Identification and expression analysis of the LRR-RLK gene family in tomato (Solanum lycopersicum) Heinz 1706

Genome ◽  
2015 ◽  
Vol 58 (4) ◽  
pp. 121-134 ◽  
Author(s):  
Zhirong Wei ◽  
Jiehua Wang ◽  
Shaohui Yang ◽  
Yingjin Song
Keyword(s):  
Gene Family ◽  
Solanum Lycopersicum ◽  
Stress Responses ◽  
Tandem Duplication ◽  
Developmental Stages ◽  
Sequence Similarity ◽  
Functional Divergence ◽  
Fleshy Fruit ◽  
Important Species ◽  
Preferential Expression

As the largest subfamily of receptor-like kinases (RLKs), leucine-rich repeat receptor-like kinases (LRR-RLKs) regulate the growth, development, and stress responses of plants. Through a reiterative process of sequence analysis and re-annotation, 234 LRR-RLK genes were identified in the genome of tomato (Solanum lycopersicum) ‘Heinz 1706’, which were further grouped into 10 major groups based on their sequence similarity. In comparison to the significant role of tandem duplication in the expansion process of this gene family in other species, only approximately 12% (29 out of 234) of SlLRR-RLK genes arose from tandem duplication. Using the multiple expectation maximization for motif elicitation (MEME) method, the motif composition and arrangement were found to be variably conserved within each SlLRR-RLK group, indicating their different extent of functional divergence. Expression profiling analyses by qRT-PCR data revealed that SlLRR-RLK genes were differentially expressed in various tomato organs and tissues, and some SlLRR-RLK genes exhibited preferential expression in fruits at distinct developmental stages, suggesting that SlLRR-RLK may take important roles in fruit development and ripening process. The results of this study provide an overview of the LRR-RLK gene family in tomato Heinz 1706, one important species of Solanaceae, and will be helpful for future functional analysis of this important protein family in fleshy fruit-bearing species.

scholarly journals The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Hao Song ◽  
Ximing Guo ◽  
Lina Sun ◽  
Qianghui Wang ◽  
Fengming Han ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Tandem Duplication ◽  
Expression Patterns ◽  
Hard Clam ◽  
Gene Repertoire ◽  
Single Chromosome ◽  
Inhibitors Of Apoptosis ◽  
History Of ◽  
Evolutionary Success

Abstract Background Inhibitors of apoptosis (IAPs) are critical regulators of programmed cell death that are essential for development, oncogenesis, and immune and stress responses. However, available knowledge regarding IAP is largely biased toward humans and model species, while the distribution, function, and evolutionary novelties of this gene family remain poorly understood in many taxa, including Mollusca, the second most speciose phylum of Metazoa. Results Here, we present a chromosome-level genome assembly of an economically significant bivalve, the hard clam Mercenaria mercenaria, which reveals an unexpected and dramatic expansion of the IAP gene family to 159 members, the largest IAP gene repertoire observed in any metazoan. Comparative genome analysis reveals that this massive expansion is characteristic of bivalves more generally. Reconstruction of the evolutionary history of molluscan IAP genes indicates that most originated in early metazoans and greatly expanded in Bivalvia through both lineage-specific tandem duplication and retroposition, with 37.1% of hard clam IAPs located on a single chromosome. The expanded IAPs have been subjected to frequent domain shuffling, which has in turn shaped their architectural diversity. Further, we observed that extant IAPs exhibit dynamic and orchestrated expression patterns among tissues and in response to different environmental stressors. Conclusions Our results suggest that sophisticated regulation of apoptosis enabled by the massive expansion and diversification of IAPs has been crucial for the evolutionary success of hard clam and other molluscan lineages, allowing them to cope with local environmental stresses. This study broadens our understanding of IAP proteins and expression diversity and provides novel resources for studying molluscan biology and IAP function and evolution.

