Genome-Wide Comparative Analysis of the Gene Family in Five Solanaceae Species and Identification of Members Regulating Carotenoid Biosynthesis in Wolfberry

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2022 Feb 26

PMID 35216373

Authors

Yue Yin

Cong Guo

Hongyan Shi

Jianhua Zhao

Fang Ma

Wei An

Xinru He

Qing Luo

Youlong Cao

Xiangqiang Zhan

Affiliations

Soon will be listed here.

Abstract

The is a large gene family involved in various plant functions, including carotenoid biosynthesis. However, this gene family lacks a comprehensive analysis in wolfberry ( L.) and other Solanaceae species. The recent sequencing of the wolfberry genome provides an opportunity for investigating the organization and evolutionary characteristics of genes in wolfberry and other Solanaceae species. A total of 610 genes were identified in five Solanaceae species, including 137 in wolfberry. The genes were grouped into 31 subgroups based on phylogenetic analysis, conserved gene structures, and motif composition. Five groups only of Solanaceae genes were functionally divergent during evolution. Dispersed and whole duplication events are critical for expanding the gene family. There were 287 orthologous gene pairs between wolfberry and the other four selected Solanaceae species. RNA-seq analysis identified the expression level of differential gene expression (DEGs) and carotenoid biosynthesis genes (CBGs) in fruit development stages. The highly expressed genes are co-expressed with CBGs during fruit development. A quantitative Real-Time (qRT)-PCR verified seven selected candidate genes. Thus, and are candidate genes regulating carotenoid biosynthesis in wolfberry. This study elucidates the evolution and function of genes in wolfberry and the four Solanaceae species.

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References

Ke Y, Abbas F, Zhou Y, Yu R, Fan Y . Auxin-Responsive R2R3-MYB Transcription Factors HcMYB1 and HcMYB2 Activate Volatile Biosynthesis in Flowers. Front Plant Sci. 2021; 12:710826. PMC: 8369990. DOI: 10.3389/fpls.2021.710826. View

Chen C, Chen H, Zhang Y, Thomas H, Frank M, He Y . TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Mol Plant. 2020; 13(8):1194-1202. DOI: 10.1016/j.molp.2020.06.009. View

Fang Q, Jiang T, Xu L, Liu H, Mao H, Wang X . A salt-stress-regulator from the Poplar R2R3 MYB family integrates the regulation of lateral root emergence and ABA signaling to mediate salt stress tolerance in Arabidopsis. Plant Physiol Biochem. 2017; 114:100-110. DOI: 10.1016/j.plaphy.2017.02.018. View

Yuan H, Zhang J, Nageswaran D, Li L . Carotenoid metabolism and regulation in horticultural crops. Hortic Res. 2015; 2:15036. PMC: 4591682. DOI: 10.1038/hortres.2015.36. View

Kim D, Langmead B, Salzberg S . HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015; 12(4):357-60. PMC: 4655817. DOI: 10.1038/nmeth.3317. View

Cao Y, Li Y, Fan Y, Li Z, Yoshida K, Wang J . Wolfberry genomes and the evolution of Lycium (Solanaceae). Commun Biol. 2021; 4(1):671. PMC: 8175696. DOI: 10.1038/s42003-021-02152-8. View

Meng Y, Wang Z, Wang Y, Wang C, Zhu B, Liu H . The MYB Activator WHITE PETAL1 Associates with MtTT8 and MtWD40-1 to Regulate Carotenoid-Derived Flower Pigmentation in . Plant Cell. 2019; 31(11):2751-2767. PMC: 6881138. DOI: 10.1105/tpc.19.00480. View

Stracke R, WERBER M, Weisshaar B . The R2R3-MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol. 2001; 4(5):447-56. DOI: 10.1016/s1369-5266(00)00199-0. View

Jian W, Cao H, Yuan S, Liu Y, Lu J, Lu W . SlMYB75, an MYB-type transcription factor, promotes anthocyanin accumulation and enhances volatile aroma production in tomato fruits. Hortic Res. 2019; 6:22. PMC: 6355774. DOI: 10.1038/s41438-018-0098-y. View

10.

Letunic I, Khedkar S, Bork P . SMART: recent updates, new developments and status in 2020. Nucleic Acids Res. 2020; 49(D1):D458-D460. PMC: 7778883. DOI: 10.1093/nar/gkaa937. View

11.

Zhao P, Li Q, Li J, Wang L, Ren Z . Genome-wide identification and characterization of R2R3MYB family in Solanum lycopersicum. Mol Genet Genomics. 2014; 289(6):1183-207. DOI: 10.1007/s00438-014-0879-4. View

12.

Wang J, Liu Y, Tang B, Dai X, Xie L, Liu F . Genome-Wide Identification and Capsaicinoid Biosynthesis-Related Expression Analysis of the Gene Family in L. Front Genet. 2021; 11:598183. PMC: 7779616. DOI: 10.3389/fgene.2020.598183. View

13.

Lu S, Wang J, Chitsaz F, Derbyshire M, Geer R, Gonzales N . CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res. 2019; 48(D1):D265-D268. PMC: 6943070. DOI: 10.1093/nar/gkz991. View

14.

Yang L, Liu H, Hao Z, Zong Y, Xia H, Shen Y . Genome-Wide Identification and Expression Analysis of Family Genes Associated with Petal Pigment Synthesis in . Int J Mol Sci. 2021; 22(20). PMC: 8538729. DOI: 10.3390/ijms222011291. View

15.

Martin C, Paz-Ares J . MYB transcription factors in plants. Trends Genet. 1997; 13(2):67-73. DOI: 10.1016/s0168-9525(96)10049-4. View

16.

Zhao Y, Yang Z, Ding Y, Liu L, Han X, Zhan J . Over-expression of an R2R3 MYB Gene, GhMYB73, increases tolerance to salt stress in transgenic Arabidopsis. Plant Sci. 2019; 286:28-36. DOI: 10.1016/j.plantsci.2019.05.021. View

17.

Liu C, Hao J, Qiu M, Pan J, He Y . Genome-wide identification and expression analysis of the MYB transcription factor in Japanese plum (Prunus salicina). Genomics. 2020; 112(6):4875-4886. DOI: 10.1016/j.ygeno.2020.08.018. View

18.

Song X, Yang Q, Liu Y, Li J, Chang X, Xian L . Genome-wide identification of Pistacia R2R3-MYB gene family and function characterization of PcMYB113 during autumn leaf coloration in Pistacia chinensis. Int J Biol Macromol. 2021; 192:16-27. DOI: 10.1016/j.ijbiomac.2021.09.092. View

19.

Ampomah-Dwamena C, Thrimawithana A, Dejnoprat S, Lewis D, Espley R, Allan A . A kiwifruit (Actinidia deliciosa) R2R3-MYB transcription factor modulates chlorophyll and carotenoid accumulation. New Phytol. 2018; 221(1):309-325. PMC: 6585760. DOI: 10.1111/nph.15362. View

20.

Anwar M, Yu W, Yao H, Zhou P, Allan A, Zeng L . , an R2R3-MYB from Narcissus, Regulates Flavonoid Biosynthesis. Int J Mol Sci. 2019; 20(21). PMC: 6862390. DOI: 10.3390/ijms20215456. View