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. 2020 Oct 22;21(1):735.
doi: 10.1186/s12864-020-07152-2.

Genome-wide study of pineapple (Ananas comosus L.) bHLH transcription factors indicates that cryptochrome-interacting bHLH2 (AcCIB2) participates in flowering time regulation and abiotic stress response

Mohammad Aslam  1   2 , Bello Hassan Jakada  1 , Beenish Fakher  3 , Joseph G Greaves  4 , Xiaoping Niu  1   2 , Zhenxia Su  1   3 , Yan Cheng  1   4 , Shijiang Cao  5 , Xiaomei Wang  6 , Yuan Qin  7   8
Affiliations

Genome-wide study of pineapple (Ananas comosus L.) bHLH transcription factors indicates that cryptochrome-interacting bHLH2 (AcCIB2) participates in flowering time regulation and abiotic stress response

Mohammad Aslam et al. BMC Genomics. .

Abstract

Background: Transcription factors (TFs) are essential regulators of growth and development in eukaryotes. Basic-helix-loop-helix (bHLHs) is one of the most significant TFs families involved in several critical regulatory functions. Cryptochrome-interacting bHLH (CIB) and cryptochromes form an extensive regulatory network to mediate a plethora of pathways. Although bHLHs regulate critical biological processes in plants, the information about pineapple bHLHs remains unexplored.

Results: Here, we identified a total of 121 bHLH proteins in the pineapple genome. The identified genes were renamed based on the ascending order of their gene ID and classified into 18 subgroups by phylogenetic analysis. We found that bHLH genes are expressed in different organs and stages of pineapple development. Furthermore, by the ectopic expression of AcCIB2 in Arabidopsis and complementation of Atcib2 mutant, we verified the involvement of AcCIB2 in photomorphogenesis and abiotic stress response.

Conclusions: Our findings revealed that AcCIB2 plays an essential role in flowering time regulation and abiotic stress response. The present study provides additional insights into the current knowledge of bHLH genes and suggests their potential role in various biological processes during pineapple development.

Keywords: Abiotic stress; CIB2; Flowering time; Pineapple; bHLH.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Phylogenetic tree showing the relationship between bHLH genes of pineapple and Arabidopsis. Different colors indicate different groups. Prefix ‘Ac’ indicates Ananas comosus and ‘AT’ refers to Arabidopsis thaliana. Red circles represent the pineapple CIB genes and the green represents Arabidopsis CIB genes
Fig. 2
Fig. 2
Chromosomal locations of pineapple bHLH genes. The bHLH genes of pineapple were mapped to different chromosomes using MapChart. Each AcbHLH is noted on the right side of its respective chromosome. Gene IDs in red represent pineapple CIB genes. The scale is in megabases (Mb)
Fig. 3
Fig. 3
Sequence characteristics of the bHLH domains. Multiple sequence alignments were conducted with the bHLH domains of all pineapple bHLH candidate and results were visualized using Weblogo online software
Fig. 4
Fig. 4
Expression profiles of the pineapple bHLH genes. Hierarchical clustering of expression profiles of bHLHs in different organs and developmental stages. Red color represents a high level of transcript abundance, and blue color represents low transcript abundance. The right side of the figure shows the scale. Different groups i.e. group I, group II and group III represent low expressed, highly expressed, and moderately expressed bHLH genes, respectively. Gene IDs in red represent pineapple CIB genes. Details of the samples are mentioned at the bottom of each lane: sepal Se1–Se4, gynoecium Gy1- Gy7, ovule Ov1–Ov7, petal Pe1–Pe3, stamen St1–St6, fruit ‘Fr_S1–Fr_S7’, root ‘Ro’, leaf ‘Le’, and flower ‘Fl’ where ‘S’ is the abbreviation for ‘stage
Fig. 5
Fig. 5
AcCIB2-GFP localizes to the nucleus. AcCIB2-GFP localization in the nucleus of seven-day-old roots of transgenic Arabidopsis plants. GFP fluorescence is represented in green and DAPI in blue channel, Scale bars = 20 μm
Fig. 6
Fig. 6
AcCIB2 regulates the photomorphogenesis. a Photograph showing the early phenotype of Arabidopsis cib2 mutant and complementation of early flowering phenotype of by AcCIB2-GFP. Plants were grown on the media plates for ten days, followed by transferring to soil in plastic pots and kept in a walk-in chamber. Plants were then photographed after 20 days of the transfer. b Relative expression of critical flowering genes (CO, FT and SOC1) and CRY-CIB genes (CRY1, CRY2, CIB1, CIB4 and CIB5) in Col-0, cib2 mutant, complemented (cib2 + 35S::AcCIB2-GFP) and in AcCIB2 overexpressing (35S::AcCIB2-GFP) lines. Gene expression is represented in fold change of expression against Arabidopsis ef1α calculated by 2−ΔΔCT. Vertical bars represent the mean ± SE of three biological replicate assays. Asterisks denote the statistical significance between control and treatment as judged by the Student’s t-test (*** P < 0.001)
Fig. 7
Fig. 7
a Relative expression of AcCIB2 in pineapple plants at different time points after osmotic (300 mM Mannitol), salt 150 (mM NaCl) and phytohormone ABA (0.5 μM) treatment. AcCIB2 expression is represented in fold change of expression against pineapple ef1α calculated by 2−ΔΔCT. Vertical bars represent the mean ± SE of three biological replicate assays. Asterisks denote the statistical significance between control and treatment as judged by the Student’s t-test (*** P < 0.001). b Overexpression of AcCIB2 results in resistance to abiotic stress. The phenotype of 3 days old cib2 mutant, complemented (cib2 + 35S::AcCIB2-GFP) and in AcCIB2 overexpressing (35S::AcCIB2-GFP) lines germinated under osmotic stress (300 mM Mannitol), salinity stress (150 mM NaCl), and ABA 0.5 μM
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References

    1. Chen WJ, Zhu T. Networks of transcription factors with roles in environmental stress response. Trends Plant Sci. 2004;9(12):591–596. doi: 10.1016/j.tplants.2004.10.007. - DOI - PubMed
    1. Lai X, Stigliani A, Vachon G, Carles C, Smaczniak C, Zubieta C, Kaufmann K, Parcy F. Building transcription factor binding site models to understand gene regulation in plants. Mol Plant. 2019;12(6):743–763. doi: 10.1016/j.molp.2018.10.010. - DOI - PubMed
    1. Carretero-Paulet L, Galstyan A, Roig-Villanova I, Martinez-Garcia JF, Bilbao-Castro JR, Robertson DL. Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae. Plant Physiol. 2010;153(3):1398–1412. doi: 10.1104/pp.110.153593. - DOI - PMC - PubMed
    1. Wang R, Zhao P, Kong N, Lu R, Pei Y, Huang C, Ma H, Chen Q. Genome-wide identification and characterization of the potato bHLH transcription factor family. Genes. 2018;9(1):54. doi: 10.3390/genes9010054. - DOI - PMC - PubMed
    1. Tian S, Li L, Wei M, Yang F. Genome-wide analysis of basic helix-loop-helix superfamily members related to anthocyanin biosynthesis in eggplant (Solanum melongena L.) PeerJ. 2019;7:e7768. doi: 10.7717/peerj.7768. - DOI - PMC - PubMed

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