Genome wide analysis of kinesin gene family in Citrullus lanatus reveals an essential role in early fruit development

Abstract Background Kinesin (KIN) as a motor protein is a versatile nano-machine and involved in diverse essential processes in plant growth and development. However, the kinesin gene family has not been identified in watermelon, a valued and nutritious fruit, and yet their functions have not been characterized. Especially, their involvement in early fruit development, which directly determines the size, shape, yield and quality of the watermelon fruit, remains unclear. Results In this study, we performed a whole-genome investigation and comprehensive analysis of kinesin genes in C. lanatus. In total, 48 kinesins were identified and categorized into 10 kinesin subfamilies groups based on phylogenetic analysis. Their uneven distribution on 11 chromosomes was revealed by distribution analysis. Conserved motif analysis showed that the ATP-binding motif of kinesins was conserved within all subfamilies, but not the microtubule-binding motif. 10 segmental duplication pairs genes were detected by the syntenic and phylogenetic approaches, which showed the expansion of the kinesin gene family in C. lanatus genome during evolution. Moreover, 5 ClKINs genes are specifically and abundantly expressed in early fruit developmental stages according to comprehensive expression profile analysis, implying their critical regulatory roles during early fruit development. Our data also demonstrated that the majority of kinesin genes were responsive to plant hormones, revealing their potential involvement in the signaling pathways of plant hormones. Conclusions Kinesin gene family in watermelon was comprehensively analyzed in this study, which establishes a foundation for further functional investigation of C. lanatus kinesin genes and provides novel insights into their biological functions. In addition, these results also provide useful information for understanding the relationship between plant hormone and kinesin genes in C. lanatus.

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Genome wide analysis of kinesin gene family in Citrullus lanatus reveals an essential role in early fruit development

10.21203/rs.3.rs-76073/v1 ◽

2020 ◽

Author(s):

Shujuan Tian ◽

Jiao Jiang ◽

Guo-qi Xu ◽

Tan Wang ◽

Qiyan Liu ◽

...

Keyword(s):

Gene Family ◽

Fruit Development ◽

Developmental Stages ◽

Citrullus Lanatus ◽

Current Data ◽

Comprehensive Analysis ◽

Binding Motif ◽

Distribution Analysis ◽

Motif Analysis ◽

Chromosomal Distribution

Abstract BackgroundKinesin (KIN) as a motor protein is a versatile nano-machine and involved in diverse essential processes in plant growth and development. However, the kinesin gene family has not been identified in watermelon, a valued and nutritious fruit, and yet their functions has not been characterized. Especially, their involvement in early fruit development, which directly determines the size, shape, yield and quality of the watermelon fruit, remains unclear.ResultsIn this study, we performed a whole-genome search and comprehensive analysis in C. lanatus. In total, 48 kinesins were identified and categorized into 10 kinesin subfamilies groups based on phylogenetic analysis. Their uneven distribution on 11 chromosomes was revealed by chromosomal distribution analysis. Conserved motif analysis showed that the ATP-binding motif of kinesins was conserved within all subfamilies, but not the microtubule-binding motif. 10 segmental duplication pairs genes were detected by the syntenic and phylogenetic approaches, which explains the expansion of the kinesin gene family in C. lanatus genome. Moreover, 5 ClKINs genes are specifically and abundantly expressed in early fruit developmental stages according to comprehensive expression profile analysis, indicating their critical regulatory roles during early fruit development. Our current data also demonstrated that the majority of kinesin genes were responsive to plant hormones, implying their involvement in the signaling pathways of plant hormones.ConclusionsThis study is the first comprehensive analysis of the kinesin gene family in watermelon, which establishes a foundation for further functional investigation of C. lanatus kinesin genes and provides novel insights into their biological functions. In addition, these results will provide a useful resource for further selecting an artificial regulator of fruit development in C. lanatus.

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Peer Review #1 of "Genome-wide identification and expression profile analysis of CCH gene family in Populus (v0.1)"

10.7287/peerj.3962v0.1/reviews/1 ◽

2017 ◽

Keyword(s):

Gene Family ◽

Peer Review ◽

Expression Profile ◽

Profile Analysis ◽

Expression Profile Analysis ◽

Genome Wide

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Genome-wide identification, annotation and expression profile analysis of SnRK2 gene family in grapevine

Australian Journal of Grape and Wine Research ◽

10.1111/ajgw.12223 ◽

2016 ◽

Vol 22 (3) ◽

pp. 478-488 ◽

Cited By ~ 12

Author(s):

J.-Y. Liu ◽

N.-N. Chen ◽

Z.-M. Cheng ◽

J.-S. Xiong

Keyword(s):

Gene Family ◽

Expression Profile ◽

Profile Analysis ◽

Expression Profile Analysis ◽

Genome Wide

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Identification and Expression Analysis of Snf2 Family Proteins in Tomato (Solanum lycopersicum)

International Journal of Genomics ◽

10.1155/2019/5080935 ◽

2019 ◽

Vol 2019 ◽

pp. 1-15 ◽

Cited By ~ 1

Author(s):

Dongdong Zhang ◽

Sujuan Gao ◽

Ping Yang ◽

Jie Yang ◽

Songguang Yang ◽

...