scholarly journals Genome-wide identification and characterization of GRAS transcription factors in tomato (Solanum lycopersicum)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3955 ◽  
Author(s):  
Yiling Niu ◽  
Tingting Zhao ◽  
Xiangyang Xu ◽  
Jingfu Li
Keyword(s):  
Gene Family ◽  
Solanum Lycopersicum ◽  
Stress Responses ◽  
Expression Patterns ◽  
Gene Families ◽  
Shoot Meristem ◽  
Axillary Shoot ◽  
Multiple Sequence ◽  
Genome Wide ◽  
First Time

Solanum lycopersicum, belonging to Solanaceae, is one of the commonly used model plants. The GRAS genes are transcriptional regulators, which play a significant role in plant growth and development, and the functions of several GRAS genes have been recognized, such as, axillary shoot meristem formation, radial root patterning, phytohormones (gibberellins) signal transduction, light signaling, and abiotic/biotic stress; however, only a few of these were identified and functionally characterized. In this study, a gene family was analyzed comprehensively with respect to phylogeny, gene structure, chromosomal localization, and expression pattern; the 54 GRAS members were screened from tomato by bioinformatics for the first time. The GRAS genes among tomato, Arabidopsis, rice, and grapevine were rebuilt to form a phylogenomic tree, which was divided into ten groups according to the previous classification of Arabidopsis and rice. A multiple sequence alignment exhibited the typical GRAS domain and conserved motifs similar to other gene families. Both the segmental and tandem duplications contributed significantly to the expansion and evolution of the GRAS gene family in tomato; the expression patterns across a variety of tissues and biotic conditions revealed potentially different functions of GRAS genes in tomato development and stress responses. Altogether, this study provides valuable information and robust candidate genes for future functional analysis for improving the resistance of tomato growth.

scholarly journals Identification and Expression Analysis of the NAC Gene Family in Coffea canephora

Agronomy ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 670 ◽  
Author(s):  
Dong ◽  
Jiang ◽  
Yang ◽  
Xiao ◽  
Bai ◽  
...  
Keyword(s):  
Cold Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Coffea Canephora ◽  
Coffee Bean ◽  
Systematic Analysis ◽  
Nac Gene Family ◽  
Basic Features

The NAC gene family is one of the largest families of transcriptional regulators in plants, and it plays important roles in the regulation of growth and development as well as in stress responses. Genome-wide analyses have been performed in diverse plant species, but there is still no systematic analysis of the NAC genes of Coffea canephora Pierre ex A. Froehner. In this study, we identified 63 NAC genes from the genome of C. canephora. The basic features and comparison analysis indicated that the NAC gene members increased via duplication events during the evolution of the plant. Phylogenetic analysis divided the NAC proteins from C. canephora, Arabidopsis and rice into 16 subgroups. Analysis of the expression patterns of CocNACs under cold stress and coffee bean development indicated that 38 CocNACs were differentially expressed under cold stress; six genes may play important roles in the process of cold acclimation, and four genes among 54 CocNACs showing a variety of expression patterns during different developmental stages of coffee beans may be positively related to the bean development. This study can expand our understanding of the functions of the CocNAC gene family in cold responses and bean development, thereby potentially intensifying the molecular breeding programs of Coffea spp. plants.

Characterization and expression analysis of GPAT gene family in maize

2019 ◽  
Vol 99 (5) ◽  
pp. 577-588
Author(s):  
Xiaoxuan Xu ◽  
Bowei Yan ◽  
Ying Zhao ◽  
Feng Wang ◽  
Xunchao Zhao ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Cold Treatment ◽  
Oil Production ◽  
Initial Step ◽  
Field Crops ◽  
Lysophospholipid Acyltransferases ◽  
Elevated Expression

