Deciphering the suaeda glauca genome: A leap towards understanding and combating soil salinity in agriculture
image: Genome size estimation and de novo genome assembly of S. glauca.
Credit: Horticulture Research
Soil salinity poses a growing threat to global agriculture, with significant land areas becoming increasingly saline. Suaeda glauca is a highly salt-tolerant halophyte with a unique ability to absorb and retain salt, particularly in the leaves, a mechanism distinct from other halophytes. While recent studies have explored various salt tolerance strategies in plants, the specific mechanisms underlying S. glauca's resilience, especially in maintaining chromosome stability under salt stress, remain unclear. Unraveling S. glauca's genome could reveal these unique adaptations and provide insights into the developing salt-resistant crops, a crucial step towards mitigating the impact of soil salinity on agriculture.
In August 2023, Horticulture Research published a research entitled by “Chromosome-scale genome sequence of Suaeda glauca sheds light on salt stress tolerance in halophytes ”.
In this study, de novo sequencing of the S. glauca genome was performed, utilizing the HiSeq 2500 PE150 platform and PacBio RSII platform, along with high-throughput chromatin conformation capture (Hi-C) for chromosome mapping. The genome, with a size of 1.02 Gb, contains 54,761 annotated genes and is marked by high heterozygosity and a significant presence of repeat sequences (70.56%). The genome analysis revealed strong synteny with Beta vulgaris and an allele-aware assembly approach was used to investigate genome-wide allele-specific expression, uncovering the role of promoter sequence diversity in consistent allele-specific expression.
Systematic analysis of the ABCE gene family reveals the formation of flower morphology, linking the dysfunction of A-class genes to the absence of petals in S. glauca. S. glauca and S. aralocaspica co-expanded gene families were significantly enriched in GO terms related to DNA repair, chromosome stability, and various other pathways, crucial for the plant's adaptation to saline environments. Transcriptome analysis under salt treatments provided detailed insights into S. glauca's salt tolerance mechanisms, particularly the upregulation of genes associated with DNA repair, chromosome stability, lipid biosynthetic processes and soprenoid metabolic processes in leaves. Furthermore, the study identified a significant expansion of the FAR1 gene family in S. glauca, although its exact role in salt tolerance remains to be explored.
Overall, the research effectively combined various sequencing technologies and analytical methods to decode the genome of S. glauca, offering valuable insights into its unique adaptations and potential applications in developing salt-tolerant crops. The findings underscore the importance of genome analysis in understanding plant adaptability and the evolutionary mechanisms underlying stress tolerance.
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References
Authors
Yan Cheng1,2,3, Jin Sun1,2,4, Mengwei Jiang1, Ziqiang Luo1, Yu Wang4, Yanhui Liu1,4, Weiming Li1, Bing Hu1,2, Chunxing Dong1,4, Kangzhuo Ye1,2, Zixian Li1,2, Fang Deng1, Lulu Wang1, Ling Cao1,3, Shijiang Cao5, Chenglang Pan6, Ping Zheng1,2, Sheng Wang3, Mohammad Aslam1,2, Hong Wang3 and Yuan Qin 1,2,*
Affiliations
1State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
2Pingtan Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350400, China
3Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
4College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
5College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
6Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
About Yuan Qin
She is currently a Professor Research at Pingtan Institute of Science and Technology, Fujian Agriculture and Forestry University. Yuan Qin’s lab focuses on the molecular control of ovule development, with an emphasis on the control of determination of the commitment of somatic cell to germline fates and the role of cell-cell communications during the ovule developmental events.