Genome-wide identification, characterization and expression analysis of the non-specific lipid transfer proteins in potato

BMC Genomics, Год журнала: 2019, Номер 20(1)

Опубликована: Май 14, 2019

Plant non-specific lipid transfer proteins (nsLTPs) are small, basic that abundant in higher plants. They have been reported to play an important role various plant physiological processes, such as transfer, signal transduction, and pathogen defense. To date, a comprehensive analysis of the potato nsLTP gene family is still lacking after completion (Solanum tuberosum L.) genome sequencing. A genome-wide characterization, classification expression StnsLTP was performed this study. In study, total 83 genes were identified categorized into eight types based on Boutrot's method. Multiple characteristics these genes, including phylogeny, structures, conserved motifs, protein domains, chromosome locations, cis-elements promoter sequences, analyzed. The distribution collinearity analyses suggested expansion greatly enhanced by tandem duplications. Ka/Ks showed 47 pairs duplicated tended undergo purifying selection during evolution. Moreover, tissues analyzed using RNA-seq data verified quantitative real-time PCR, revealing mainly expressed younger tissues. These results indicated StnsLTPs may played significant functionally varied roles development different we comprehensively nsLTPs potato, providing valuable information better understand functions pathways, especially response abiotic stress.

Язык: Английский

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Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress

Frontiers in Plant Science, Год журнала: 2020, Номер 11

Опубликована: Ноя. 12, 2020

Drought stress is an important abiotic factor limiting common bean yield, with great impact on the production worldwide. Understanding genetic basis regulating beans’ yield and seed weight (SW) a fundamental prerequisite for development of superior cultivars. The main objectives this work were to conduct genome-wide marker discovery by genotyping Mesoamerican panel germplasm, containing cultivated landrace accessions broad origin, followed identification genomic regions associated productivity under two water regimes using different association study (GWAS) approaches. A total 11,870 markers genotyped 339 genotypes, which 3,213 SilicoDArT 8,657 SNPs derived from DArT CaptureSeq. estimated linkage disequilibrium extension, corrected structure relatedness ( r 2 sv ), was 98.63 124.18 kb landraces breeding lines, respectively. Germplasm structured into lines/cultivars. We carried out GWASs 100-SW in field environments without 3 consecutive years, single-, segment-, gene-based models. Higher number associations at high stringency identified SW trait irrigation, totaling ∼185 QTLs both single- segment-based, whereas showed ∼220 ∼650 genes. For drought, 18 segment-based 35 genes GWASs. 25 identified, drought 10 In addition consistent detected across experiments, these GWAS approaches provided complementary QTL information (∼221 QTLs; 650 genes; 0.01% 32%). Several mined within or near candidate playing significant role productivity, providing better understanding mechanisms underlying traits making available molecular tools be used marker-assisted breeding. findings also allowed material (germplasm) performance promising program. Finally, availability highly diverse scientific value analysis any relevant bean.

Язык: Английский

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Comprehensive Bioinformatics and Expression Analysis of the TLP Gene Family Revealed Its Role in Regulating the Response of Oryza sativa to Nilaparvata lugens, Laodelphax striatellus, and Jinggangmycin

Agronomy, Год журнала: 2022, Номер 12(6), С. 1297 - 1297

Опубликована: Май 28, 2022

Thaumatin-like proteins (TLPs), which belong to pathogenesis-related (PR) protein family 5 (PR5), are involved in the plant host defense and developmental processes. Detailed information regarding TLP gene rice remains elusive. Here, we identified 43 OsTLP genes from genome database. The silico analysis comprised of evolutionary tree, structure, conserved motifs, chemical properties highlighted key aspects genes. By phylogenetic analysis, were classified into ten groups (OsTLPI-OsTLPX). Gene ontology (GO) showed that regulate growth response various environmental stimuli. Moreover, most expressed almost all tissues. Microarray data differential expression trends under salinity stress hormonal treatments, whereas BPH, SSB, RFL, only OsTLP1, OsTLP2 OsTLP27 expressed. qRT-PCR as prominent gene, displayed by its upregulated JGM. Our results provide detailed knowledge resistance plants, believe current study will facilitate development cultivars resistant biotic/abiotic stress, particularly caused chewing sucking insect pests.

Язык: Английский

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Lipid transfer proteins: structure, classification and prospects of genetic engineering for improved disease resistance in plants

Plant Cell Tissue and Organ Culture (PCTOC), Год журнала: 2023, Номер 153(1), С. 3 - 17

Опубликована: Янв. 14, 2023

Язык: Английский

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From Gene to Transcript and Peptide: A Deep Overview on Non-Specific Lipid Transfer Proteins (nsLTPs)

Antibiotics, Год журнала: 2023, Номер 12(5), С. 939 - 939

Опубликована: Май 21, 2023

Non-specific lipid transfer proteins (nsLTPs) stand out among plant-specific peptide superfamilies due to their multifaceted roles in plant molecular physiology and development, including protective functions against pathogens. These antimicrobial agents have demonstrated remarkable efficacy bacterial fungal The discovery of plant-originated, cysteine-rich peptides such as nsLTPs has paved the way for exploring mentioned organisms potential biofactories synthesizing compounds. Recently, been focus a plethora research reviews, providing functional overview activity. present work compiles relevant information on nsLTP omics evolution, it adds meta-analysis nsLTPs, including: (1) genome-wide mining 12 genomes not studied before; (2) latest common ancestor analysis (LCA) expansion mechanisms; (3) structural proteomics, scrutinizing nsLTPs’ three-dimensional structure/physicochemical characteristics context classification; (4) broad spatiotemporal transcriptional using soybean study case. Combining critical review with original results, we aim integrate high-quality single source clarify unexplored aspects this important gene/peptide family.

