Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L

Ning Li,Minjie Tao,Shufen Li,Wujun Gao,Yueyuan Wang,Ziwei Meng,Yulan Zhang,Chuanliang Deng

doi:10.1186/s12864-020-07277-4

Abstract

BackgroundDioecious spinach (Spinacia oleracea L.), a commercial and nutritional vegetable crop, serves as a model for studying the mechanisms of sex determination and differentiation in plants. However, this mechanism is still unclear. Herein, based on PacBio Iso-seq and Illumina RNA-seq data, comparative transcriptome analysis of male and female flowers were performed to explore the sex differentiation mechanism in spinach.ResultsCompared with published genome of spinach, 10,800 transcripts were newly annotated; alternative splicing, alternative polyadenylation and lncRNA were analyzed for the first time, increasing the diversity of spinach transcriptome. A total of 2965 differentially expressed genes were identified between female and male flowers at three early development stages. The differential expression of RNA splicing-related genes, polyadenylation-related genes and lncRNAs suggested the involvement of alternative splicing, alternative polyadenylation and lncRNA in sex differentiation. Moreover, 1946 male-biased genes and 961 female-biased genes were found and several candidate genes related to gender development were identified, providing new clues to reveal the mechanism of sex differentiation. In addition, weighted gene co-expression network analysis showed that auxin and gibberellin were the common crucial factors in regulating female or male flower development; however, the closely co-expressed genes of these two factors were different between male and female flower, which may result in spinach sex differentiation.ConclusionsIn this study, 10,800 transcripts were newly annotated, and the alternative splicing, alternative polyadenylation and long-noncoding RNA were comprehensively analyzed for the first time in spinach, providing valuable information for functional genome study. Moreover, candidate genes related to gender development were identified, shedding new insight on studying the mechanism of sex determination and differentiation in plant.

Highlights

Dioecious spinach (Spinacia oleracea L.), a commercial and nutritional vegetable crop, serves as a model for studying the mechanisms of sex determination and differentiation in plants
Our study show that sex differentiation may be regulated by the crosstalk among sugar, auxin and gibberellin signaling; different transcription factors between female and male may receive signals and target cell development-related genes to modulate floral whorl initiation
(See figure on previous page.) Fig. 1 Summary of Iso-seq data. a CCS read length distribution, the X-axis represents the read length, the Y-axis on the left represents the column graph coordinate, indicating the number of reads with a certain length (X-axis), and the Y-axis on the right is the curve coordinate, indicating the number of reads whose length is bigger than a certain X-axis value. b The percentage of high quality isoforms mapped to the reference genome. c Classification and number of isoforms mapped to the reference genome

Summary

Introduction

Dioecious spinach (Spinacia oleracea L.), a commercial and nutritional vegetable crop, serves as a model for studying the mechanisms of sex determination and differentiation in plants. Only a few sex-determining genes have been reported in plants, such as Diospyros lotus [10, 11], Asparagus officinalis [12, 13], Date palm [14], Actinidia chinensis [15], Vitis vinifera [16, 17], Ficus carica [18], Populus trichocarpa [19] and Fragaria octoploids [20]. These identified genes are involved in or determine the emergence of unisexual flower, the exact mechanism of sex determination in plants remains unclear

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