Comprehensive characterization and gene expression patterns of LBD gene family in Gossypium

Yu, Jingwen; Xie, Qianwen; Cheng, Li; Dong, Yifan; Zhu, Shuijin; Chen, Jinhong

doi:10.1007/s00425-020-03364-8

Cited by 28 publications

(29 citation statements)

References 66 publications

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“…2018 ; Yu et al, 2020a ; Yu et al, 2020b ). The stability of the internal nodes was measured by bootstrap analysis of 1,000 replicates ( Yu et al, 2020a ; Yu et al, 2020b ). The illusion of “Long-branch Attraction” (LBA) exists widely in molecular phylogenetic analysis.…”

Section: Methodsmentioning

confidence: 99%

“…tauschii) were performed with ClustalW using the default options in MEGA-X (Kumar et al, 2018). Phylogenetic trees were constructed based on bootstrap neighbor-joining (NJ) algorithms with the Kimura two-parameter model of MEGAX (Grimplet et al, 2017;Liu et al, 2019;Lu et al, 2018;Rui-Min et al 2018;Yu et al, 2020a;Yu et al, 2020b). The stability of the internal nodes was measured by bootstrap analysis of 1,000 replicates (Yu et al, 2020a;Yu et al, 2020b).…”

Section: Phylogenetic Gene Structure and Motif Composition Analysismentioning

confidence: 99%

“…Phylogenetic trees were constructed based on bootstrap neighbor-joining (NJ) algorithms with the Kimura two-parameter model of MEGAX (Grimplet et al, 2017;Liu et al, 2019;Lu et al, 2018;Rui-Min et al 2018;Yu et al, 2020a;Yu et al, 2020b). The stability of the internal nodes was measured by bootstrap analysis of 1,000 replicates (Yu et al, 2020a;Yu et al, 2020b). The illusion of ''Long-branch Attraction'' (LBA) exists widely in molecular phylogenetic analysis.…”

Section: Phylogenetic Gene Structure and Motif Composition Analysismentioning

confidence: 99%

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Genome-wide identification and characterization of the Lateral Organ Boundaries Domain (LBD) gene family in polyploid wheat and related species

Tao

et al. 2021

PeerJ

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Background Wheat (Triticum aestivum) originated from three different diploid ancestral grass species and experienced two rounds of polyploidization. Exploring how certain wheat gene subfamilies have expanded during the evolutionary process is of great importance. The Lateral Organ Boundaries Domain (LBD) gene family encodes plant-specific transcription factors that share a highly conserved LOB domain and are prime candidates for this, as they are involved in plant growth, development, secondary metabolism and stress in various species. Methods Using a genome-wide analysis of high-quality polyploid wheat and related species genome sequences, a total of 228 LBD members from five Triticeae species were identified, and phylogenetic relationship analysis of LBD members classified them into two main classes (classes I and II) and seven subgroups (classes I a–e, II a and II b). Results The gene structure and motif composition analyses revealed that genes that had a closer phylogenetic relationship in the same subgroup also had a similar gene structure. Macrocollinearity and microcollinearity analyses of Triticeae species suggested that some LBD genes from wheat produced gene pairs across subgenomes of chromosomes 4A and 5A and that the complex evolutionary history of TaLBD4B-9 homologs was a combined result of chromosome translocation, polyploidization, gene loss and duplication events. Public RNA-seq data were used to analyze the expression patterns of wheat LBD genes in various tissues, different developmental stages and following abiotic and biotic stresses. Furthermore, qRT-PCR results suggested that some TaLBDs in class II responded to powdery mildew, regulated reproductive growth and were involved in embryo sac development in common wheat.

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Section: Methodsmentioning

confidence: 99%

Section: Phylogenetic Gene Structure and Motif Composition Analysismentioning

confidence: 99%

Section: Phylogenetic Gene Structure and Motif Composition Analysismentioning

confidence: 99%

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Genome-wide identification and characterization of the Lateral Organ Boundaries Domain (LBD) gene family in polyploid wheat and related species

