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

BACKGROUND: 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. However, this mechanism is still unclear. Herein, based on PacBio Iso-seq and Illumina RNA-seq data, co...

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Autores principales: Li, Ning, Meng, Ziwei, Tao, Minjie, Wang, Yueyuan, Zhang, Yulan, Li, Shufen, Gao, Wujun, Deng, Chuanliang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7708156/
https://www.ncbi.nlm.nih.gov/pubmed/33256615
http://dx.doi.org/10.1186/s12864-020-07277-4
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author Li, Ning
Meng, Ziwei
Tao, Minjie
Wang, Yueyuan
Zhang, Yulan
Li, Shufen
Gao, Wujun
Deng, Chuanliang
author_facet Li, Ning
Meng, Ziwei
Tao, Minjie
Wang, Yueyuan
Zhang, Yulan
Li, Shufen
Gao, Wujun
Deng, Chuanliang
author_sort Li, Ning
collection PubMed
description BACKGROUND: 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. 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. RESULTS: Compared 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. CONCLUSIONS: In 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-020-07277-4.
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spelling pubmed-77081562020-12-02 Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L Li, Ning Meng, Ziwei Tao, Minjie Wang, Yueyuan Zhang, Yulan Li, Shufen Gao, Wujun Deng, Chuanliang BMC Genomics Research Article BACKGROUND: 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. 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. RESULTS: Compared 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. CONCLUSIONS: In 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-020-07277-4. BioMed Central 2020-12-01 /pmc/articles/PMC7708156/ /pubmed/33256615 http://dx.doi.org/10.1186/s12864-020-07277-4 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Li, Ning
Meng, Ziwei
Tao, Minjie
Wang, Yueyuan
Zhang, Yulan
Li, Shufen
Gao, Wujun
Deng, Chuanliang
Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L
title Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L
title_full Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L
title_fullStr Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L
title_full_unstemmed Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L
title_short Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L
title_sort comparative transcriptome analysis of male and female flowers in spinacia oleracea l
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7708156/
https://www.ncbi.nlm.nih.gov/pubmed/33256615
http://dx.doi.org/10.1186/s12864-020-07277-4
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