Genome of extreme halophyte Puccinellia tenuiflora

Rui Guo,Kaijian Zhang,Dan Gao,Long Zhao,Chunwu Yang

doi:10.1186/s12864-020-6727-5

Abstract

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 10× genomic technique. We generated 43.2× PacBio long reads, 123.87× 10× genomic reads, and 312.6× Illumina reads. Finally, we assembled 2638 scaffolds with a total size of 1.107 Gb, contig N50 of 117 kb, and scaffold N50 of 950 kb. We predicted 39,725 protein-coding genes, and identified 692 tRNAs, 68 rRNAs, 702 snRNAs, 1376 microRNAs, and 691 Mb 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.

Highlights

Puccinellia tenuiflora, a forage grass, is considered a model halophyte given its strong tolerance for multiple stress conditions and its close genetic relationship with cereals
Most botanists believe that these salt-sensitive glycophytes may provide limited insights into mechanisms of salinity tolerance, and that extreme halophytes may have enormous values for improving our understanding of salinity tolerance mechanisms [4,5,6]
Our K-mer analysis showed that the genome size of extreme halophyte P. tenuiflora was 1.303 Gb (2n = 14) and the genome was complex, with 1.56% heterozygosity and 65.5% repeat content (Table 1)

Summary

Introduction

Puccinellia tenuiflora, a forage grass, is considered a model halophyte given its strong tolerance for multiple stress conditions and its close genetic relationship with cereals. Our K-mer analysis showed that the genome size of extreme halophyte P. tenuiflora was 1.303 Gb (2n = 14) and the genome was complex, with 1.56% heterozygosity and 65.5% repeat content (Table 1). We sequenced 56.12 Gb of PacBio long reads and 161.03 Gb of 10× genomics barcoded reads (Table 2).

Results

Conclusion