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SCIENCE CHINA Life Sciences, https://doi.org/10.1007/s11427-020-1662-x

A high-quality genome sequence of alkaligrass provides insights into halophyte stress tolerance

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  • ReceivedJan 16, 2020
  • AcceptedMar 1, 2020
  • PublishedMar 12, 2020

Abstract

Alkaligrass (Puccinellia tenuiflora) is a monocotyledonous halophytic forage grass widely distributed in Northern China. It belongs to the Gramineae family and shares a close phylogenetic relationship with the cereal crops, wheat and barley. Here, we present a high-quality chromosome-level genome sequence of alkaligrass assembled from Illumina, PacBio and 10× Genomics reads combined with genome-wide chromosome conformation capture (Hi-C) data. The ~1.50 Gb assembled alkaligrass genome encodes 38,387 protein-coding genes, and 54.9% of the assembly are transposable elements, with long terminal repeats being the most abundant. Comparative genomic analysis coupled with stress-treated transcriptome profiling uncovers a set of unique saline- and alkaline-responsive genes in alkaligrass. The high-quality genome assembly and the identified stress related genes in alkaligrass provide an important resource for evolutionary genomic studies in Gramineae and facilitate further understanding of molecular mechanisms underlying stress tolerance in monocotyledonous halophytes. The alkaligrass genome data is freely available at http://xhhuanglab.cn/data/alkaligrass.html.


Funded by

grants from the National Key Research and Development Program of China(2018YFA090060)

the Foundation of Shanghai Science and Technology Committee(17391900600)

the Fund of Shanghai Engineering Research Center of Plant Germplasm Resources(17DZ2252700)

and the Natural Science Foundation of Heilongjiang Province(ZD2019C003)


Acknowledgment

The authors thank Dr. Zhangjun Fei from Cornell University for critical reading and editing of the manuscript. This work was supported by grants from the National Key Research and Development Program of China (2018YFA090060), the Foundation of Shanghai Science and Technology Committee (17391900600), the Fund of Shanghai Engineering Research Center of Plant Germplasm Resources (17DZ2252700), and the Natural Science Foundation of Heilongjiang Province (ZD2019C003).


Interest statement

The author(s) declare that they have no conflict of interest.


Supplement

SUPPORTING INFORMATION

Figure S1 Morphology of alkaligrass.

Figure S2 Genome size estimation in alkaligrass by flow cytometry.

Figure S3 Genome size estimation by K-mer analysis.

Figure S4 Hi-C map of the alkaligrass genome showing genome-wide chromatin interactions.

Figure S5 Integrated work-flow for the assembly of the alkaligrass genome.

Figure S6 Insertion time of (A) intact LTRs, (B) Copia/LTRs and (C) Gypsy/LTRs in seven BOP species.

Figure S7 Phylogenetic tree of the most expanded family (F-box/FBD/LRR-repeat protein) in alkaligrass.

Figure S8 Comparative genomic analysis.

Figure S9 Inter-genomic comparison of (A) alkaligrass vs. Triticum urartu (B) alkaligrass vs. Oryza sativa.

Table S1 Estimation of nuclear DNA amount in P. tenuiflora by flow cytometry

Table S2 Genome survey of alkaligrass

Table S3 Summary of the final genome assemblies of alkaligrass

Table S4 Length and gene number statistics for each chromosome

Table S5 Coverage statistics of alkaligrass genome

Table S6 Assessment of completeness of gene annotation using BUSCO

Table S7 Summary of repetitive sequence in the assembled alkaligrass genome

Table S8 LTR subclass ratio in whole genome sequences

Table S9 Assembly summary of alkaligrass genome

Table S10 Statistics of gene function annotation alkaligrass genome

Table S11 Statistics of synteny blocks within alkaligrass and other species

Table S12 Data statistics of samples used for RNA-seq

Supplemental file 1 Abbreviations of the protein names in the pathways in Figure 4C.

Supplemental file 2 FIMO analysis result of four FER promoter sequence.

Supplemental file 3 Primer sequences of the alkaligrass genes for qRT-PCR.

The supporting information is available online at http://life.scichina.com and https://link.springer.com. The supporting materials are published as submitted, without typesetting or editing. The responsibility for scientific accuracy and content remains entirely with the authors.


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  • Figure 1

    Landscape of the alkaligrass genome. Circos plot of the alkaligrass genome assembly. Circles from the outside inwards: (a) pseudochromosomes, (b) gene density, (c) LTR/Gypsy density, (d) LTR/Copia density, and (e) GC content. These density metrics were calculated with 1 Mb sliding windows. Genome syntenic blocks are illustrated with colored lines.

  • Figure 2

    Evolution of the alkaligrass genome. A, Phylogenetic tree of 12 species constructed based on 102 single-copy genes, with A. thaliana as the outgroup. Divergence times were estimated using the divergence time of monocot-dicot (140–150 Mya) as the calibration point. Blue bars on the nodes are the estimated range of divergence times (Mya). B, Distribution of synonymous substitution rates (Ks) among collinear paralogs in six BOP plants. C, Frequency distributions of Ks of collinear orthologs among four BOP plants (A. tauschii, T. urartu, H. vulgare, and O. sativa), one PACMAD plant (C. americanus) and alkaligrass.

  • Figure 3

    Comparative analysis of gene families in alkaligrass. A, Gene family expansions and contractions (left panel) and proportion of expanded/contracted/remained gene families in each plant species (pie charts). MRCA, most recent common ancestor. The right panel displays the distribution of single-copy, multiple-copy, unique and other orthologs. B, Gene ontology (GO) functional classification. “Expand” indicates GO term annotations of expanded genes. “Reference” indicates GO term annotations of all alkaligrass genes. C, Venn diagram showing the number of gene families shared among six Poaceae species.

  • Figure 4

    Salt-responsive genes and pathways in alkaligrass. A, Visualization of correlation matrix of root (R) and leaf (L) samples under the treatments of Na2CO3, NaHCO3, and NaCl for 0.5 h, 6 h and 7 d, based on gene expression profiles. B, Relative expression levels of PutANN1 and PutBIK in root and leaf under NaCl treatment evaluated by RT-qPCR analysis. C, Receptor-like kinase FER and FLS2 related pathways in roots were involved in salinity and alkali tolerance. Transcriptome profiling revealed that FER and HERK1, as well as their interacting protein encoding genes (LLG1, RALF1, LRX2, AGB1, and ROPGEF1) were induced by saline-alkaline. The downstream members (i.e., GTPROP5, ABI2, and SnRK2.2) in ABA signaling were also up-regulated under certain stress conditions. FLS2 and its related genes (EFR, BAK1, BIK1, SCD1, BSK1, and GRP7) were all up-regulated. In addition, genes encoding ROS-generated protein Rboh A/B/E/J, as well as the members of kinase signaling (MEKK1, MKK1/2/4/5, and MPK3/4), Ca2+ signaling (ANN1 and NORTIA), and transcription factors WRKY22/25/29 were conditionally up-regulated in response to saline-alkaline stress. D, Relative expression levels of PutMEKK and PutFLS2 in root under NaCl treatment. E, Expression profiles of four alkaligrass FER homologs in root under different treatments. R2 in B and D represents the correlation values between the real-time PCR and RNA-Seq data. See Supplemental file 1 in Supporting Information for gene abbreviations.

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