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Comparative Transcriptome Analysis of Pecan Female and Male Inflorescences

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Abstract

Pecan (Carya illinoinensis (Wangenh.) K.Koch) is a popular long-lived diploid tree insilviculture and horticulture. Pecan is a wind pollinated monoecious tree exhibiting heterodichogamy, and the location and timing of functioning female and male organs are different. The limited availability of pecan genomic information has hindered research on the mechanisms underlying its flower development. In this study, we obtained the first de novo assembly of pecan transcriptome and performed acomparative analysis of pecan female and male inflorescences using RNA-seq technology. A final dataset containing 53894 unigenes in the female pecan inflorescence was obtained, with an N50 length of 1411 bp, while only small differences existed among female and male inflorescence unigenes. Using the bioinformatics approach, we identified 11813 simple sequence repeats in unigenes and developed primers for 7725 of them. A total of 5826 differentially expressed genes were identified between pecan female and male inflorescences. A large number of them were linked to plant hormone regulation, especially revolved in the gibberellin biosynthesis (GA2OX and GA20OX), gibberellin signal reception (GID1) and gibberellin regulation (GASA, GRF, GRAS). In addition, almost onetenth (569) of unigenes encoding transcription factors in pecan differentially expressed. At least 15 ARF, 3 bZIP, 33 bHLH, 8 GH3, 13 MADS-box, 92 MYB, 28 NAC and 14 zf-Dof transcription factors were associated with pecan flower sex differentiation. This assembly of pecan transcriptome could contribute to enhancing understanding of the gene specialization in flowers of different sexes, and also be particularly useful for pecan germplasm management and breeding programs.

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Abbreviations

DEG:

Differentially Expressed Gene

NCBI:

National Center for Biotechnology Information, United States

NCBI-Nr:

NCBI Non-redundant Protein Database

NCBI-Nt:

NCBI Non-redundant Nucleotide Database

qPCR:

Real-time quantitative Polymerase Chain Reaction

RPKM:

Reads Per Kilobase Of Xxon Model Per Million Mapped Reads

SSR:

Simple Sequence Repeat

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Author notes

  1. These authors contributed equally to this work.

Authors and Affiliations

  1. Research Center of Economic Plants, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu Province, 210014, China

    Z. Jia, G. Wang, J. Xuan, J. Zhang, M. Zhai, X. Jia & Zh. Guo

  2. Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China

    M. Li

Authors
  1. Z. Jia
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  2. G. Wang
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  3. J. Xuan
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  4. J. Zhang
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  5. M. Zhai
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  6. X. Jia
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  7. Zh. Guo
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  8. M. Li
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Correspondence to J. Xuan.

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Jia, Z., Wang, G., Xuan, J. et al. Comparative Transcriptome Analysis of Pecan Female and Male Inflorescences. Russ J Plant Physiol 65, 186–196 (2018). https://doi.org/10.1134/S1021443718020139

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  • DOI: https://doi.org/10.1134/S1021443718020139

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