Genome-Wide Analysis of the Lateral Organ Boundaries Domain (LBD) Gene Family in Solanum tuberosum

Abstract

Lateral organ boundaries domain (LBD) proteins belong to a particular class of transcription factors of lateral organ boundary (LOB) specific domains that play essential roles in plant growth and development. However, a potato phylogenetic analysis of the LBD family has not been fully studied by scholars and researchers. In this research, bioinformatics methods and the growth of potatoes were used to identify 43 StLBD proteins. We separated them into seven subfamilies: Ia, Ib, Ic, Id, Ie, IIa and IIb. The number of amino acids encoded by the potato LBD family ranged from 94 to 327. The theoretical isoelectric point distribution ranged from 4.16 to 9.12 Kda, and they were distributed among 10 chromosomes. The results of qRT-PCR showed that the expression levels of StLBD2-6 and StLBD3-5 were up-regulated under drought stress in the stem. The expression levels of StLBD1-5 and StLBD2-6 were down-regulated in leaves. We hypothesized that StLBD1-5 was down-regulated under drought stress, and that StLBD2-6 and StLBD3-5 up-regulation might help to maintain the normal metabolism of potato and enhance the potatoes’ resistance to drought.

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

“…Additionally, the MdLBD13 protein can inhibit anthocyanin synthesis and nitrogen uptake in apple (Li et al 2017). Genome-wide analysis of LBD gene family have been studied in plants like Camellia sinensis (Zhang et al 2019), Solanum tuberosum (Liu et al 2019), Eucalyptus grandis (Lu et al 2018), Brassica rapa (Huang et al 2018), grapevine (Grimplet et al 2017), and soybean (Yang et al 2017). However, the function of the LBD genes in Gossypium remains largely unexplored.…”

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

“…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).…”

“…In the present study, most of the analyzed taxa were closely related species of Triticeae, it is accorded with the content of the method ''breaking long branch method'' to reduce the problem of ''LBA'', in other words, taxonomic elements with close relationship were added for phylogenetic analysis. Secondly, in order to avoid the great difference among species, and refered to the method described by Zhao et al (2019), the conseved LOB domain were used for construct the evolutionary tree, which would further reduces the possibility of ''LBA'' (Bergsten, 2005;Zhao et al, 2019). The phylogenetic tree was visualized with EvolView (https://www.evolgenius.info/) (He et al, 2016).…”

“…The expression patterns of gene family members are helpful to predict their potential biological functions (Zhao et al, 2019). In order to elucidate the potential role of TaLBDs, their expression patterns were studied by qRT-PCR or in silico expression profiling.…”

“…Full-size DOI: 10.7717/peerj.11811/fig-5 reproductive stages), under two abiotic stresses (drought and heat) and one biotic stress (powdery mildew pathogen E09) were analyzed using the wheat RNA-seq data from public databases (Borrill, Ramirez-Gonzalez & Uauy, 2016;Pearce et al, 2015). The expression level was measured as tags per million (TPM), and we assumed that expression was high if TPM ≥ 2.5; moderate if 2.5 >TPM ≥ 1.5; low if 1.5 >TPM >0; and undetectable if TPM = 0, as reported by Zhao et al (2019) . Cluster analysis showed diverse expression patterns in LBDs of common wheat (Fig.…”