Tao

et al. 2021

PeerJ

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“…This family has been comprehensively analyzed in many species, such as Arabidopsis thaliana ( Liu et al, 2005 ), Malus domestica ( Wang et al, 2013 ), Glycine max ( Yang et al, 2017 ), Eucalyptus grandis ( Lu et al, 2018 ), Brassica rapa ( Huang et al, 2018 ), Camellia sinensis ( Teng et al, 2018 ), Gossypium spp. ( Yu et al, 2020 ), and Pyrus bretschneideri ( Song et al, 2020 ). LBD genes show a key role in the regulation of plant organ development and in the response to abiotic and biotic stresses ( Xu et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

“…LBD genes show a key role in the regulation of plant organ development and in the response to abiotic and biotic stresses ( Xu et al, 2016 ). They are involved in the establishment of organ boundaries ( Rast and Simon, 2012 ), leaf formation ( Semiarti et al, 2001 ), pulvinus differentiation and petiole development ( Chen et al, 2012 ), regulation of lateral root organogenesis ( Okushima et al, 2007 ), root and stem development ( Yu et al, 2020 ), development of sepal and petal primordia of flowers ( Xu et al, 2008 ), pollen development ( Kim et al, 2015 ), regulation of light/dark-dependent hypocotyl elongation ( Mangeon et al, 2011 ), and secondary phloem growth ( Yordanov et al, 2010 ). Moreover, LOB genes are also involved in pathogen and abiotic response ( Thatcher et al, 2012 ; Grimplet et al, 2017 ; Yu et al, 2020 ), and they can act as repressor of anthocyanin biosynthesis and affect nitrogen response ( Rubin et al, 2009 ).…”

Section: Introductionmentioning

confidence: 99%

RNAi of a Putative Grapevine Susceptibility Gene as a Possible Downy Mildew Control Strategy

et al. 2021

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Downy mildew, caused by the oomycete Plasmopara viticola, is one of the diseases causing the most severe economic losses to grapevine (Vitis vinifera) production. To date, the application of fungicides is the most efficient method to control the pathogen and the implementation of novel and sustainable disease control methods is a major challenge. RNA interference (RNAi) represents a novel biotechnological tool with a great potential for controlling fungal pathogens. Recently, a candidate susceptibility gene (VviLBDIf7) to downy mildew has been identified in V. vinifera. In this work, the efficacy of RNAi triggered by exogenous double-stranded RNA (dsRNA) in controlling P. viticola infections has been assessed in a highly susceptible grapevine cultivar (Pinot noir) by knocking down VviLBDIf7 gene. The effects of dsRNA treatment on this target gene were assessed by evaluating gene expression, disease severity, and development of vegetative and reproductive structures of P. viticola in the leaf tissues. Furthermore, the effects of dsRNA treatment on off-target (EF1α, GAPDH, PEPC, and PEPCK) and jasmonic acid metabolism (COI1) genes have been evaluated. Exogenous application of dsRNA led to significant reductions both in VviLBDIf7 gene expression, 5 days after the treatment, and in the disease severity when artificial inoculation was carried out 7 days after dsRNA treatments. The pathogen showed clear alterations to both vegetative (hyphae and haustoria) and reproductive structures (sporangiophores) that resulted in stunted growth and reduced sporulation. Treatment with dsRNA showed signatures of systemic activity and no deleterious off-target effects. These results demonstrated the potential of RNAi for silencing susceptibility factors in grapevine as a sustainable strategy for pathogen control, underlying the possibility to adopt this promising biotechnological tool in disease management strategies.

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Cloning and functional identification of apple LATERAL ORGAN BOUNDARY DOMAIN 3 (LBD3) transcription factor in the regulation of drought and salt stress

Liu,

An,

Liu

et al. 2024

Planta

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Comprehensive characterization and gene expression patterns of LBD gene family in Gossypium

Abstract: Main conclusion A comprehensive account of the LBD gene family of Gossypium was provided in this work. Expression analysis and functional characterization revealed that LBD genes might play different roles in G. hirsutum and G. barbadense.

Cited by 28 publications

References 66 publications

Genome-wide identification and characterization of the Lateral Organ Boundaries Domain (LBD) gene family in polyploid wheat and related species

Genome-wide identification and characterization of the Lateral Organ Boundaries Domain (LBD) gene family in polyploid wheat and related species

RNAi of a Putative Grapevine Susceptibility Gene as a Possible Downy Mildew Control Strategy

Cloning and functional identification of apple LATERAL ORGAN BOUNDARY DOMAIN 3 (LBD3) transcription factor in the regulation of drought and salt stress

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