Dataset Information

Genomic Analysis of the ASMT Gene Family in Solanum lycopersicum.

ABSTRACT: Acetylserotonin methyltransferase (ASMT) is the last enzyme of melatonin biosynthesis and may play a rate-limiting role in the melatonin production of plants. In this study, systematic analysis of the ASMT gene family in tomato (Solanum lycopersicum Mill) has been presented by the integration of the structural features, phylogenetic relationships, exon/intron configuration, and expression profile during growth and development, as well as biotic stresses. The results revealed that the tomato genome encoded a minimum of 14 members, containing three probable encoded pseudogenes. Chromosome mapping indicated that the family had probably expanded via tandem duplication events. Genome-wide RNA-seq and qRT-PCR based gene expression analysis revealed that almost half of the SlASMT genes were expressed in at least one of the experimental stages studied and also showed differential accumulation. Furthermore, the tandem duplicated SlASMT genes showed differential expression levels, which indicated probable functional divergence during the course of the evolution. Finally, this study also determined that some SlASMT genes were induced by multiple pathogens. The results suggested that these genes could be involved in tomato plant response to biotic stresses.

SUBMITTER: Liu W

PROVIDER: S-EPMC6150316 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature

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Genomic Analysis of the ASMT Gene Family in Solanum lycopersicum.

Liu Weicheng W Zhao Dake D Zheng Chunfang C Chen Chen C Peng Xin X Cheng Yuan Y Wan Hongjian H

Molecules (Basel, Switzerland) 20171116 11

Acetylserotonin methyltransferase (ASMT) is the last enzyme of melatonin biosynthesis and may play a rate-limiting role in the melatonin production of plants. In this study, systematic analysis of the ASMT gene family in tomato (<i>Solanum lycopersicum</i> Mill) has been presented by the integration of the structural features, phylogenetic relationships, exon/intron configuration, and expression profile during growth and development, as well as biotic stresses. The results revealed that the toma ...[more]

PMID: 29144405

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Project description:BACKGROUND:Cytochrome P450 (P450) is a functionally diverse and multifamily class of enzymes which catalyses vast variety of biochemical reactions. P450 genes play regulatory role in growth, development and secondary metabolite biosynthesis. Solanum lycopersicum L. (Tomato) is an economically important crop plant and model system for various studies with massive genomic data. The comprehensive identification and characterization of P450 genes was lacking. Probing tomato genome for P450 identification would provide valuable information about the functions and evolution of the P450 gene family. RESULTS:In the present study, we have identified 233 P450 genes from tomato genome along with conserved motifs. Through the phylogenetic analysis of Solanum lycopersicum P450 (SlP450) protein sequences, they were classified into two major clades and nine clans further divided into 42 families. RT-qPCR analysis of selected six candidate genes were corroborated with digital expression profile. Out of 233 SlP450 genes, 73 showed expression evidence in 19 tissues of tomato. Out of 22 intron gain/loss positions, two positions were conserved in tomato P450 genes supporting intron late theory of intron evolution in SlP450 families. The comparison between tomato and other related plant P450s families showed that CYP728, CYP733, CYP80, CYP92, CYP736 and CYP749 families have been evolved in tomato and few higher plants whereas lost from Arabidopsis. The global promoter analysis of SlP450 against all the protein coding genes, coupled with expression data, revealed statistical overrepresentation of few promoter motifs in SlP450 genes which were highly expressed in specific tissue of tomato. Hence, these identified promoter motifs can be pursued further as tissue specific promoter that are driving expression of respective SlP450. CONCLUSIONS:The phylogenetic analysis and expression profiles of tomato P450 gene family offers essential genomic resource for their functional characterization. This study allows comparison of SlP450 gene family with other Solanaceae members which are also economically important and attempt to classify functionally important SlP450 genes into groups and families. This report would enable researchers working on Tomato P450 to select appropriate candidate genes from huge repertoire of P450 genes depending on their phylogenetic class, tissue specific expression and promoter prevalence.

Dataset Information

Genomic Analysis of the ASMT Gene Family in Solanum lycopersicum.

Publications

Genomic Analysis of the ASMT Gene Family in Solanum lycopersicum.

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