Язык: Английский

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Non-Specific Lipid Transfer Proteins in Triticum kiharae Dorof. et Migush.: Identification, Characterization and Expression Profiling in Response to Pathogens and Resistance Inducers

Pathogens, Год журнала: 2019, Номер 8(4), С. 221 - 221

Опубликована: Ноя. 5, 2019

Non-specific lipid-transfer proteins (nsLTPs) represent a family of plant antimicrobial peptides (AMPs) implicated in diverse physiological processes. However, their role induced resistance (IR) triggered by non-pathogenic fungal strains and metabolites is poorly understood. In this work, using RNA-seq data our AMP search pipeline, we analyzed the repertoire nsLTP genes wheat Triticum kiharae studied expression response to Fusarium oxysporum infection treatment with intracellular sambucinum FS-94. A total 243 putative nsLTPs were identified, which classified into five structural types characterized. Expression analysis showed that 121 TkLTPs including sets paralogs identical mature displayed specific patters different treatments pointing roles development. We speculate upregulated are involved protection due activity or signaling functions. Furthermore, discovered IR-displaying plants, vast majority downregulated, suggesting as negative regulators immune mechanisms activated FS-94 elicitors. The results obtained add knowledge IR provide candidate molecules for genetic engineering crops enhance disease resistance.

Язык: Английский

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Genome-Wide Identification and Expression Analysis of nsLTP Gene Family in Rapeseed (Brassica napus) Reveals Their Critical Roles in Biotic and Abiotic Stress Responses

International Journal of Molecular Sciences, Год журнала: 2022, Номер 23(15), С. 8372 - 8372

Опубликована: Июль 28, 2022

Non-specific lipid transfer proteins (nsLTPs) are small cysteine-rich basic which play essential roles in plant growth, development and abiotic/biotic stress response. However, there is limited information about the nsLTP gene (BnLTP) family rapeseed (Brassica napus). In this study, 283 BnLTP genes were identified rapeseed, distributed randomly 19 chromosomes of rapeseed. Phylogenetic analysis showed that divided into seven groups. Exon/intron structure MEME motifs both remained highly conserved each group. Segmental duplication hybridization rapeseed’s two sub-genomes mainly contributed to expansion family. Various potential cis-elements respond development, biotic/abiotic stresses, phytohormone signals existed promoters. Transcriptome expressed various tissues/organs with different levels also involved response heat, drought, NaCl, cold, IAA ABA as well treatment fungal pathogens (Sclerotinia sclerotiorum Leptosphaeria maculans). The qRT-PCR assay validated results RNA-seq expression top Sclerotinia-responsive genes, BnLTP129 BnLTP161. Moreover, batches BnLTPs might be regulated by BnTT1 BnbZIP67 metabolism or adaptability seed coat embryo This work provides an important basis for further functional study quality improvement resistance.

Язык: Английский

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Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence–structure–function analysis

PeerJ, Год журнала: 2019, Номер 7, С. e7504 - e7504

Опубликована: Авг. 14, 2019

Non-specific Lipid Transfer Proteins (nsLTPs) are widely distributed in the plant kingdom and constitute a superfamily of related proteins. Several hundreds different nsLTP sequences-and counting-have been characterized so far, but their biological functions remain unclear. It has clear for years that they present certain interest agronomic nutritional issues. Deciphering means collecting analyzing variety data from gene sequence to protein structure, cellular localization physiological role. As huge growing number new sequences available nowadays, extracting meaningful knowledge sequence-structure-function relationships calls development tools approaches. nsLTPs show high evolutionary divergence, conserved common right handed superhelix structural fold, as involved large key roles defense, stimulating case study validating such an approach. In this study, we comprehensively investigated 797 sequences, including phylogenetic analysis on canonical three-dimensional structure modeling functional annotation using several well-established bioinformatics programs. Additionally, two integrative methodologies original were developed. The first was method detection (i) amino acid residues stabilization (ii) potentially ligand interaction. second structure-function classification based trace display tree visualization interface. We also tool visualizing trees. Following protocol, updated established hypothesis is suggested. Lastly, work allows better representation diversity terms sequence, function.

Язык: Английский

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Transcriptome Analysis of Jojoba (Simmondsia chinensis) during Seed Development and Liquid Wax Ester Biosynthesis

Plants, Год журнала: 2020, Номер 9(5), С. 588 - 588

Опубликована: Май 4, 2020

Jojoba is one of the main two known plant source natural liquid wax ester for use in various applications, including cosmetics, pharmaceuticals, and biofuel. Due to lack transcriptomic genomic data on lipid biosynthesis accumulation, molecular marker breeding has been used improve jojoba oil production quality. In current study, transcriptome developing seeds was investigated using Illunina NovaSeq 6000 system, 100 × 106 paired end reads, an average length bp, a sequence depth 12 Gb per sample. A total 176,106 unigenes were detected with contig 201 bp. Gene Ontology (GO) showed that distributed three GO groups biological processes (BP, 5.53%), cellular component (CC, 6.06%), functions (MF, 5.88%) 67 functional groups. The pathway established based expression genes, fatty acid (FA) biosynthesis, FA desaturation, elongation, alcohol triacylglycerol (TAG) phospholipid metabolism, transfer storage genes. detection these categories genes confirms presence efficient accumulation system seeds. results this study will significantly enhance understanding biology open new routes improvement quality through biotechnology applications.

Язык: Английский

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Triterpenic and phenolic acids production changed in Salvia officinalis via in vitro and in vivo polyploidization: A consequence of altered genes expression

Phytochemistry, Год журнала: 2021, Номер 189, С. 112803 - 112803

Опубликована: Июнь 16, 2021

Язык: Английский

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