Genome-wide Identification, Classification, and Expression Analysis of the Gene Family in Pineapple ()

Overview

Journal PeerJ

Specialties Biology
Environmental Health
General Medicine

Date 2021 May 14

PMID 33987013

Citations 6

Authors

Lulu Wang

Yanhui Liu

Mengnan Chai

Huihuang Chen

Mohammad Aslam

Xiaoping Niu

Yuan Qin

Hanyang Cai

Affiliations

Soon will be listed here.

Abstract

Transcription factors (TFs), such as heat shock transcription factors (HSFs), usually play critical regulatory functions in plant development, growth, and response to environmental cues. However, no HSFs have been characterized in pineapple thus far. Here, we identified 22 genes from the pineapple genome. Gene structure, motifs, and phylogenetic analysis showed that families were distinctly grouped into three subfamilies (12 in Group A, seven in Group B, and four in Group C). The promoters contained various -elements associated with stress, hormones, and plant development processes, for instance, STRE, WRKY, and ABRE binding sites. The majority of were expressed in diverse pineapple tissues and developmental stages. The expression of / and were enriched in the ovules and fruits, respectively. Six genes ( , , , , and ) were transcriptionally modified by cold, heat, and ABA. Our results provide an overview and lay the foundation for future functional characterization of the pineapple gene family.

Citing Articles

Genome-Wide Identification and Expression Analysis of the Gene Family in .

Zhao S, Qing J, Yang Z, Tian T, Yan Y, Li H Curr Issues Mol Biol. 2024; 46(10):11375-11393.

PMID: 39451558 PMC: 11505871. DOI: 10.3390/cimb46100678.

Comparative transcriptome analysis reveals candidate genes for cold stress response and early flowering in pineapple.

Yow A, Laosuntisuk K, Young R, Doherty C, Gillitt N, Perkins-Veazie P Sci Rep. 2023; 13(1):18890.

PMID: 37919298 PMC: 10622448. DOI: 10.1038/s41598-023-45722-y.

Identification, classification, and expression profile analysis of heat shock transcription factor gene family in .

Liu R, Zou P, Yan Z, Chen X PeerJ. 2022; 10:e14464.

PMID: 36523473 PMC: 9745953. DOI: 10.7717/peerj.14464.

Functional Characterization of Heat Shock Factor () Families Provide Comprehensive Insight into the Adaptive Mechanisms of (Sw.) DC. to Tropical Coral Islands.

Zhang M, Wang Z, Jian S Int J Mol Sci. 2022; 23(20).

PMID: 36293211 PMC: 9604225. DOI: 10.3390/ijms232012357.

Evolution and co-evolution: insights into the divergence of plant heat shock factor genes.

Parakkunnel R, Bhojaraja Naik K, Susmita C, Girimalla V, Bhaskar K, Sripathy K Physiol Mol Biol Plants. 2022; 28(5):1029-1047.

PMID: 35722513 PMC: 9203654. DOI: 10.1007/s12298-022-01183-7.

References

Guo M, Yin Y, Ji J, Ma B, Lu M, Gong Z . Cloning and expression analysis of heat-shock transcription factor gene CaHsfA2 from pepper (Capsicum annuum L.). Genet Mol Res. 2014; 13(1):1865-75. DOI: 10.4238/2014.March.17.14. View

Hu Y, Han Y, Wei W, Li Y, Zhang K, Gao Y . Identification, isolation, and expression analysis of heat shock transcription factors in the diploid woodland strawberry Fragaria vesca. Front Plant Sci. 2015; 6:736. PMC: 4569975. DOI: 10.3389/fpls.2015.00736. View

Xue G, Sadat S, Drenth J, McIntyre C . The heat shock factor family from Triticum aestivum in response to heat and other major abiotic stresses and their role in regulation of heat shock protein genes. J Exp Bot. 2013; 65(2):539-57. PMC: 3904712. DOI: 10.1093/jxb/ert399. View

Li W, Cui X, Meng Z, Huang X, Xie Q, Wu H . Transcriptional regulation of Arabidopsis MIR168a and argonaute1 homeostasis in abscisic acid and abiotic stress responses. Plant Physiol. 2012; 158(3):1279-92. PMC: 3291255. DOI: 10.1104/pp.111.188789. View

Giesguth M, Sahm A, Simon S, Dietz K . Redox-dependent translocation of the heat shock transcription factor AtHSFA8 from the cytosol to the nucleus in Arabidopsis thaliana. FEBS Lett. 2015; 589(6):718-25. DOI: 10.1016/j.febslet.2015.01.039. View

