Genome-wide identification, and phylogenetic and expression profiling analyses, of XTH gene families in Brassica rapa L. and Brassica oleracea L.

Abstract Background Xyloglucan endotransglucosylase/hydrolase genes (XTHs) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. Brassica rapa and Brassica oleracea contain XTHs, but detailed identification and characterization of the XTH family in these species, and analysis of their tissue expression profiles, have not previously been carried out. Results In this study, 53 and 38 XTH genes were identified in B. rapa and B. oleracea respectively, which contained some novel members not observed in previous studies. All XTHs of B. rapa, B. oleracea and Arabidopsis thaliana could be classified into three groups, Group I/II, III and the Early diverging group, based on phylogenetic relationships. Gene structures and motif patterns were similar within each group. All XTHs in this study contained two characteristic conserved domains (Glyco_hydro and XET_C). XTHs are located mainly in the cell wall but some are also located in the cytoplasm. Analyses of the mechanisms of gene family expansion revealed that whole-genome triplication (WGT) events and tandem duplication (TD) may have been the major mechanisms accounting for the expansion of the XTH gene family. Interestingly, TD genes all belonged to Group I/II, suggesting that TD was the main reason for the largest number of genes being in these groups. B. oleracea had lost more of the XTH genes, the conserved domain XET_C and the conserved active-site motif EXDXE compared with B. rapa, consistent with asymmetrical evolution between the two Brassica genomes. A majority of XTH genes exhibited different tissue-specific expression patterns based on RNA-seq data analyses. Moreover, there was differential expression of duplicated XTH genes in the two species, indicating that their functional differentiation occurred after B. rapa and B. oleracea diverged from a common ancestor. Conclusions We carried out the first systematic analysis of XTH gene families in B. rapa and B. oleracea. The results of this investigation can be used for reference in further studies on the functions of XTH genes and the evolution of this multigene family.

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Genome-wide identification, and phylogenetic and expression profiling analyses, of XTH gene families in Brassica rapa L. and Brassica oleracea L.

10.21203/rs.3.rs-62331/v2 ◽

2020 ◽

Author(s):

Di Wu ◽

Anqi Liu ◽

Xiaoyu Qu ◽

Jiayi Liang ◽

Min Song

Keyword(s):

Cell Wall ◽

Gene Family ◽

Brassica Oleracea ◽

Brassica Rapa ◽

Multigene Family ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Families ◽

Specific Expression ◽

Group I

Abstract Background: Xyloglucan endotransglucosylase/hydrolase genes ( XTHs ) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. Brassica rapa and Brassica oleracea contain XTHs, but detailed identification and characterization of the XTH family in these species, and analysis of their tissue expression profiles, have not previously been carried out. Results: In this study, 53 and 38 XTH genes were identified in B. rapa and B. oleracea respectively, which contained some novel members not observed in previous studies. All XTHs of B. rapa , B. oleracea and Arabidopsis thaliana could be classified into three groups, Group I/II, III and the Early diverging group, based on phylogenetic relationships. Gene structures and motif patterns were similar within each group. All XTHs in this study contained two characteristic conserved domains (Glyco_hydro and XET_C). XTHs are located mainly in the cell wall but some are also located in the cytoplasm. Analyses of the mechanisms of gene family expansion revealed that whole-genome triplication (WGT) events and tandem duplication (TD) may have been the major mechanisms accounting for the expansion of the XTH gene family. Interestingly, TD genes all belonged to Group I/II, suggesting that TD was the main reason for the largest number of genes being in these groups. B. oleracea had lost more of the XTH genes, the conserved domain XET_C and the conserved active-site motif EXDXE compared with B. rapa , consistent with asymmetrical evolution between the two Brassica genomes. A majority of XTH genes exhibited different tissue-specific expression patterns based on RNA-seq data analyses. Moreover, there was differential expression of duplicated XTH genes in the two species, indicating that their functional differentiation occurred after B. rapa and B. oleracea diverged from a common ancestor. Conclusions: We carried out the first systematic analysis of XTH gene families in B. rapa and B. oleracea . The results of this investigation can be used for reference in further studies on the functions of XTH genes and the evolution of this multigene family.

