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Additional file 1: Table S1. Summary of the sequencing and mapping results. Table S2. The number of differentially expressed genes in the wild type (WT) and Wannianjin (YL). Table S3. The Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation of differently expressed genes in chlorophyll metabolism. Table S4. The Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation of differently expressed genes in photosynthesis. Table S5. The Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation of differently expressed genes in carotenoid metabolism. Table S6. Quantitative real-time PCR primers of differentially expressed genes. Fig. S1. The differentially expressed genes between wild type (WT) and Wannianjin (YL) at the spring, summer, and autumn stages, respectively. Fig. S2. The most enriched Gene Ontology terms of differentially expressed genes between wild type (WT) and Wannianjin (YL) at the spring, summer, and autumn stages, respectively. Fig. S3. The Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation of differentially expressed genes between wild type (WT) and Wannianjin (YL) at the spring, summer, and autumn stages, respectively.

This dataset describes the modelled distribution range of latitude and depth for 5619 marine fish. In addition, the maximum body sizes and trophic levels of 5619 marine fish.

(1) 20220304-binary dataset of all fish in 100 m and 10 m depth bands-This dataset was used for caluculation of averaged phylogenetic diversity (AvPD) for 5619 marine fish in 100m depth bands. -This dataset was used for doing the Jaccard similarity for 5619 marine fish in 100 m depth bands (0 - 3500 m) and 10n bands (0-500m).(2) 20220304-binary dataset of marine fish in 5 degree latitude bands in the depth zones-This detaset was used for calculation of latitudinal averaged phylogenetic diversity (AvPD) in 5 degree latitude bands for all (5619 species), bony (5117 species), and cartilaginous fish (470 species) in four depth zones (0-6000m, 0-200m, 201-1000m, 1001-6000m).(3) 20220304-Dataset of taxon richness in 5-degree latitude and 100-m depth bands-This dataset was used for plotting the species richness of all, bony, and cartilaginous fish in 5-degree latitude and 100m depth bands.-This dataset was used for calculation of the sum of the higher taxonomic levels (STL) and the sum of the higher taxonomic levels divided by the number of species (STL/spp) for all, bony, and cartilaginous fish in 5-degree latitude and 100m depth bands.

This dataset describes the modelled distribution range of latitude and depth for 5619 marine fish. In addition, the maximum body sizes and trophic levels of 5619 marine fish.

Sexual dimorphism like dioecy (separate male and female individuals) have evolved in diverse multicellular eukaryotes while the molecular mechanisms underlying the development of such a key biological trait remains elusive (1). The living fossil Ginkgo biloba represents an early diverged lineage of land plants with dioecy. However, its sex-determination system and molecular basis have long been controversial or unknown. In the present research, we assembled the first and largest to date chromosome-level genome of a non-model tree species using Hi-C data. With this reference genome, we addressed both questions using genome resequencing data gathered from 97 male and 265 female trees of ginkgo, as well as transcriptome data from three developmental stages for both sexes. Our results support vertebrate-like XY chromosomes for ginkgo and five potential sex-determination genes, which may originate ~14 million years ago. This is the earliest diverged sex determination region in all reported plants as yet. The present research resolved a long-term controversy, lay a foundation for future studies on the origin and evolution of plant sexes, and provide genetic markers for sex identification of ginkgo which will be valuable for both nurseries and field ecology of ginkgo.