LMI1 homeodomain protein regulates organ proportions by spatial modulation of endoreduplication

Vuolo, Francesco; Kierzkowski, Daniel; Runions, Adam; Hajheidari, Mohsen; Mentink, Remco A.; Gupta, Mainak Das; Zhang, Zhongjuan; Vlad, Daniela; Wang, Yi; Pečinka, Aleš; Gan, Xiangchao; Hay, Angela; Huijser, Peter; Tsiantis, Miltos

doi:10.1101/gad.318212.118

Cited by 31 publications

(19 citation statements)

References 35 publications

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“…According to the predicted interaction network, NtHDZI3, 8, 10, and 18 might play a similar role in N. tabacum. Similarly, NtHDZI24 and 25 might function as a LATE MERISTEM IDENTITY1 (LMI1) homeodomain protein to regulate stipular ratio similar to the role of ATHB51 [51], whereas NtHDZI1, 2, 4, 6, 13, 16, 17, and 21 might be involved in regulating the response to water-deficit in an ABA-dependent manner similar to the function of ATHB6 [45].…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of HD-ZIP I Gene Subfamily in Nicotiana tabacum

Bai

Feng

et al. 2019

Genes

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The homeodomain-leucine zipper (HD-Zip) gene family, whose members play vital roles in plant growth and development, and participate in responding to various stresses, is an important class of transcription factors currently only found in plants. Although the HD-Zip gene family, especially the HD-Zip I subfamily, has been extensively studied in many plant species, the systematic report on HD-Zip I subfamily in cultivated tobacco (Nicotiana tabacum) is lacking. In this study, 39 HD-Zip I genes were systematically identified in N. tabacum (Nt). Interestingly, that 64.5% of the 31 genes with definite chromosome location information were found to originate from N. tomentosoformis, one of the two ancestral species of allotetraploid N. tabacum. Phylogenetic analysis divided the NtHD-Zip I subfamily into eight clades. Analysis of gene structures showed that NtHD-Zip I proteins contained conserved homeodomain and leucine-zipper domains. Three-dimensional structure analysis revealed that most NtHD-Zip I proteins in each clade, except for those in clade η, share a similar structure to their counterparts in Arabidopsis. Prediction of cis-regulatory elements showed that a number of elements responding to abscisic acid and different abiotic stresses, including low temperature, drought, and salinity, existed in the promoter region of NtHD-Zip I genes. The prediction of Arabidopsis ortholog-based protein–protein interaction network implied that NtHD-Zip I proteins have complex connections. The expression profile of these genes showed that different NtHD-Zip I genes were highly expressed in different tissues and could respond to abscisic acid and low-temperature treatments. Our study provides insights into the evolution and expression patterns of NtHD-Zip I genes in N. tabacum and will be useful for further functional characterization of NtHD-Zip I genes in the future.

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Section: Resultsmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of HD-ZIP I Gene Subfamily in Nicotiana tabacum

Bai

Feng

et al. 2019

Genes

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“…Further, fine mapping with reduced-coverage genome sequences of 131 individuals in the NILs (near iso-genic lines, BC 3 F 6 ) (~59) derived from the cross of ZFF 2 ( Figure S11) and narrowed down the locus controlling leaf shape to a region between 54.21 and 54.36 Mb within tig00018960 with six predicted genes. Of the six genes, the gene Hca.13G0013000 (HcLMI1) was orthologous to the transcription factor, LATE MERISTEM IDENTITY1 (LMI1, AT5G03790) (Vuolo et al, 2018) with 51.8% protein similarity ( Figure S12), encoding a homeodomain leucine zipper class I (HD-Zip I) meristem identity regulator that acts together with LFY to induce CAL expression. Two deletions of 1-bp, 955 and 981 bp, respectively, in the 3rd exon were found in round-leaf Hclmi1 compared with the gene sequence of lobed-leaf HcLMI1 (Figure 2c).…”