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Genome-wide identification, and phylogenetic and expression profiling analyses of XTH gene families in Brassica rapa L. and Brassica oleracea L.

10.21203/rs.3.rs-62331/v1 ◽

2020 ◽

Author(s):

Min Song ◽

Di Wu ◽

Anqi Liu ◽

Xiaoyu Qu ◽

Jiayi Liang

Keyword(s):

Cell Wall ◽

Gene Family ◽

Brassica Rapa ◽

Expression Patterns ◽

Gene Families ◽

Functional Differentiation ◽

Specific Expression ◽

Major Mechanism ◽

Group I ◽

Gene Structures

Abstract Background Xyloglucan endotransglucosylase/hydrolase genes (XTHs) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. XTH genes of Brassica have not been reported. Results In this study, 53 and 38 XTH genes were identified in Brassica rapa and Brassica olerecea, respectively. All XTHs of B. rapa, B. oleracea and Arabidopsis thaliana can be classified into three groups including Group I/II, III and Ancestral Group based on phylogenetic relationships. Gene structures and motif patterns were similar in the same group. All XTHs in this study contained two characteristic conserved domains (Glyco_hydro and XET_C). XTHs mainly located in the cell wall and some also located in cytoplasm. Expansion mechanism analyses uncovered that whole-genome triplication (WGT) events and tandem duplication (TD) may be the major mechanism accounting for the expansion of XTH gene family. Interestingly, TD genes were all belong to Group I/II, which suggested TD was the main reason for the largest number of genes in the groups. B. oleracea had a higher loss rate of XTH genes, conserved domain XET_C and conserved motif EXDXE compared with B. rapa, consistent with the asymmetrical evolution between the two Brassica genomes. A majority of XTH genes exhibited different tissue-specific expression patterns based on RNA-seq data analyses. Moreover, the differential expressions of duplicated XTH genes in the two species were found and indicated their functional differentiation occurred after B. rapa and B. olerecea diverged from a common ancestor. Conclusions We first systematic analyzed XTH gene families in B. rapa and B. oleracea. The results of this paper can be used for reference to further study the function of XTH gene and the evolution pattern of multi gene family.

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Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments

Genome ◽

10.1139/gen-2017-0163 ◽

2018 ◽

Vol 61 (2) ◽

pp. 121-130 ◽

Cited By ~ 4

Author(s):

Chenghao Zhang ◽

Wenqi Dong ◽

Zong-an Huang ◽

MyeongCheoul Cho ◽

Qingcang Yu ◽

...

Keyword(s):

Capsicum Annuum ◽

Abiotic Stresses ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Families ◽

Environmental Stresses ◽

Transcriptional Level ◽

Specific Expression ◽

Capsicum Annuum L ◽

Genome Wide

Auxin plays key roles in regulating plant growth and development as well as in response to environmental stresses. The intercellular transport of auxin is mediated by the following four gene families: ATP-binding cassette family B (ABCB), auxin resistant1/like aux1 (AUX/LAX), PIN-formed (PIN), and PIN-like (PILS). Here, the latest assembled pepper (Capsicum annuum L.) genome was used to characterise and analyse the CaLAX and CaPIN gene families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships, and intron/exon structures, were performed. In total, 4 CaLAX and 10 CaPIN genes were mapped to 10 chromosomes. Most of these genes exhibited varied tissue-specific expression patterns assessed by quantitative real-time PCR. The expression profiles of the CaLAX and CaPIN genes under various abiotic stresses (salt, drought, and cold), exogenous phytohormones (IAA, 6-BA, ABA, SA, and MeJA), and polar auxin transport inhibitor treatments were evaluated. Most CaLAX and CaPIN genes were altered by abiotic stress at the transcriptional level in both shoots and roots, and many CaLAX and CaPIN genes were regulated by exogenous phytohormones. Our study helps to identify candidate auxin transporter genes and to further analyse their biological functions in pepper development and in its adaptation to environmental stresses.

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Genome-Wide Analysis of Basic Helix–Loop–Helix Superfamily Members Reveals Organization and Chilling-Responsive Patterns in Cabbage (Brassica oleracea var. capitata L.)

