Genome of extreme halophyte Puccinellia tenuiflora
Genome of extreme halophyte Puccinellia tenuiflora
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DOI：
10.1186/s12864-020-6727-5
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发表时间：
2020-04-19
期刊：
影响因子：
4.4
通讯作者：
Yang, Chunwu
中科院分区：
文献类型：
--
作者：
Guo, Rui;Zhao, Long;Yang, Chunwu
研究背景星星草是一种牧草，具有较强的抗逆性，与禾本科植物亲缘关系密切，被认为是一种模式盐生植物。这种盐生植物对于提高我们对耐盐机制的理解具有巨大的价值。结果采用Illumina、PacBio和10x基因组技术相结合的策略，对2n=14的星星草基因组进行了测序和组装。我们生成了43.2x PacBio长读段、123.87x 10x基因组读段和312.6x Illumina读段。最终，我们组装了2638个支架，总大小为1.107 Gb，重叠群N50为117 kb，支架N50为950 kb。预测了39，725个蛋白质编码基因，鉴定了692个tRNAs、68个rRNAs、702个snRNAs、1376个microRNAs和691 Mb转座元件。本研究为提高植物的耐盐性提供了丰富的遗传资源，也为提高禾谷类作物的耐盐性和耐旱性提供了重要的理论依据。
BackgroundPuccinellia tenuiflora, a forage grass, is considered a model halophyte given its strong tolerance for multiple stress conditions and its close genetic relationship with cereals. This halophyte has enormous values for improving our understanding of salinity tolerance mechanisms. The genetic information of P. tenuiflora also is a potential resource that can be used for improving the salinity tolerance of cereals.ResultsHere, we sequenced and assembled the P. tenuiflora genome (2n=14) through the combined strategy of Illumina, PacBio, and 10x genomic technique. We generated 43.2x PacBio long reads, 123.87x10x genomic reads, and 312.6x Illumina reads. Finally, we assembled 2638 scaffolds with a total size of 1.107 Gb, contig N50 of 117kb, and scaffold N50 of 950kb. We predicted 39,725 protein-coding genes, and identified 692 tRNAs, 68 rRNAs, 702 snRNAs, 1376 microRNAs, and 691Mb transposable elements.ConclusionsWe deposited the genome sequence in NCBI and the Genome Warehouse in National Genomics Data Center. Our work may improve current understanding of plant salinity tolerance, and provides extensive genetic resources necessary for improving the salinity and drought tolerance of cereals.