Section: Phylogenetic Analysis and Whole-genome Duplicationsmentioning

confidence: 99%

The genome of kenaf (Hibiscus cannabinus L.) provides insights into bast fibre and leaf shape biogenesis

Zhang

et al. 2020

Plant Biotechnology Journal

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Kenaf is an annual crop that is widely cultivated as a source of bast (phloem) fibres, the phytoremediation of heavy metal-contaminated farmlands and textile-relevant compounds. Leaf shape played a unique role in kenaf improvement, due to the inheritance as a single locus and the association with fibre development in typical lobed-leaf varieties. Here we report a highquality genome assembly and annotation for var. 'Fuhong 952' with 1078 Mbp genome and 66 004 protein-coding genes integrating single-molecule real-time sequencing, a high-density genetic map and high-throughput chromosome conformation capture techniques. Gene mapping assists the identification of a homeobox transcription factor LATE MERISTEM IDENTITY 1 (HcLMI1) gene controlling lobed-leaf. Virus-induced gene silencing (VIGS) of HcLMI1 in a lobed-leaf variety was critical to induce round (entire)-like leaf formation. Candidate genes involved in cell wall formation were found in quantitative trait loci (QTL) for fibre yield and quality-related traits. Comparative genomic and transcriptome analyses revealed key genes involved in bast fibre formation, among which there are twice as many cellulose synthase A (CesA) genes due to a recent whole-genome duplication after divergence from Gossypium. Population genomic analysis showed two recent population bottlenecks in kenaf, suggesting domestication and improvement process have led to an increase in fibre biogenesis and yield. This chromosome-scale genome provides an important framework and toolkit for sequencedirected genetic improvement of fibre crops. 1796

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“…In recent years, the development of live-imaging tools to capture quantitative data from living organisms has increased exponentially and has enabled us to precisely monitor cell division and cell growth in a 4D scale (2). The triumvirate of live imaging, classic developmental genetics, and computational modeling fuels our understanding of growth during plant morphogenesis (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14).…”

mentioning

confidence: 99%

Growth dynamics of the Arabidopsis fruit is mediated by cell expansion

Ripoll

Zhu

Brocke

et al. 2019

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

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Fruit have evolved a sophisticated tissue and cellular architecture to secure plant reproductive success. Postfertilization growth is perhaps the most dramatic event during fruit morphogenesis. Several studies have proposed that fertilized ovules and developing seeds initiate signaling cascades to coordinate and promote the growth of the accompanying fruit tissues. This dynamic process allows the fruit to conspicuously increase its size and acquire its final shape and means for seed dispersal. All these features are key for plant survival and crop yield. Despite its importance, we lack a high-resolution spatiotemporal map of how postfertilization fruit growth proceeds at the cellular level. In this study, we have combined live imaging, mutant backgrounds in which fertilization can be controlled, and computational modeling to monitor and predict postfertilization fruit growth in Arabidopsis. We have uncovered that, unlike leaves, sepals, or roots, fruit do not exhibit a spatial separation of cell division and expansion domains; instead, there is a separation into temporal stages with fertilization as the trigger for transitioning to cell expansion, which drives postfertilization fruit growth. We quantified the coordination between fertilization and fruit growth by imaging no transmitting tract (ntt) mutants, in which fertilization fails in the bottom half of the fruit. By combining our experimental data with computational modeling, we delineated the mobility properties of the seed-derived signaling cascades promoting growth in the fruit. Our study provides the basis for generating a comprehensive understanding of the molecular and cellular mechanisms governing fruit growth and shape.

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LMI1 homeodomain protein regulates organ proportions by spatial modulation of endoreduplication

Cited by 31 publications

References 35 publications

Genome-Wide Identification and Expression Analysis of HD-ZIP I Gene Subfamily in Nicotiana tabacum

Genome-Wide Identification and Expression Analysis of HD-ZIP I Gene Subfamily in Nicotiana tabacum

The genome of kenaf (Hibiscus cannabinus L.) provides insights into bast fibre and leaf shape biogenesis

Growth dynamics of the Arabidopsis fruit is mediated by cell expansion

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