Nishizawa-Yokoi A, Nosaka R, Hayashi H, Tainaka H, Maruta T, Tamoi M . HsfA1d and HsfA1e involved in the transcriptional regulation of HsfA2 function as key regulators for the Hsf signaling network in response to environmental stress. Plant Cell Physiol. 2011; 52(5):933-45. DOI: 10.1093/pcp/pcr045. View

Singh A, Mittal D, Lavania D, Agarwal M, Mishra R, Grover A . OsHsfA2c and OsHsfB4b are involved in the transcriptional regulation of cytoplasmic OsClpB (Hsp100) gene in rice (Oryza sativa L.). Cell Stress Chaperones. 2011; 17(2):243-54. PMC: 3273560. DOI: 10.1007/s12192-011-0303-5. View

Liu Z, Wu Z, Li X, Huang Y, Li H, Wang Y . Identification, classification, and expression profiles of heat shock transcription factors in tea plant (Camellia sinensis) under temperature stress. Gene. 2015; 576(1 Pt 1):52-9. DOI: 10.1016/j.gene.2015.09.076. View

Cheng Q, Zhou Y, Liu Z, Zhang L, Song G, Guo Z . An alternatively spliced heat shock transcription factor, OsHSFA2dI, functions in the heat stress-induced unfolded protein response in rice. Plant Biol (Stuttg). 2014; 17(2):419-29. DOI: 10.1111/plb.12267. View

10.

Ming R, VanBuren R, Wai C, Tang H, Schatz M, Bowers J . The pineapple genome and the evolution of CAM photosynthesis. Nat Genet. 2015; 47(12):1435-42. PMC: 4867222. DOI: 10.1038/ng.3435. View

11.

Letunic I, Doerks T, Bork P . SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res. 2011; 40(Database issue):D302-5. PMC: 3245027. DOI: 10.1093/nar/gkr931. View

12.

Le Hir H, Nott A, Moore M . How introns influence and enhance eukaryotic gene expression. Trends Biochem Sci. 2003; 28(4):215-20. DOI: 10.1016/S0968-0004(03)00052-5. View

13.

Shaul O . How introns enhance gene expression. Int J Biochem Cell Biol. 2017; 91(Pt B):145-155. DOI: 10.1016/j.biocel.2017.06.016. View

14.

Zhu J . Abiotic Stress Signaling and Responses in Plants. Cell. 2016; 167(2):313-324. PMC: 5104190. DOI: 10.1016/j.cell.2016.08.029. View

15.

Wang L, Li Y, Jin X, Liu L, Dai X, Liu Y . Floral transcriptomes reveal gene networks in pineapple floral growth and fruit development. Commun Biol. 2020; 3(1):500. PMC: 7483743. DOI: 10.1038/s42003-020-01235-2. View

16.

Pereira A . Plant Abiotic Stress Challenges from the Changing Environment. Front Plant Sci. 2016; 7:1123. PMC: 4962010. DOI: 10.3389/fpls.2016.01123. View

17.

Chidambaranathan P, Jagannadham P, Satheesh V, Kohli D, Basavarajappa S, Chellapilla B . Genome-wide analysis identifies chickpea (Cicer arietinum) heat stress transcription factors (Hsfs) responsive to heat stress at the pod development stage. J Plant Res. 2017; 131(3):525-542. DOI: 10.1007/s10265-017-0948-y. View

18.

Priyadarshani S, Hu B, Li W, Ali H, Jia H, Zhao L . Simple protoplast isolation system for gene expression and protein interaction studies in pineapple ( L.). Plant Methods. 2018; 14:95. PMC: 6205801. DOI: 10.1186/s13007-018-0365-9. View

19.

Barral B, Chillet M, Lechaudel M, Lartaud M, Verdeil J, Conejero G . An Imaging Approach to Identify Mechanisms of Resistance to Pineapple Fruitlet Core Rot. Front Plant Sci. 2019; 10:1065. PMC: 6747042. DOI: 10.3389/fpls.2019.01065. View

20.

Chauhan H, Khurana N, Agarwal P, Khurana P . Heat shock factors in rice (Oryza sativa L.): genome-wide expression analysis during reproductive development and abiotic stress. Mol Genet Genomics. 2011; 286(2):171-87. DOI: 10.1007/s00438-011-0638-8. View