylogeny Website (APG) and NCBI databases ( Leebens-Mack et al, 2019 ).…”

Section: Methodsmentioning

confidence: 99%

Exploring the evolution of CHS gene family in plants

Yang,

Zhang,

Chu

et al. 2024

Front. Genet.

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Chalcone synthase (CHS) is a key enzyme that catalyzes the first committed step of flavonoid biosynthetic pathway. It plays a vital role not only in maintaining plant growth and development, but also in regulating plant response to environmental hazards. However, the systematic phylogenomic analysis of CHS gene family in a wide range of plant species has not been reported yet. To fill this knowledge gap, a large-scale investigation of CHS genes was performed in 178 plant species covering green algae to dicotyledons. A total of 2,011 CHS and 293 CHS-like genes were identified and phylogenetically divided into four groups, respectively. Gene distribution patterns across the plant kingdom revealed the origin of CHS can be traced back to before the rise of algae. The gene length varied largely in different species, while the exon structure was relatively conserved. Selection pressure analysis also indicated the conserved features of CHS genes on evolutionary time scales. Moreover, our synteny analysis pinpointed that, besides genome-wide duplication and tandem duplication, lineage specific transposition events also occurred in the evolutionary trajectory of CHS gene family. This work provides novel insights into the evolution of CHS gene family and may facilitate further research to better understand the regulatory mechanism of traits relating to flavonoid biosynthesis in diverse plants.

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“…In addition to calculating the statistical significance of the colocalization between miscanthus SQTLs and QTLs, the cell wall genes in colocalizing regions were identified by using the set of angiosperm cell wall genes developed in our previous SQTL study [ 1 ]. Moreover, angiosperm-wide syntenic conservation of those genes was analyzed by retrieving their syntenic homologs from the synteny network developed by Pancaldi, et al [ 75 ] and Pancaldi, Vlegels, Rijken, van Loo, and Trindade [ 1 ].…”

Section: Methodsmentioning

confidence: 99%

Syntenic Cell Wall QTLs as Versatile Breeding Tools: Intraspecific Allelic Variability and Predictability of Biomass Quality Loci in Target Plant Species

Pancaldi

Loo

Senio

et al. 2023

Plants

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Syntenic cell wall QTLs (SQTLs) can identify genetic determinants of biomass traits in understudied species based on results from model crops. However, their effective use in plant breeding requires SQTLs to display intraspecific allelic variability and to predict causative loci in other populations/species than the ones used for SQTLs identification. In this study, genome assemblies from different accessions of Arabidopsis, rapeseed, tomato, rice, Brachypodium and maize were used to evaluate the intraspecific variability of SQTLs. In parallel, a genome-wide association study (GWAS) on cell wall quality traits was performed in miscanthus to verify the colocalization between GWAS loci and miscanthus SQTLs. Finally, an analogous approach was applied on a set of switchgrass cell wall QTLs retrieved from the literature. These analyses revealed large SQTLs intraspecific genetic variability, ranging from presence–absence gene variation to SNPs/INDELs and changes in coded proteins. Cell wall genes displaying gene dosage regulation, such as PAL and CAD, displayed presence–absence variation in Brachypodium and rapeseed, while protein INDELs were detected for the Brachypodium homologs of the rice brittle culm-like 8 locus, which may likely impact cell wall quality. Furthermore, SQTLs significantly colocalized with the miscanthus and switchgrass QTLs, with relevant cell wall genes being retained in colocalizing regions. Overall, SQTLs are useful tools to screen germplasm for relevant genes and alleles to improve biomass quality and can increase the efficiency of plant breeding in understudied biomass crops.

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Genomic Architecture and Evolution of the Cellulose synthase Gene Superfamily as Revealed by Phylogenomic Analysis

Cited by 12 publications

References 70 publications

Cellulose synthase-like D movement in the plasma membrane requires enzymatic activity

Cellulose synthase-like D movement in the plasma membrane requires enzymatic activity

Exploring the evolution of CHS gene family in plants

Syntenic Cell Wall QTLs as Versatile Breeding Tools: Intraspecific Allelic Variability and Predictability of Biomass Quality Loci in Target Plant Species

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