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Phylogenomic analysis of cytochrome P450 multigene family and their differential expression analysis in Solanum lycopersicum L. suggested tissue specific promoters.
BMC Genomics. 2019 Feb 07; 20(1):116.BG

Abstract

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.

Authors+Show Affiliations

Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.Department of Botany, Savitribai Phule Pune University, Pune, 411007, India. bvitthal@unipune.ac.in.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30732561

Citation

Vasav, A P., and V T. Barvkar. "Phylogenomic Analysis of Cytochrome P450 Multigene Family and Their Differential Expression Analysis in Solanum Lycopersicum L. Suggested Tissue Specific Promoters." BMC Genomics, vol. 20, no. 1, 2019, p. 116.
Vasav AP, Barvkar VT. Phylogenomic analysis of cytochrome P450 multigene family and their differential expression analysis in Solanum lycopersicum L. suggested tissue specific promoters. BMC Genomics. 2019;20(1):116.
Vasav, A. P., & Barvkar, V. T. (2019). Phylogenomic analysis of cytochrome P450 multigene family and their differential expression analysis in Solanum lycopersicum L. suggested tissue specific promoters. BMC Genomics, 20(1), 116. https://doi.org/10.1186/s12864-019-5483-x
Vasav AP, Barvkar VT. Phylogenomic Analysis of Cytochrome P450 Multigene Family and Their Differential Expression Analysis in Solanum Lycopersicum L. Suggested Tissue Specific Promoters. BMC Genomics. 2019 Feb 7;20(1):116. PubMed PMID: 30732561.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Phylogenomic analysis of cytochrome P450 multigene family and their differential expression analysis in Solanum lycopersicum L. suggested tissue specific promoters. AU - Vasav,A P, AU - Barvkar,V T, Y1 - 2019/02/07/ PY - 2018/07/17/received PY - 2019/01/28/accepted PY - 2019/2/9/entrez PY - 2019/2/9/pubmed PY - 2019/5/23/medline KW - Cytochrome P450 KW - Genome-wide promoter analysis KW - Intron map KW - Phylogeny KW - Tissue specific promoter SP - 116 EP - 116 JF - BMC genomics JO - BMC Genomics VL - 20 IS - 1 N2 - 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. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/30732561/Phylogenomic_analysis_of_cytochrome_P450_multigene_family_and_their_differential_expression_analysis_in_Solanum_lycopersicum_L__suggested_tissue_specific_promoters_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5483-x DB - PRIME DP - Unbound Medicine ER -