Glycerol-3-phosphate acyltransferase (GPAT) catalyzes the initial step of glycerolipids biosynthesis and contributes to oil production, membrane stabilization, and stress responses in plants. In major field crops, little information on the GPAT gene family and their potential stress-related functions were available. In this study, 15 GPAT gene family members were identified from the maize genome and designated as ZmGPAT1–ZmGPAT14 and ZMS1. The ZmGPAT proteins contained 371–557 amino acids and had a molecular weight between 42.7 and 61.2 kDa. Phylogenetic analysis revealed that ZmGPATs fell into four clusters. All 15 ZmGPAT proteins possessed conserved PlsC/LPLAT (phosphate acyltransferases/lysophospholipid acyltransferases) domains and featured multiple acyltransferase motifs. The expression profiles of ZmGPAT genes were different in various tissues of maize and the elevated expression of several ZmGPAT genes occurred at early seed developmental stages. In response to environmental stresses, differential expression of ZmGPATs had been observed, highlighted by the significant induction of transcripts accumulation of some ZmGPATs under cold treatment. This study will help to better understand the potential roles of GPAT in oil production and development and abiotic stress responses in field crops.

scholarly journals Genome-wide analysis of wheat DNA-binding with one finger (Dof) transcription factor genes: evolutionary characteristics and diverse abiotic stress responses

2020 ◽  
Author(s):  
Yue Liu ◽  
Nannan Liu ◽  
Xiong Deng ◽  
Dongmiao Liu ◽  
Mengfei Li ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Abiotic Stress ◽  
Positive Selection ◽  
Gene Family ◽  
Stress Responses ◽  
Functional Divergence ◽  
Acid Sites ◽  
Genome Wide Analysis ◽  
Dof Transcription Factor ◽  
Genome Wide

Abstract Background: DNA binding with one finger (Dof) transcription factors play important roles in plant growth and abiotic stress responses. Although genome-wide identification and analysis of the DOF transcription factor family has been reported in other species, no relevant studies have emerged in wheat. The aim of this study was to investigate the evolutionary and functional characteristics associated with plant growth and abiotic stress responses by genome-wide analysis of the wheat Dof transcription factor gene family. Results: Using the recently released wheat genome database (IWGSC RefSeq v1.1), we identified 96 wheat Dof gene family members, which were phylogenetically clustered into five distinct subfamilies. Gene duplication analysis revealed a broad and heterogeneous distribution of TaDofs on the chromosome groups 1 to 7, and obvious tandem duplication genes were present on chromosomes 2 and 3.Members of the same gene subfamily had similar exon-intron structures, while members of different subfamilies had obvious differences. Functional divergence analysis indicated that type-II functional divergence played a major role in the differentiation of the TaDof gene family. Positive selection analysis revealed that the Dof gene family experienced different degrees of positive selection pressure during the process of evolution, and five significant positive selection sites (30A, 31T, 33A, 102G and 104S) were identified. Additionally, nine groups of coevolving amino acid sites, which may play a key role in maintaining the structural and functional stability of Dof proteins, were identified. The results from the RNA-seq data and qRT-PCR analysis revealed that TaDof genes exhibited obvious expression preference or specificity in different organs and developmental stages, as well as in diverse abiotic stress responses. Most TaDof genes were significantly upregulated by heat, PEG and heavy metal stresses. Conclusions: The genome-wide analysis and identification of wheat DOF transcription factor family and the discovery of important amino acid sites are expected to provide new insights into the structure, evolution and function of the plant Dof gene family.

scholarly journals Genome-Wide Analysis of LRR-RLK Gene Family in Four Gossypium Species and Expression Analysis during Cotton Development and Stress Responses

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 592
Author(s):  
Ruibin Sun ◽  
Shaohui Wang ◽  
Dan Ma ◽  
Chuanliang Liu
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Functional Divergence ◽  
Comprehensive Analysis ◽  
Functional Study ◽  
Gossypium Species ◽  
Genome Wide ◽  
Plant Pathogen Interaction ◽  
Gossypium Raimondii ◽  
Plant Hormone Signaling