Keyword(s):

Amino Acid ◽

Solanum Lycopersicum ◽

Developmental Stages ◽

Profile Analysis ◽

Nucleosome Position ◽

Fruit Fly ◽

Amino Acid Residues ◽

Expression Profile Analysis ◽

Wide Range ◽

Chromatin Remodeling Complexes

As part of chromatin-remodeling complexes (CRCs), sucrose nonfermenting 2 (Snf2) family proteins alter chromatin structure and nucleosome position by utilizing the energy of ATP, which allows other regulatory proteins to access DNA. Plant genomes encode a large number of Snf2 proteins, and some of them have been shown to be the key regulators at different developmental stages in Arabidopsis. Yet, little is known about the functions of Snf2 proteins in tomato (Solanum lycopersicum). In this study, 45 Snf2s were identified by the homologous search using representative sequences from yeast (S. cerevisiae), fruit fly (D. melanogaster), and Arabidopsis (A. thaliana) against the tomato genome annotation dataset. Tomato Snf2 proteins (also named SlCHRs) could be clustered into 6 groups and distributed on 11 chromosomes. All SlCHRs contained a helicase-C domain with about 80 amino acid residues and a SNF2-N domain with more variable amino acid residues. In addition, other conserved motifs were also identified in SlCHRs by using the MEME program. Expression profile analysis indicated that tomato Snf2 family genes displayed a wide range of expressions in different tissues and some of them were regulated by the environmental stimuli such as salicylic acid, abscisic acid, salt, and cold. Taken together, these results provide insights into the functions of SlCHRs in tomato.

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Comprehensive sequence and expression profile analysis of Hsp20 gene family in rice

Plant Molecular Biology ◽

10.1007/s11103-009-9477-y ◽

2009 ◽

Vol 70 (3) ◽

pp. 341-357 ◽

Cited By ~ 60

Author(s):

Yidan Ouyang ◽

Jiongjiong Chen ◽

Weibo Xie ◽

Lei Wang ◽

Qifa Zhang

Keyword(s):

Gene Family ◽

Expression Profile ◽

Profile Analysis ◽

Expression Profile Analysis ◽

Hsp20 Gene Family

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Genome-wide identification and evolution of HECT genes in wheat

PeerJ ◽

10.7717/peerj.10457 ◽

2020 ◽

Vol 8 ◽

pp. e10457

Author(s):

Xianwen Meng ◽

Ting Yang ◽

Jing Liu ◽

Mingde Zhao ◽

Jiuli Wang

Keyword(s):

Gene Family ◽

Stress Responses ◽

Segmental Duplication ◽

Profile Analysis ◽

Purifying Selection ◽

Expression Profile Analysis ◽

Genome Wide ◽

A Genome ◽

Ubiquitin Proteasome ◽

Proteasome Pathway

Background As an important class of E3 ubiquitin ligases in the ubiquitin proteasome pathway, proteins containing homologous E6-AP carboxyl terminus (HECT) domains are crucial for growth, development, metabolism, and abiotic and biotic stress responses in plants. However, little is known about HECT genes in wheat (Triticum aestivum L.), one of the most important global crops. Methods Using a genome-wide analysis of high-quality wheat genome sequences, we identified 25 HECT genes classified into six groups based on the phylogenetic relationship among wheat, rice, and Arabidopsis thaliana. Results The predicted HECT genes were distributed evenly in 17 of 21 chromosomes of the three wheat subgenomes. Twenty-one of these genes were hypothesized to be segmental duplication genes, indicating that segmental duplication was significantly associated with the expansion of the wheat HECT gene family. The Ka/Ks ratios of the segmental duplication of these genes were less than 1, suggesting purifying selection within the gene family. The expression profile analysis revealed that the 25 wheat HECT genes were differentially expressed in 15 tissues, and genes in Group II, IV, and VI (UPL8, UPL6, UPL3) were highly expressed in roots, stems, and spikes. This study contributes to further the functional analysis of the HECT gene family in wheat.

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Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat (Triticum aestivum)

10.7287/peerj.preprints.27402v1 ◽

2018 ◽

Author(s):

Wenqiang J. Jiang ◽

Lei Y. Yang ◽

Yiqin H. He ◽

Haotian Z. Zhang ◽

Wei L. Li ◽

...

Keyword(s):

Gene Family ◽

Phylogenetic Analyses ◽

Composition Analysis ◽

Distribution Analysis ◽

Motif Analysis ◽

Chromosomal Distribution ◽

Critical Function ◽

Genome Wide ◽

A Genome ◽

Sod Gene Family

Superoxide dismutases (SODs) are a key antioxidant enzyme family, which plays a critical function in plant growth and development. Previously, this gene family has been investigated in Arabidopsis and rice. In the present study, it was the first time for us to perform a genome-wide analysis of SOD gene family in wheat. And using bioinformatics-based methods, 26 SOD genes were identified from the whole genome of wheat, including 17 Cu/Zn-SODs, 6 Fe-SODs, and 3 Mn-SODs. The chromosomal distribution analysis revealed that SOD genes are only distributed on 2, 4 and 7 chromosomes of wheat. Phylogenetic analyses with SODs from wheat and several other species revealed that these SOD proteins can divided into two major categories. SOD1 is mainly composed of Cu/Zn-SODs, and SOD2 is mainly composed of Fe-SODs and Mn-SODs. Gene structure and motif analysis indicated that most of the SOD genes have relatively conserved exon/intron arrangement and motif composition. Analysis of transcriptional data indicated that most of the wheat SOD genes are expressed in almost all the tested tissues and it possibly have important function in abiotic stress. Taken together, our results provide a basis for further functional research on SOD gene family in wheat and facilitate their potential applications in the genetic improvement of wheat.

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