Genes ◽

10.3390/genes10110914 ◽

2019 ◽

Vol 10 (11) ◽

pp. 914

Author(s):

Shan ◽

Zhang ◽

Yu ◽

Wang ◽

Li ◽

...

Keyword(s):

Brassica Oleracea ◽

Expression Profiles ◽

Phylogenetic Analyses ◽

Chilling Stress ◽

Expression Patterns ◽

Comprehensive Analysis ◽

Bhlh Transcription Factor ◽

Specific Expression ◽

Basic Helix Loop Helix ◽

Helix Loop Helix

Basic helix–loop–helix (bHLH) transcription factor (TF) family is commonly found in eukaryotes, which is one of the largest families of regulator proteins. It plays an important role in plant growth and development, as well as various biotic and abiotic stresses. However, a comprehensive analysis of the bHLH family has not been reported in Brassica oleracea. In this study, we systematically describe the BobHLHs in the phylogenetic relationships, expression patterns in different organs/tissues, and in response to chilling stress, and gene and protein characteristics. A total of 234 BobHLH genes were identified in the B. oleracea genome and were further clustered into twenty-three subfamilies based on the phylogenetic analyses. A large number of BobHLH genes were unevenly located on nine chromosomes of B. oleracea. Analysis of RNA-Seq expression profiles revealed that 21 BobHLH genes exhibited organ/tissue-specific expression. Additionally, the expression of six BobHLHs (BobHLH003, -048, -059, -093, -109, and -148) were significantly down-regulated in chilling-sensitive cabbage (CS-D9) and chilling-tolerant cabbage (CT-923). At 24h chilling stress, BobHLH054 was significantly down-regulated and up-regulated in chilling-treated CS-D9 and CT-923. Conserved motif characterization and exon/intron structural patterns showed that BobHLH genes had similar structures in the same subfamily. This study provides a comprehensive analysis of BobHLH genes and reveals several candidate genes involved in chilling tolerance of B. oleracea, which may be helpful to clarify the roles of bHLH family members and understand the regulatory mechanisms of BobHLH genes in response to the chilling stress of cabbage.

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Genome-Wide Characterization of the sHsp Gene Family in Salix suchowensis Reveals Its Functions under Different Abiotic Stresses

International Journal of Molecular Sciences ◽

10.3390/ijms19103246 ◽

2018 ◽

Vol 19 (10) ◽

pp. 3246 ◽

Cited By ~ 9

Author(s):

Jianbo Li ◽

Jin Zhang ◽

Huixia Jia ◽

Zhiqiang Yue ◽

Mengzhu Lu ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Expression Profiles ◽

Expression Patterns ◽

Purifying Selection ◽

Molecular Characteristics ◽

Specific Expression ◽

Cis Acting ◽

Shsp Gene ◽

Duplication Events

Small heat shock proteins (sHsps) function mainly as molecular chaperones that play vital roles in response to diverse stresses, especially high temperature. However, little is known about the molecular characteristics and evolutionary history of the sHsp family in Salix suchowensis, an important bioenergy woody plant. In this study, 35 non-redundant sHsp genes were identified in S. suchowensis, and they were divided into four subfamilies (C, CP, PX, and MT) based on their phylogenetic relationships and predicted subcellular localization. Though the gene structure and conserved motif were relatively conserved, the sequences of the Hsp20 domain were diversified. Eight paralogous pairs were identified in the Ssu-sHsp family, in which five pairs were generated by tandem duplication events. Ka/Ks analysis indicated that Ssu-sHsps had undergone purifying selection. The expression profiles analysis showed Ssu-Hsps tissue-specific expression patterns, and they were induced by at least one abiotic stress. The expression correlation between two paralogous pairs (Ssu-sHsp22.2-CV/23.0-CV and 23.8-MT/25.6-MT) were less than 0.6, indicating that they were divergent during the evolution. Various cis-acting elements related to stress responses, hormone or development, were detected in the promoter of Ssu-sHsps. Furthermore, the co-expression network revealed the potential mechanism of Ssu-sHsps under stress tolerance and development. These results provide a foundation for further functional research on the Ssu-sHsp gene family in S. suchowensis.

