Achnatherum splendens Trin. (Gramineae) is a constructive species of the arid grassland ecosystem in Northwest China and is a major forage grass. It has good tolerance of salt and drought stress in alkaline habitats. Here, we report its chromosome-level genome, determined through a combination of Illumina HiSeq sequencing, PacBio sequencing and Hi-C technology. The final assembly of the ~1.17 Gb genome sequence had a super-scaffold N50 of 40.3 Mb. A total of 57 374 protein-coding genes were annotated, of which 54 426 (94.5%) genes have functional protein annotations. Approximately 735 Mb (62.37%) of the assembly were identified as repetitive elements, and among these, LTRs (40.53%) constitute the highest proportion, having made a major contribution to the expansion of genome size in A. splendens. Phylogenetic analysis revealed that A. splendens diverged from the Brachypodium distachyon–Hordeum vulgare–Aegilops tauschii subclade around 37 million years ago (Ma) and that a clade comprising these four species diverged from the Phyllostachys edulis clade ~47 Ma. Genomic synteny indicates that A. splendens underwent an additional species-specific whole-genome duplication (WGD) 18–20 Ma, which further promoted an increase in copies of numerous saline–alkali-related gene families in the A. splendens genome. By transcriptomic analysis, we further found that many of these duplicated genes from this extra WGD exhibited distinct functional divergence in response to salt stress. This WGD, therefore, contributed to the strong resistance to salt stress and widespread arid adaptation of A. splendens.

中文翻译：

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基因组序列提供了对碱性草原建群种芨芨草（禾本科）耐盐性的见解

芨芨草属芨芨草属Trin。禾本科（Gramineae）是我国西北干旱草原生态系统的建群种，是主要饲草。在碱性生境中具有良好的耐盐和干旱胁迫能力。在这里，我们报告了其染色体水平的基因组，通过 Illumina HiSeq 测序、PacBio 测序和 Hi-C 技术的组合确定。约 1.17 Gb 基因组序列的最终组装具有 40.3 Mb 的超级支架 N50。总共注释了57 374个蛋白质编码基因，其中54 426个（94.5%）基因具有功能蛋白质注释。大约735 Mb（62.37%）的组装被鉴定为重复元件，其中LTR（40.53%）所占比例最高，对芨芨草基因组大小的扩展做出了重大贡献。系统发育分析显示，A. splendens在大约 3700 万年前 (Ma)从Brachypodium distachyon – Hordeum vulgare – Aegilops tauschii分支中分化出来，并且由这四个物种组成的分支在 ~47 Ma 中从Phyllostachys edulis分支中分化出来。基因组同线性表明芨芨草经历了一次额外的物种特异性全基因组复制（WGD）18-20 Ma，这进一步促进了芨芨草基因组中众多与盐碱相关的基因家族的拷贝数增加。通过转录组分析，我们进一步发现来自额外 WGD 的许多重复基因在响应盐胁迫时表现出明显的功能差异。因此，这种WGD有助于芨芨草对盐胁迫的强大抵抗力和广泛的干旱适应。