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Transcriptional sequencing and analysis of major genes involved in the adventitious root formation of mango cotyledon segments

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Abstract

Main conclusion

A total of 74,745 unigenes were generated and 1975 DEGs were identified. Candidate genes that may be involved in the adventitious root formation of mango cotyledon segment were revealed.

Adventitious root formation is a crucial step in plant vegetative propagation, but the molecular mechanism of adventitious root formation remains unclear. Adventitious roots formed only at the proximal cut surface (PCS) of mango cotyledon segments, whereas no roots were formed on the opposite, distal cut surface (DCS). To identify the transcript abundance changes linked to adventitious root development, RNA was isolated from PCS and DCS at 0, 4 and 7 days after culture, respectively. Illumina sequencing of libraries generated from these samples yielded 62.36 Gb high-quality reads that were assembled into 74,745 unigenes with an average sequence length of 807 base pairs, and 33,252 of the assembled unigenes at least had homologs in one of the public databases. Comparative analysis of these transcriptome databases revealed that between the different time points at PCS there were 1966 differentially expressed genes (DEGs), while there were only 51 DEGs for the PCS vs. DCS when time-matched samples were compared. Of these DEGs, 1636 were assigned to gene ontology (GO) classes, the majority of that was involved in cellular processes, metabolic processes and single-organism processes. Candidate genes that may be involved in the adventitious root formation of mango cotyledon segment are predicted to encode polar auxin transport carriers, auxin-regulated proteins, cell wall remodeling enzymes and ethylene-related proteins. In order to validate RNA-sequencing results, we further analyzed the expression profiles of 20 genes by quantitative real-time PCR. This study expands the transcriptome information for Mangifera indica and identifies candidate genes involved in adventitious root formation in cotyledon segments of mango.

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Abbreviations

Aux/IAA:

Auxin/indole-3-acetic acid

DCS:

Distal cut surface

DEGs:

Differentially expressed genes

ERF:

Ethylene-responsive transcription factor

GH3:

Gretchen Hagen 3

GO:

Gene ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

KOG:

euKaryotic Ortholog Groups

Nr:

NCBI non-redundant protein sequences

Nt:

NCBI non-redundant nucleotide sequences

PAT:

Polar auxin transport

PCS:

Proximal cut surface

PIN:

PIN-FORMED

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Acknowledgements

This work was financially supported by the National Natural Science Foundation of China (31372053), the Agriculture and Food Research Initiative competitive Grant (# 2015-06811 to GKM) of the United States Department of Agriculture National Institute of Food and Agriculture, China Scholarship Council (201503260005).

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  1. South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, No. 1 Huxiu Road, Zhanjiang, 524091, China

    Yun-He Li, Hong-Na Zhang & Qing-Song Wu

  2. Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang, 524091, China

    Yun-He Li

  3. Department of Biology, Wake Forest University, Winston-Salem, NC, 27109, USA

    Yun-He Li & Gloria K. Muday

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  1. Yun-He Li
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Li, YH., Zhang, HN., Wu, QS. et al. Transcriptional sequencing and analysis of major genes involved in the adventitious root formation of mango cotyledon segments. Planta 245, 1193–1213 (2017). https://doi.org/10.1007/s00425-017-2677-9

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