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Genome Identification of B-BOX Gene Family Members in Seven Rosacea Species and Their Expression Analysis in Response to Flower Induction in Malus domestica

Molecules ◽

10.3390/molecules23071763 ◽

2018 ◽

Vol 23 (7) ◽

pp. 1763 ◽

Cited By ~ 2

Author(s):

Abdullah Shalmani ◽

Sheng Fan ◽

Peng Jia ◽

Guofang Li ◽

Izhar Muhammad ◽

...

Keyword(s):

Gene Family ◽

Malus Domestica ◽

Growth And Development ◽

Expression Profiles ◽

Expression Patterns ◽

Chemical Properties ◽

Structural Features ◽

Flower Induction ◽

Specific Expression ◽

Flowering Induction

BBX proteins play important roles in regulating plant growth and development including photomorphogenesis, photoperiodic regulation of flowering, and responses to biotic and abiotic stresses. At present, the genomes of seven Rosacea fruit species have been fully sequenced. However, little is known about the BBX gene family and their evolutionary history in these Rosacea species. Therefore, in this study total, 212 BBX genes were investigated from seven Rosacea species (67 from Malus × domestica, 40 from Pyruscommunis, 22 from Rosa Chinesis, 20 from Prunuspersica, 21 from Fragariavesca, 22 from Prunusavium, and 20 from Rubusoccidentalis). The chemical properties, gene structures, and evolutionary relationships of the BBX genes were also studied. All the BBX genes were grouped into six subfamilies on the basis of their phylogenetic relationships and structural features. Analysis of gene structure, segmental and tandem duplication, gene phylogeny, and tissue-specific expression with the ArrayExpress database showed their diversification in function, quantity, and structure. The expression profiles of 19 MdBBX genes in different tissues were evaluated through qRT-PCR. These genes showed distinct transcription level among the tested tissues (bud, flower, fruit, stem, and leaf). Moreover, expression patterns of 19 MdBBX genes were examined during flowering induction time under flowering-related hormones and treatments (GA3, 6-BA, and sucrose). The expressions of the candidates BBX genes were affected and showed diverse expression profile. Furthermore, changes in response to these flowering-related hormones and treatment specifying their potential involvement in flowering induction. Based on these findings, BBX genes could be used as potential genetic markers for the growth and development of plants particularly in the area of functional analysis, and their involvement in flower induction in fruit plants.

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Analysis of the ASMT Gene Family in Pepper (Capsicum annuum L.): Identification, Phylogeny, and Expression Profiles

International Journal of Genomics ◽

10.1155/2019/7241096 ◽

2019 ◽

Vol 2019 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Luzhao Pan ◽

Jiaqiu Zheng ◽

Jia Liu ◽

Jun Guo ◽

Fawan Liu ◽

...

Keyword(s):

Gene Family ◽

Capsicum Annuum ◽

Abiotic Stresses ◽

Expression Profiles ◽

Expression Patterns ◽

Evolutionary Relationship ◽

Pepper Plant ◽

Rna Seq ◽

Qrt Pcr ◽

Group I

Acetylserotonin methyltransferase (ASMT) in plant species, one of the most important enzymes in melatonin biosynthesis, plays a rate-limiting role in the melatonin production. In this study, based on the whole genome sequence, we performed a systematic analysis for the ASMT gene family in pepper (Capsicum annuum L.) and analyzed their expression profiles during growth and development, as well as abiotic stresses. The results showed that at least 16 CaASMT genes were identified in the pepper genome. Phylogenetic analyses of all the CaASMTs were divided into three groups (group I, group II, and group III) with a high bootstrap value. Through the online MEME tool, six distinct motifs (motif 1 to motif 6) were identified. Chromosome location found that most CaASMT genes were mapped in the distal ends of the pepper chromosomes. In addition, RNA-seq analysis revealed that, during the vegetative and reproductive development, the difference in abundance and distinct expression patterns of these CaASMT genes suggests different functions. The qRT-PCR analysis showed that high abundance of CaASMT03, CaASMT04, and CaASMT06 occurred in mature green fruit and mature red fruit. Finally, using RNA-seq and qRT-PCR technology, we also found that several CaASMT genes were induced under abiotic stress conditions. The results will not only contribute to elucidate the evolutionary relationship of ASMT genes but also ascertain the biological function in pepper plant response to abiotic stresses.