Leucine-rich repeat receptor-like kinases (LRR-RLKs) have been reported to play important roles in plant growth, development, and stress responses. However, no comprehensive analysis of this family has been performed in cotton (Gossypium spp.), which is an important economic crop that suffers various stresses in growth and development. Here we conducted a comprehensive analysis of LRR-RLK family in four Gossypium species (Gossypium arboreum, Gossypium barbadense, Gossypium hirsutum, and Gossypium raimondii). A total of 1641 LRR-RLK genes were identified in the four Gossypium species involved in our study. The maximum-likelihood phylogenetic tree revealed that all the LRR-RLK genes were divided into 21 subgroups. Exon-intron organization structure of LRR-RLK genes kept relatively conserved within subfamilies and between Arabidopsis and Gossypium genomes. Notably, subfamilies XI and XII were found dramatically expanded in Gossypium species. Tandem duplication acted as an important mechanism in expansion of the Gossypium LRR-RLK gene family. Functional analysis suggested that Gossypium LRR-RLK genes were enriched for plant hormone signaling and plant-pathogen interaction pathways. Promoter analysis revealed that Gossypium LRR-RLK genes were extensively regulated by transcription factors (TFs), phytohormonal, and various environmental stimuli. Expression profiling showed that Gossypium LRR-RLK genes were widely involved in stress defense and diverse developmental processes including cotton fiber development and provides insight into potential functional divergence within and among subfamilies. Our study provided valuable information for further functional study of Gossypium LRR-RLK genes.

scholarly journals An integrated multi-level comparison highlights common aspects and specific features between distantly-related species: Tomato and Grapevine

2016 ◽  
Author(s):  
Luca Ambrosino ◽  
Hamed Bostan ◽  
Valentino Ruggieri ◽  
Maria Luisa Chiusano
Keyword(s):  
Comparative Genomics ◽  
Developmental Stages ◽  
Gene Annotation ◽  
Sequence Similarity ◽  
Gene Families ◽  
Plant Evolution ◽  
Loss Of Function ◽  
Evolutionary Mechanisms ◽  
Important Species ◽  
Similarity Searches

Motivation. Even after years from the first completion of genomes by sequencing, comparative genomics still remains a challenge, also enhanced by the availability of numerous draft genomes with still poor annotation quality. The detection of ortholog genes between different species is a key approach for comparative genomics. For example, ortholog gene detection may support investigations on mechanisms that shaped the organization of the genomes, highlighting on gain or loss of function and on gene annotation. On the other hand, the detection of paralog genes is fundamental for understanding the evolutionary mechanisms that drove gene function innovation and support gene families analyses. Here we report on the gene comparison between two distantly related plants, Solanum lycopersicum (Tomato) (The Tomato Genome Consortium 2012) and Vitis vinifera (Grapevine) (Jaillon et al. 2007), considered as economically important species from asterids and rosids clades, respectively. The strategy was accompanied by integration of multilevel analyses, from domain investigations to expression profiling, to get to the most reliable results and to offer powerful resources, in order to understand different useful aspects of plant evolution and physiology and to dissect traits and molecular aspects that could provide novel tools for agriculture applications and biotechnologies. Methods. In order to predict best putative orthologs and paralogs between Tomato and Grapevine, and to overcome possible annotation issues, all-against-all sequence similarity searches between genes, mRNAs and proteins collections of both species were performed. A Bidirectional Best Hit approach was implemented to detect the best orthologs between the two species. Moreover we developed a dedicated algorithm in Python programming language able to define more extended alignments between mRNA sequences. NetworkX package (Hagberg et al. 2008) was used to define networks of paralogs and orthologs. Proteins domain prediction was carried out on the entire Tomato and Grapevine protein collection by using InterProScan program (Jones et al. 2014). The enzyme classification was obtained by sequence similarity searches between Tomato and Grapevine mRNA collections and the entire UniProt reviewed protein collection (UniProt consortium 2015). The metabolic pathways associated to the detected enzymes were identified exploiting the KEGG Database (Kanehisa and Goto 2000). Expression level of three developmental stages of Tomato (2 cm fruit, breaker and mature red) and the corresponding stages of Grapevine (post-setting, veraison, mature berry) was defined on the basis of the iTAG loci (Shearer et al. 2014) and v1 vitis loci, respectively. The expression was normalized by Reads Per Kilobases per Million (RPKM) for each tissue/stage. Abstract truncated at 3,000 characters - the full version is available in the pdf file

scholarly journals Comparative Analysis of Developmental Transcriptome Maps of Arabidopsis thaliana and Solanum lycopersicum

