Draft genomes of two outcrossing wild rice, Oryza rufipogon and O. longistaminata, reveal genomic features associated with mating‐system evolution
Wei Li,
Qun‐Jie Zhang,
Ting Zhu,
Yan Tong,
Kui Li,
Cong Shi,
Yun Zhang,
Yun‐Long Liu,
Jian‐Jun Jiang,
Yuan Liu,
En‐Hua Xia,
Hui Huang,
Li‐Ping Zhang,
Dan Zhang,
Chao Shi,
Wen‐Kai Jiang,
You‐Jie Zhao,
Shu‐Yan Mao,
Jun‐ying Jiao,
Ping‐Zhen Xu,
Li‐Li Yang,
Li‐Zhi Gao
Affiliations
Wei Li
Institution of Genomics and Bioinformatics South China Agricultural University Guangzhou China
Qun‐Jie Zhang
Institution of Genomics and Bioinformatics South China Agricultural University Guangzhou China
Ting Zhu
Institution of Genomics and Bioinformatics South China Agricultural University Guangzhou China
Yan Tong
Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of Sciences Kunming China
Kui Li
Institution of Genomics and Bioinformatics South China Agricultural University Guangzhou China
Cong Shi
Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of Sciences Kunming China
Yun Zhang
Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of Sciences Kunming China
Yun‐Long Liu
Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of Sciences Kunming China
Jian‐Jun Jiang
Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of Sciences Kunming China
Yuan Liu
Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of Sciences Kunming China
En‐Hua Xia
Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of Sciences Kunming China
Hui Huang
Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of Sciences Kunming China
Li‐Ping Zhang
Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of Sciences Kunming China
Dan Zhang
Institution of Genomics and Bioinformatics South China Agricultural University Guangzhou China
Chao Shi
Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of Sciences Kunming China
Wen‐Kai Jiang
Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of Sciences Kunming China
You‐Jie Zhao
Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of Sciences Kunming China
Shu‐Yan Mao
Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of Sciences Kunming China
Jun‐ying Jiao
Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of Sciences Kunming China
Ping‐Zhen Xu
Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of Sciences Kunming China
Li‐Li Yang
Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of Sciences Kunming China
Li‐Zhi Gao
Institution of Genomics and Bioinformatics South China Agricultural University Guangzhou China
Abstract Oryza rufipogon and O. longistaminata are important wild relatives of cultivated rice, harboring a promising source of novel genes for rice breeding programs. Here, we present de novo assembled draft genomes and annotation of O. rufipogon and O. longistaminata. Our analysis reveals a considerable number of lineage‐specific gene families associated with the self‐incompatibility (SI) and formation of reproductive separation. We show how lineage‐specific expansion or contraction of gene families with functional enrichment of the recognition of pollen, thus enlightening their reproductive diversification. We documented a large number of lineage‐specific gene families enriched in salt stress, antifungal response, and disease resistance. Our comparative analysis further shows a genome‐wide expansion of genes encoding NBS‐LRR proteins in these two outcrossing wild species in contrast to six other selfing rice species. Conserved noncoding sequences (CNSs) in the two wild rice genomes rapidly evolve relative to selfing rice species, resulting in the reduction of genomic variation owing to shifts of mating systems. We find that numerous genes related to these rapidly evolving CNSs are enriched in reproductive structure development, flower development, and postembryonic development, which may associate with SI in O. rufipogon and O. longistaminata.
