The Cycas genome and the early evolution of seed plants

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Authors

Liu, Yang
Wang, Sibu
Li, Linzhou
Yang, Ting
Dong, Shanshan
Wei, Tong
Wu, Shengdan
Liu, Yongbo
Gong, Yiqing
Feng, Xiuyan

Journal Title

Journal ISSN

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Publisher

Nature Research

Abstract

Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of Cycas panzhihuaensis, complemented by the transcriptomes of 339 cycad species. Nuclear and plastid phylogenomic analyses strongly suggest that cycads and Ginkgo form a clade sister to all other living gymnosperms, in contrast to mitochondrial data, which place cycads alone in this position. We found evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms. The Cycas genome contains four homologues of the fitD gene family that were likely acquired via horizontal gene transfer from fungi, and these genes confer herbivore resistance in cycads. The male-specific region of the Y chromosome of C. panzhihuaensis contains a MADS-box transcription factor expressed exclusively in male cones that is similar to a system reported in Ginkgo, suggesting that a sex determination mechanism controlled by MADS-box genes may have originated in the common ancestor of cycads and Ginkgo. The C. panzhihuaensis genome provides an important new resource of broad utility for biologists.

Description

DATA AVAILABILITY : The genome and transcriptome data, genome assemblies and annotations can be found at https://db.cngb.org/codeplot/datasets/public_dataset?id=PwRftGHfPs5q G3gE. The raw genomic, transcriptomic and Hi-C data generated in this study were deposited in the NCBI Sequence Read Archive (SRA, BioProject PRJNA734434) and the CNGB data center (https://db.cngb.org/) under project number CNP0001756. Source data are provided with this paper.
SUPPLEMENTARY INFORMATION : Supplementary notes and figures for additional information of the manuscript.
SUPPLEMENTARY VIDEO 1 : A swimming sperm of Cycas.
SUPPLEMENTARY TABLE 1 : Supplementary tables.
SUPPLEMENTARY DATA : Raw gels figure for Supplementary Fig. 39.

Keywords

Cycads, Seed plants, Ginkgo, MADS-box, SDG-15: Life on land

Sustainable Development Goals

Citation

Liu, Y., Wang, S., Li, L. et al. 2022, 'The Cycas genome and the early evolution of seed plants', Nature Plants, vol. 8, pp. 389-401. DOI :10.1038/s41477-022-01129-7.