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Genome-wide Identification and Expression Pattern Analysis of the HD-Zip Transcription Factor Family in Pineapple (Ananas Comosus)

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Abstract

The Homeodomain leucine zipper (HD-Zip) transcription factor family is one of the most important transcription factor families in the plant kingdom and it plays pivotal roles in plant development, growth as well as response to all kinds of stresses. However, the HD-Zip gene family has not been characterized in pineapple yet. Pineapple is one of the most economically important tropical fruit in the world. Here, we identified a total of 33 HD-Zip genes in pineapple by a genome-wide study. These 33 genes were divided into 4 subgroups and variably located on 14 chromosomes and one scaffold_1724. The gene structure and conserved motifs of these genes relatively share similar characteristics in a subfamily. We found at least two abiotic stress responding cis-elements in the promoter region of AcoHDzip genes, the light-responsive element is the most abundant cis-element that can be found in all the genes. Besides, transcriptome analysis showed the expression profile of 33 genes in different developmental stages. We identified the nine genes with higher expression in gynoecium and two genes with highly expressed in ovules and flowers respectively. Our studies will provide valuable information about the HD-Zip transcription factor family in pineapple, which would be useful for further functional studies in plant growth, plant development, and stress response.

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Abbreviations

ACO:

Ananas comosus

AT:

Arabidopsis thaliana

OS:

Oryza sativa

HD-Zip:

Homeodomain leucine zipper

TFs:

Transcription Factors

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Funding

This work was supported by NSFC (U1605212; 31970333) and a Guangxi Distinguished Experts Fellowship to Y.Q.

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Authors and Affiliations

  1. Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Sciences, College of Agriculture, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China

    Qiao Zhou, Liping Liu, Han Cheng, Zeyun Li, MyatHnin Wai, Tiantian Luo, Xingyue Jin, Heming Zhao, S. V. G. N. Priyadarshani & Yuan Qin

  2. State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China

    Yuan Qin

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  1. Qiao Zhou
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Contributions

Q.Z. and L.L. performed the experiment, and manuscript writing; H.C. performed the experiment, data analyse;Z.l., M.H.W., T.L. helped to design the figure; H.Z. and S. V. G. N. P. revised and edited the manuscript; Q.Y. Fund acquisition and revising manuscript.

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Correspondence to Yuan Qin.

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Communicated by: Ray Ming.

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Supplementary Information

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12042_2020_9279_MOESM1_ESM.docx

Supplementary file1 Table S1. Characterization of HD-Zip gene superfamily in pineapple. Table S2. The primers of the selected genes of HD-Zip family for RT-qPCR (DOCX 19 KB)

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Zhou, Q., Liu, L., Cheng, H. et al. Genome-wide Identification and Expression Pattern Analysis of the HD-Zip Transcription Factor Family in Pineapple (Ananas Comosus). Tropical Plant Biol. 14, 120–131 (2021). https://doi.org/10.1007/s12042-020-09279-8

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