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Identification and expression profile analysis of the sucrose phosphate synthase gene family in Litchi chinensis Sonn.

PeerJ ◽

10.7717/peerj.4379 ◽

2018 ◽

Vol 6 ◽

pp. e4379 ◽

Cited By ~ 5

Author(s):

Dan Wang ◽

Jietang Zhao ◽

Bing Hu ◽

Jiaqi Li ◽

Yaqi Qin ◽

...

Keyword(s):

Gene Family ◽

Profile Analysis ◽

Functional Divergence ◽

Expression Patterns ◽

Sucrose Phosphate Synthase ◽

Gene Families ◽

Specific Expression ◽

Litchi Chinensis ◽

Sucrose Phosphate ◽

Phosphate Synthase

Sucrose phosphate synthase (SPS, EC 2.4.1.14) is a key enzyme that regulates sucrose biosynthesis in plants. SPS is encoded by different gene families which display differential expression patterns and functional divergence. Genome-wide identification and expression analyses of SPS gene families have been performed in Arabidopsis, rice, and sugarcane, but a comprehensive analysis of the SPS gene family in Litchi chinensis Sonn. has not yet been reported. In the current study, four SPS gene (LcSPS1, LcSPS2, LcSPS3, and LcSPS4) were isolated from litchi. The genomic organization analysis indicated the four litchi SPS genes have very similar exon-intron structures. Phylogenetic tree showed LcSPS1-4 were grouped into different SPS families (LcSPS1 and LcSPS2 in A family, LcSPS3 in B family, and LcSPS4 in C family). LcSPS1 and LcSPS4 were strongly expressed in the flowers, while LcSPS3 most expressed in mature leaves. RT-qPCR results showed that LcSPS genes expressed differentially during aril development between cultivars with different hexose/sucrose ratios. A higher level of expression of LcSPS genes was detected in Wuheli, which accumulates higher sucrose in the aril at mature. The tissue- and developmental stage-specific expression of LcSPS1-4 genes uncovered in this study increase our understanding of the important roles played by these genes in litchi fruits.

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Structure and Evolution of the Actin Gene Family in Arabidopsis thaliana

Genetics ◽

10.1093/genetics/142.2.587 ◽

1996 ◽

Vol 142 (2) ◽

pp. 587-602 ◽

Cited By ~ 8

Author(s):

John M McDowell ◽

Shurong Huang ◽

Elizabeth C McKinney ◽

Yong-Qiang An ◽

Richard B Meagher

Keyword(s):

Arabidopsis Thaliana ◽

Gene Family ◽

Higher Plants ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Gene Families ◽

Plant Evolution ◽

Actin Gene ◽

Specific Expression ◽

Phylogenetic Structure

Abstract Higher plants contain families of actin-encoding genes that are divergent and differentially expressed. Progress in understanding the functions and evolution of plant actins has been hindered by the large size of the actin gene families. In this study, we characterized the structure and evolution of the actin gene family in Arabidopsis thaliana. DNA blot analyses with gene-specific probes suggested that all 10 of the Arabidopsis actin gene family members have been isolated and established that Arabidopsis has a much simpler actin gene family than other plants that have been examined. Phylogenetic analyses suggested that the Arabidopsis gene family contains at least two ancient classes of genes that diverged early in land plant evolution and may have separated vegetative from reproductive actins. Subsequent divergence produced a total of six distinct subclasses of actin, and five showed a distinct pattern of tissue specific expression. The concordance of expression patterns with the phylogenetic structure is discussed. These subclasses appear to be evolving independently, as no evidence of gene conversion was found. The Arabidopsis actin proteins have an unusually large number of nonconservative amino acid substitutions, which mapped to the surface of the actin molecule, and should effect protein-protein interactions.

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