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Global comparative analysis of expressed genes in ovules and leaves of Ginkgo biloba L.

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Abstract

Ovules are an essential reproductive structure in all seed plants. However, limited information is available on the genetics and genomics of ovules in gymnosperms. Here, we used Illumina sequencing to derive comprehensive gene expression profiles for ovules and leaves in the extant basal gymnosperm Ginkgo biloba. A total of 100,124 transcripts, including 77,898 unigenes, were obtained by de novo assembly from leaf cDNA samples. These transcripts were functionally annotated by comparing their sequences to public protein databases as references. For the comparative analysis of gene expression levels between ovules and leaves, digital gene expression tag profiling was used. An analysis of the expressed genes revealed a high proportion of functional genes commonly expressed in both ovules and leaves. Functional gene expression analyses and microscopic observations implied that ovules and leaves share the photosynthetic structures of chloroplasts and stomata, indicating that they are homologous structures. Interestingly, many homologous genes associated with floral development were expressed in ovules, indicating that gymnosperm ovules share some gene regulatory mechanisms with angiosperm floral organs. The genes that showed highly differential expression levels between leaves and ovules were involved in flavonoid biosynthesis, cell division, hormone transport, transcriptional regulation, and starch and sucrose metabolism, and they indicated higher cell growth and division activity in the ovule. Thus, these results provide valuable gene expression information, which will contribute to an enhanced understanding of the diverse biological mechanisms in the ovules and leaves of G. biloba and provide important molecular insights into ovule evolution in early seed plants.

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Acknowledgments

This work was financially supported by the National Natural Science Foundation of China (No. 31200145), the Three New Forestry Engineering Foundation of Jiangsu Province (No. lysx[2013]05 and lysx[2014]12), and the Graduate Practice Innovation Projects of Jiangsu Province (No._SJLX15_0672).

Author contributions

L.W. and B.J. designed the project; Z.G.L performed the experiments; W.X.L., J.X., K.G.L., W.C.L., and L.Z participated in some experiments. L.W., Z.G.L, and B.J. drafted the paper.

Data archiving statement

All of the raw data from the Illumina sequencing have been deposited in NCBI Sequence Read Archive (SRA) under accession number SRP051312, and all raw and processed DGE data are available at Gene Expression Omnibus (GEO) database accession number GSE64502.

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Authors and Affiliations

  1. College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China

    Li Wang, Zhaogeng Lu, Weixing Li, Jing Xu, Kaige Luo, Weichao Lu, Li Zhang & Biao Jin

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  1. Li Wang
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  2. Zhaogeng Lu
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  3. Weixing Li
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Correspondence to Biao Jin.

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Communicated by J.L. Wegrzyn

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Wang, L., Lu, Z., Li, W. et al. Global comparative analysis of expressed genes in ovules and leaves of Ginkgo biloba L.. Tree Genetics & Genomes 12, 29 (2016). https://doi.org/10.1007/s11295-016-0989-8

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