Genome and Transcriptome Analyses Reveal Genes Involved in the Formation of Fine Ridges on Petal Epidermal Cells in Hibiscus Trionum

Overview

Journal DNA Res

Publisher Oxford University Press

Specialties Genetics
Molecular Biology

Date 2023 Sep 11

PMID 37691489

Authors

Shizuka Koshimizu

Sachiko Masuda

Arisa Shibata

Takayoshi Ishii

Ken Shirasu

Atsushi Hoshino

Masanori Arita

Affiliations

Soon will be listed here.

Abstract

Hibiscus trionum, commonly known as the 'Flower of an Hour', is an easily cultivated plant in the Malvaceae family that is widespread in tropical and temperate regions, including drylands. The purple base part of its petal exhibits structural colour due to the fine ridges on the epidermal cell surface, and the molecular mechanism of ridge formation has been actively investigated. We performed genome sequencing of H. trionum using a long-read sequencing technology with transcriptome and pathway analyses to identify candidate genes for fine structure formation. The ortholog of AtSHINE1, which is involved in the biosynthesis of cuticular wax in Arabidopsis thaliana, was significantly overexpressed in the iridescent tissue. In addition, orthologs of AtCUS2 and AtCYP77A, which contribute to cutin synthesis, were also overexpressed. Our results provide important insights into the formation of fine ridges on epidermal cells in plants using H. trionum as a model.

Citing Articles

Genome assembly of Hibiscus sabdariffa L. provides insights into metabolisms of medicinal natural products.

Kim T, Lee J, Seo H, Moh S, Choi S, Kim J G3 (Bethesda). 2024; 14(8).

PMID: 38995814 PMC: 11304979. DOI: 10.1093/g3journal/jkae134.

References

Inglis P, Pappas M, Resende L, Grattapaglia D . Fast and inexpensive protocols for consistent extraction of high quality DNA and RNA from challenging plant and fungal samples for high-throughput SNP genotyping and sequencing applications. PLoS One. 2018; 13(10):e0206085. PMC: 6193717. DOI: 10.1371/journal.pone.0206085. View

Kuznetsov D, Tegenfeldt F, Manni M, Seppey M, Berkeley M, Kriventseva E . OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity. Nucleic Acids Res. 2022; 51(D1):D445-D451. PMC: 9825584. DOI: 10.1093/nar/gkac998. View

Plackett A, Powers S, Fernandez-Garcia N, Urbanova T, Takebayashi Y, Seo M . Analysis of the developmental roles of the Arabidopsis gibberellin 20-oxidases demonstrates that GA20ox1, -2, and -3 are the dominant paralogs. Plant Cell. 2012; 24(3):941-60. PMC: 3336139. DOI: 10.1105/tpc.111.095109. View

Vignolini S, Moyroud E, Hingant T, Banks H, Rudall P, Steiner U . The flower of Hibiscus trionum is both visibly and measurably iridescent. New Phytol. 2014; 205(1):97-101. DOI: 10.1111/nph.12958. View

Sun J, Nishiyama T, Shimizu K, Kadota K . TCC: an R package for comparing tag count data with robust normalization strategies. BMC Bioinformatics. 2013; 14:219. PMC: 3716788. DOI: 10.1186/1471-2105-14-219. View

Da-Costa-Rocha I, Bonnlaender B, Sievers H, Pischel I, Heinrich M . Hibiscus sabdariffa L. - a phytochemical and pharmacological review. Food Chem. 2014; 165:424-43. DOI: 10.1016/j.foodchem.2014.05.002. View

Moyroud E, Wenzel T, Middleton R, Rudall P, Banks H, Reed A . Disorder in convergent floral nanostructures enhances signalling to bees. Nature. 2017; 550(7677):469-474. DOI: 10.1038/nature24285. View

Simao F, Waterhouse R, Ioannidis P, Kriventseva E, Zdobnov E . BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31(19):3210-2. DOI: 10.1093/bioinformatics/btv351. View

Baumann K, Perez-Rodriguez M, Bradley D, Venail J, Bailey P, Jin H . Control of cell and petal morphogenesis by R2R3 MYB transcription factors. Development. 2007; 134(9):1691-701. DOI: 10.1242/dev.02836. View

10.

Gabriel L, Hoff K, Bruna T, Borodovsky M, Stanke M . TSEBRA: transcript selector for BRAKER. BMC Bioinformatics. 2021; 22(1):566. PMC: 8620231. DOI: 10.1186/s12859-021-04482-0. View

11.

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K . BLAST+: architecture and applications. BMC Bioinformatics. 2009; 10:421. PMC: 2803857. DOI: 10.1186/1471-2105-10-421. View

12.

Hong L, Brown J, Segerson N, Rose J, Roeder A . CUTIN SYNTHASE 2 Maintains Progressively Developing Cuticular Ridges in Arabidopsis Sepals. Mol Plant. 2017; 10(4):560-574. DOI: 10.1016/j.molp.2017.01.002. View

13.

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View

14.

Gou J, Yu X, Liu C . A hydroxycinnamoyltransferase responsible for synthesizing suberin aromatics in Arabidopsis. Proc Natl Acad Sci U S A. 2009; 106(44):18855-60. PMC: 2773987. DOI: 10.1073/pnas.0905555106. View

15.

Rieu I, Ruiz-Rivero O, Fernandez-Garcia N, Griffiths J, Powers S, Gong F . The gibberellin biosynthetic genes AtGA20ox1 and AtGA20ox2 act, partially redundantly, to promote growth and development throughout the Arabidopsis life cycle. Plant J. 2007; 53(3):488-504. DOI: 10.1111/j.1365-313X.2007.03356.x. View

16.

Tohge T, Nishiyama Y, Hirai M, Yano M, Nakajima J, Awazuhara M . Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. Plant J. 2005; 42(2):218-35. DOI: 10.1111/j.1365-313X.2005.02371.x. View

17.

Li B, Dewey C . RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011; 12:323. PMC: 3163565. DOI: 10.1186/1471-2105-12-323. View

18.

Morita Y, Hoshino A, Kikuchi Y, Okuhara H, Ono E, Tanaka Y . Japanese morning glory dusky mutants displaying reddish-brown or purplish-gray flowers are deficient in a novel glycosylation enzyme for anthocyanin biosynthesis, UDP-glucose:anthocyanidin 3-O-glucoside-2''-O-glucosyltransferase, due to 4-bp.... Plant J. 2005; 42(3):353-63. DOI: 10.1111/j.1365-313X.2005.02383.x. View

19.

Li P, Li Y, Zhang F, Zhang G, Jiang X, Yu H . The Arabidopsis UDP-glycosyltransferases UGT79B2 and UGT79B3, contribute to cold, salt and drought stress tolerance via modulating anthocyanin accumulation. Plant J. 2016; 89(1):85-103. DOI: 10.1111/tpj.13324. View

20.

Morita Y, Takagi K, Fukuchi-Mizutani M, Ishiguro K, Tanaka Y, Nitasaka E . A chalcone isomerase-like protein enhances flavonoid production and flower pigmentation. Plant J. 2014; 78(2):294-304. DOI: 10.1111/tpj.12469. View