The Spartina alterniflora genome sequence provides insights into the salt-tolerance mechanisms of exo-recretohalophytes
文献类型： 外文期刊
作者： Chen, Shoukun 1 ; Du, Tingting 1 ; Huang, Zhangping 1 ; He, Kunhui 1 ; Yang, Maogeng 1 ; Gao, Shang 1 ; Yu, Tingxi 1 ; Zhang, Hao 1 ; Li, Xiang 5 ; Chen, Shihua 4 ; Liu, Chun-Ming 1 ; Li, Huihui 1 ;
作者机构： 1.Chinese Acad Agr Sci CAAS, Inst Crop Sci, State Key Lab Crop Gene Resources & Breeding, Beijing, Peoples R China
2.CAAS, Nanfan Res Inst, Sanya, Hainan, Peoples R China
3.Hainan Seed Ind Lab, Sanya, Hainan, Peoples R China
4.Yantai Univ, Coll Life Sci, Key Lab Plant Mol & Dev Biol, Yantai, Shandong, Peoples R China
5.Chinese Acad Sci, State Key Lab Plant Genom, Beijing, Peoples R China
6.Chinese Acad Sci, Inst Genet & Dev Biol, Innovat Acad Seed Design, Natl Ctr Plant Gene Res, Beijing, Peoples R China
7.Chinese Acad Sci, Inst Bot, Key Lab Plant Mol Physiol, Beijing, Peoples R China
8.Univ Chinese Acad Sci, Coll Life Sci, Beijing, Peoples R China
9.Peking Univ, Sch Adv Agr Sci, Beijing, Peoples R China
关键词： Spartina alterniflora; genome; salinity adaptation; evolution; glutathione metabolism
期刊名称：PLANT BIOTECHNOLOGY JOURNAL （ 影响因子：13.8； 五年影响因子：13.2 ）
ISSN： 1467-7644
年卷期： 2024 年
页码：
收录情况： SCI
摘要： Spartina alterniflora is an exo-recretohalophyte Poaceae species that is able to grow well in seashore, but the genomic basis underlying its adaptation to salt tolerance remains unknown. Here, we report a high-quality, chromosome-level genome assembly of S. alterniflora constructed through PacBio HiFi sequencing, combined with high-throughput chromosome conformation capture (Hi-C) technology and Illumina-based transcriptomic analyses. The final 1.58 Gb genome assembly has a contig N50 size of 46.74 Mb. Phylogenetic analysis suggests that S. alterniflora diverged from Zoysia japonica approximately 21.72 million years ago (MYA). Moreover, whole-genome duplication (WGD) events in S. alterniflora appear to have expanded gene families and transcription factors relevant to salt tolerance and adaptation to saline environments. Comparative genomics analyses identified numerous species-specific genes, significantly expanded genes and positively selected genes that are enriched for 'ion transport' and 'response to salt stress'. RNA-seq analysis identified several ion transporter genes including the high-affinity K+ transporters (HKTs), SaHKT1;2, SaHKT1;3 and SaHKT1;8, and high copy number of Salt Overly Sensitive (SOS) up-regulated under high salt conditions, and the overexpression of SaHKT2;4 in Arabidopsis thaliana conferred salt tolerance to the plant, suggesting specialized roles for S. alterniflora to adapt to saline environments. Integrated metabolomics and transcriptomics analyses revealed that salt stress activate glutathione metabolism, with differential expressions of several genes such as gamma-ECS, GSH-S, GPX, GST and PCS in the glutathione metabolism. This study suggests several adaptive mechanisms that could contribute our understanding of evolutional basis of the halophyte.
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