Abstract
Tapiscia sinensis (Tapisciaceae) possesses an unusual androdioecious breeding system that has attracted considerable interest from evolutionary biologists. Key aspects of T. sinensis biology, including its biogeography, genomics, and sex-linked genes, are unknown. Here, we report the first de novo assembly of the genome of T. sinensis. The genome size was 410 Mb, with 22,251 predicted genes. Based on whole-genome resequencing of 55 trees from 10 locations, an analysis of population genetic structure indicated that T. sinensis has fragmented into five lineages, with low intrapopulation genetic diversity and little gene flow among populations. By comparing whole-genome scans of male versus hermaphroditic pools, we identified 303 candidate sex-linked genes, 79 of which (25.9%) were located on scaffold 25. A 24-kb region was absent in hermaphroditic individuals, and five genes in that region, TsF-box4, TsF-box10, TsF-box13, TsSUT1, and TsSUT4, showed expression differences between mature male and hermaphroditic flowers. The results of this study shed light on the breeding system evolution and conservation genetics of the Tapisciaceae.
Highlights
Introduction Tapiscia sinensisOliv. (Tapisciaceae), is a woody, perennial, androdioecious species[1,2,3,4,5,6]
We identified 229 T. sinensis-specific genes that did not cluster with any genes from any of 17 other plant species: Morus notabilis, Ziziphus jujuba, Prunus persica, Oryza sativa, Arabidopsis thaliana, Juglans regia, Vitis vinifera, Jatropha curcas, Glycine max, Populus trichocarpa, Gossypium raimondii, Theobroma cacao, Fraxinus chinensis, Carica papaya, Solanum lycopersicum, Olea europaea and Citrus sinensis (Supplementary Table 11)
Analysis of gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that male and hermaphroditic plants were enriched in different annotations; for example, in males, we found that the greatest number of enriched genes were related to metabolic process, catalytic activity, and hydrolase activity, whereas enrichment in the hermaphroditic plant genome was in binding genes (Fig. 4b and Supplementary Figs. 5, 6 and Supplementary Table 17)
Summary
Introduction Tapiscia sinensisOliv. (Tapisciaceae), is a woody, perennial, androdioecious species[1,2,3,4,5,6]. Androdioecy is a rare breeding system in which populations consist of only male and hermaphroditic individuals[7,8]. Hermaphroditic individuals have both male and female functions[9]. Functional androdioecy is found in less than 0.005% of angiosperms[10], including Mercurialis annua[11], Datisca glomerata[11,12], Schizopepon bryoniaefolius[9], Laguncularia racemosa[13], and Osmanthus fragrans[14,15]. T. sinensis has research value as a model for the study of the evolution and maintenance of androdioecy[1,2,4]. In T. sinensis, floral buds on hermaphroditic individuals initiate differentiation in May, flower in late June, and are fertilized in early
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