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 50 ◽  
Author(s):  
Aleksey A. Penin ◽  
Anna V. Klepikova ◽  
Artem S. Kasianov ◽  
Evgeny S. Gerasimov ◽  
Maria D. Logacheva
Keyword(s):  
Arabidopsis Thaliana ◽  
Comparative Analysis ◽  
Solanum Lycopersicum ◽  
Developmental Stages ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Model Organisms ◽  
Additional Information ◽  
Starting Point ◽  
Gene Functions

The knowledge of gene functions in model organisms is the starting point for the analysis of gene function in non-model species, including economically important ones. Usually, the assignment of gene functions is based on sequence similarity. In plants, due to a highly intricate gene landscape, this approach has some limitations. It is often impossible to directly match gene sets from one plant species to another species based only on their sequences. Thus, it is necessary to use additional information to identify functionally similar genes. Expression patterns have great potential to serve as a source of such information. An important prerequisite for the comparative analysis of transcriptomes is the existence of high-resolution expression maps consisting of comparable samples. Here, we present a transcriptome atlas of tomato (Solanum lycopersicum) consisting of 30 samples of different organs and developmental stages. The samples were selected in a way that allowed for side-by-side comparison with the Arabidopsis thaliana transcriptome map. Newly obtained data are integrated in the TraVA database and are available online, together with tools for their analysis. In this paper, we demonstrate the potential of comparing transcriptome maps for inferring shifts in the expression of paralogous genes.

scholarly journals Genome-Wide Analysis, Characterization, and Expression Profile of the Basic Leucine Zipper Transcription Factor Family in Pineapple

2020 ◽  
Vol 2020 ◽  
pp. 1-14 ◽  
Author(s):  
Yanhui Liu ◽  
Mengnan Chai ◽  
Man Zhang ◽  
Qing He ◽  
Zhenxia Su ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Leucine Zipper ◽  
Developmental Stages ◽  
Functional Characterization ◽  
Sequencing Data ◽  
Basic Leucine Zipper ◽  
Expression Levels ◽  
Duplication Events

This study identified 57 basic leucine zipper (bZIP) genes from the pineapple genome, and the analysis of these bZIP genes was focused on the evolution and divergence after multiple duplication events in relation to the pineapple genome fusion. According to bioinformatics analysis of a phylogenetic tree, the bZIP gene family was divided into 11 subgroups in pineapple, Arabidopsis, and rice; gene structure and conserved motif analyses showed that bZIP genes within the same subgroup shared similar intron-exon organizations and motif composition. Further synteny analysis showed 17 segmental duplication events with 27 bZIP genes. The study also analyzed the pineapple gene expression of bZIP genes in different tissues, organs, and developmental stages, as well as in abiotic stress responses. The RNA-sequencing data showed that AcobZIP57 was upregulated in all tissues, including vegetative and reproductive tissues. AcobZIP28 and AcobZIP43 together with the other 25 bZIP genes did not show high expression levels in any tissue. Six bZIP genes were exposed to abiotic stress, and the relative expression levels were detected by quantitative real-time PCR. A significant response was observed for AcobZIP24 against all kinds of abiotic stresses at 24 and 48 h in pineapple root tissues. Our study provides a perspective for the evolutionary history and general biological involvement of the bZIP gene family of pineapple, which laid the foundation for future functional characterization of the bZIP genes in pineapple.

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