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Molecular characterization of miRNA genes and their expression in Dimocarpus longan Lour

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Abstract

Main conclusion

A genome-wide analysis of longan miRNA genes was conducted, and full-length pri-miRNA transcripts were cloned. Bioinformatics and expression analyses contributed to the functional characterization of longan miRNA genes.

MicroRNAs are important for the post-transcriptional regulation of target genes. However, little is known about the transcription and regulation of miRNA genes in longan (Dimocarpus longan Lour.). In this study, 80 miRNA precursors (pre-miRNA) were predicted, and their secondary structure, size, conservation, and diversity were analyzed. Furthermore, the full-length cDNA sequences of 13 longan primary miRNAs (pri-miRNAs) were amplified by RLM-RACE and SMART-RACE and analyzed, which revealed that longan pri-miRNA transcripts have multiple transcription start sites (TSSs) and the downstream pre-miRNAs are polymorphic. Accordingly, the longan pri-miRNAs and protein-encoding genes may have similar transcriptional specificities. An analysis of the longan miRNA gene promoter elements indicated that the three most abundant cis-acting elements were light-responsive, stress-responsive, and hormone-responsive elements. A quantitative real-time PCR assay elucidated the potential spatial and temporal expression patterns of longan pre-miRNAs during the early stages of somatic embryogenesis (SE) and in different longan organs/tissues. This is the first report regarding the molecular characterization of miRNA genes and their expression profiles in longan. The generated data may serve as a foundation for future research aimed at clarifying the longan miRNA gene functions.

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Abbreviations

CpECGE:

Compact pro-embryogenic cultures globular embryos

EC:

Embryogenic callus

GE:

Globular embryos

ICpEC:

Incomplete compact pro-embryogenic cultures

MIR genes:

MiRNA genes

NEC:

Non-embryonic callus

pre-miRNAs:

Precursor miRNAs

pri-miRNAs:

Primary miRNAs

SE:

Somatic embryogenesis

TSSs:

Transcription start sites

RLM-RACE:

RNA ligase-mediated rapid amplification of cDNA ends

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (31672127), the Constructions of Plateau Discipline of Fujian Province (102/71201801101), the Technology Innovation Fund of Fujian agriculture and forestry university (CXZX2017187 and CXZX2018078). We thank Liwen Bianji, Edanz Editing China (www.liwenbianji.cn/ac) for editing the English text of a draft of this manuscript.

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  1. Yuling Lin and Yan Chen equal contributors.

Authors and Affiliations

  1. Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China

    Yuling Lin, Yan Chen, Youjing Zeng, Shuting Zhang, Zihao Zhang, YuKun Chen & Zhongxiong Lai

  2. Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China

    Jiawei Gong

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  1. Yuling Lin
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Contributions

ZXL and YLL conceived the idea and designed the experiments. YLL, YJZ, YKC, and YC performed the experiments. STZ, ZHZ, and JWG prepared the materials. YLL and YC wrote the manuscript, and ZXL finalized the manuscript.

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Correspondence to Zhongxiong Lai.

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Supplementary Information

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425_2021_3564_MOESM1_ESM.png

Supplementary file1 Suppl. Fig. S1 Consensus structures of pre-miRNA families in D .longan, the consensus structure is generated by RNAalifold. a pre-miR156 family; b pre-miR160 family; c pre-miR167 family; d pre-miR171 family; e pre-miR319 family; f pre-miR390 family; g pre-miR393 family; h pre-miR394 family; i pre-miR395 family; j pre-miR398 family; k pre-miR399 family; l pre-miR477 family; m pre-miR482 family; n pre-miR1863 family; o pre-miR3627 family. (PNG 1137 KB)

425_2021_3564_MOESM2_ESM.png

Supplementary file2 Suppl. Fig. S2 Gel electrophoresis of the cloned sequence of longan pri-miRNA. a pri-miR156(scaffold29); b pri-miR156(Unigene5849); c pri-miR166(scaffold338); d pri-miR395(scaffold6); e pri-miR396(scaffold38); f pri-miR170(scaffold1266); g pri-miR390(scaffold24); h pri-miR398b(scaffold58); i pri-miR394(scaffold3884); j pri-miR482(scaffold26); k pri-miR170(scaffold1266); l pri-miR408(Unigene40210); m pri-miR156(scaffold38). (PNG 425 KB)

425_2021_3564_MOESM3_ESM.png

Supplementary file3 Suppl. Fig. S3 Analysis of stem-loop hairpin structures of pri-miRNAs in D. longan. a pri-miR156(scaffold29); b pri-miR398a; c pri-miR160; d pri-miR167; e pri-miR482(scaffold26); f pri-miR156(scaffold38); g pri-miR156(Unigene5849); h pri-miR166(scaffold78); i pri-miR166(scaffold338); j pri-miR168(scaffold2621); k pri-miR170(scaffold1266); l pri-miR170 (scaffold1537); m pri-miR319(Unigene13717); n pri-miR398b(scaffold58); o pri-miR390(scaffold24); p pri-miR393(scaffold978); q pri-miR394(scaffold3884); r pri-miR395(scaffold6); s pri-miR396(scaffold38); t pri-miR397(scaffold21); u pri-miR408(Unigene40210). The green font is the position of the miRNA-5p and miRNA-3p. (PNG 1032 KB)

425_2021_3564_MOESM4_ESM.pdf

Supplementary file4 Suppl. Fig. S4 The location of a single transcription start site (TSSs) in D. longan. Red letter on behalf the TSS is G; blue represent TSSs as A; purple represent TSSs as T. (PDF 31 KB)

Supplementary file5 Suppl. Table S1 Primers and related information of 16 pri-miRNAs. (XLSX 40 KB)

Supplementary file6 Suppl. Table S2 Primer information of 19 pre-miRNAs for qRT-PCR. (XLSX 38 KB)

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Lin, Y., Chen, Y., Zeng, Y. et al. Molecular characterization of miRNA genes and their expression in Dimocarpus longan Lour. Planta 253, 41 (2021). https://doi.org/10.1007/s00425-021-03564-w

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