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Genome-wide identification of lncRNAs during hickory (Carya cathayensis) flowering

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Abstract

Non-coding RNAs with lengths greater than 200 bp are known as long non-coding RNAs (lncRNAs), and these RNAs play important role in gene regulation and plant development. However, to date, little is known regarding the role played by lncRNAs during flowering in hickory (Carya cathayensis). Here, we performed whole transcriptome RNA-sequencing of samples from hickory female and male floral buds, in which three samples (H0311PF, H0318PF, and H0402PF) represent pre-flowering, flowering, and post-flowering, respectively, while eight male samples collected from May 8th to June 13th as this time course are the key stage for male floral bud differentiation. We identified 2163 lncRNAs in hickory during flowering, containing 213 intronic, 1488 intergenic, and 462 antisense lncRNAs. We noticed that 510 and 648 lncRNAs were differentially expressed corresponding to female and male floral buds, respectively. And some of the lncRNAs were in a tightly tissue-specific or stage-specific manner. To further understand the roles of the lncRNAs, we predicted the function of the lncRNAs in cis- and trans-acting modes. The results showed that 924 lncRNAs were cis-correlated with 1536 protein-coding genes, while 1207 lncRNAs co-expressed (trans-acting) with 7432 protein-coding genes (R > 0.95 or R < − 0.95). These lncRNAs were all enriched in flower development-associated biological processes, i.e., circadian rhythm, vernalization response, response to gibberellin, inflorescence development, floral organ development, etc. To further understand the relationships between lncRNAs and floral-core genes, we build a co-expressing lncRNA-mRNA flowering network. We classified these floral genes into different pathway (photoperiod, vernalization, gibberellin, autonomous, and sucrose pathway) according to their particular functions. We found a set of lncRNAs that preferentially expressed in these pathways. The network showed that some lncRNAs (i.e., XLOC_038669, XLOC_017938) functioned in a particular flowering time pathway, while others (i.e., XLOC_011251, XLOC_04110) were involved in multiple pathway. Furthermore, some lncRNAs (i.e., XLOC_038669, XLOC_009597, and XLOC_049539) played roles in single or multiple pathways via interaction with each other. This study provides a genome-wide survey of hickory flower-related lncRNAs and will contribute to further understanding of the molecular mechanism underpinning flowering in hickory.

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Data availability statement

The raw RNA-seq datasets analyzed during the current study were deposited in National Center for Biotechnology Information (NCBI) Short Read Archive (SRA) accession SRP134709 (https://www.ncbi.nlm.nih.gov/sra/SRP134709).

Funding

The research was financially supported by the National Natural Science Foundation of China (31570666, 31971672, 31670682, and 31600547), the Natural Science Foundation of Zhejiang Province (LY18C150002).

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Authors and Affiliations

  1. State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, 311300, People’s Republic of China

    Tongqiang Fan, Qixiang Zhang, Yuanyuan Hu, Zhengjia Wang & Youjun Huang

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  1. Tongqiang Fan
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  2. Qixiang Zhang
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  3. Yuanyuan Hu
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  4. Zhengjia Wang
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Contributions

Youjun Huang and Zhengjia Wang designed the experiment. Qixiang Zhang participated in discussion part. Tongqiang Fan, Youjun Huang, Yuanyuan Hu, Qixiang Zhang, and Zhengjia Wang participated in the revision of manuscript. Tongqiang Fan carried out statistical analysis and manuscript draft. All authors have read and approved the final manuscript.

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Correspondence to Zhengjia Wang or Youjun Huang.

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Ethics statement

No specific permissions were required for these locations/activities because all samples were collected from Caray cathayensis flower buds of Donghu Campus of Zhejiang A&F University (30°N, 119°W), Lin’an, China. We collected flower buds from hickory for research, and also confirmed that the field studies did not involve any endangered or protected species.

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The authors declare that they have no conflict of interest.

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Table S1

Summary of the RNA-seq data and reads mapped to the Carya cathayensis reference genome (XLSX 13 kb)

Table S2

List of the lncRNAs identified in Carya cathayensis pistillate and staminate bud libraries (XLSX 100 kb)

Table S3

List of differentially expressed lncRNAs from three female floral bud libraries (XLSX 101 kb)

Table S4

List of differentially expressed lncRNAs from eight male floral bud libraries (XLSX 214 kb)

Table S5

Detected protein-coding genes 10 kb upstream and downstream of all the identified lncRNAs (XLSX 484 kb)

Table S6

Functional enrichment analysis of protein-coding genes targeted by cis-acting lncRNAs (XLSX 102 kb)

Table S7

Functional enrichment analysis of protein-coding genes targeted by cis-acting lncRNAs that were involved in some key processes (XLSX 20 kb)

Table S8

Co-expression analysis of protein-coding genes and lncRNAs with PCC (Pearson’s correlation coefficient) > 0.95 or <− 0.95 (XLSX 1390 kb)

Table S9

Functional enrichment analysis of protein-coding genes that co-expressed with lncRNAs (XLSX 190 kb)

Table S10

Co-expression analysis of lncRNAs and mRNA involved in floral development (XLSX 23 kb)

Table S11

(XLSX 35 kb)

Table S12

(XLSX 4576 kb)

Table S13

(XLSX 11 kb)

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Fan, T., Zhang, Q., Hu, Y. et al. Genome-wide identification of lncRNAs during hickory (Carya cathayensis) flowering. Funct Integr Genomics 20, 591–607 (2020). https://doi.org/10.1007/s10142-020-00737-w

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  • DOI: https://doi.org/10.1007/s10142-020-00737-w

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