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Summary: 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. [ABSTRACT FROM AUTHOR]

Medicago ruthenica has been recently cultivated as a new forage crop and has been recognized as a source of genes to improve abiotic stress tolerance in cultivated alfalfa because of its remarkable tolerance to drought, salinity‐alkalinity, and cold and snowy winters. Here, we reveal a chromosome‐scale genome sequence of M. ruthenica based on Illumina, PacBio, and Hi‐C data. The assembled genome consists of 903.56 Mb with 50,268 annotated protein‐coding genes, which is larger and contains relatively more genes than Medicago truncatula (420 Mb and 44,623 genes) and Medicago sativa spp. caerulea (793 Mb and 47,202 genes). All three species shared the ancestral Papilionoideae whole‐genome duplication event before their divergence. The more recent expansion of repetitive elements compared to that in the other two species was determined to have contributed greatly to the larger genome size of M. ruthenica. We further found that multiple gene and transcription factor families (e.g., SOS homologous genes, NAC, C2H2, and CAMTA) have expanded in M. ruthenica, which might have led to its enhanced tolerance to abiotic stress. In addition, M. ruthenica harbors more genes involved in the lignin and cellulose biosynthesis pathways than the other two species. Finally, population genomic analyses revealed two genetic lineages, reflecting the west and east of its geographical distribution, respectively. The two lineages probably diverged during the last glaciation and survived in multiple refugia at the last glacial maximum, followed by recent expansion. Our genomic data provide a genetic basis for further molecular breeding research on M. ruthenica and alfalfa. [ABSTRACT FROM AUTHOR]

Genome size varies greatly across the flowering plants and has played an important role in shaping their evolution. It has been reported that many factors correlate with the variation in genome size, but few studies have systematically explored this at the genomic level. Here, we scan genomic information for 74 species from 74 families in 38 orders covering the major groups of angiosperms (the taxonomic information was acquired from the latest Angiosperm Phylogeny Group (APG IV) system) to evaluate the correlation between genome size variation and different genome characteristics: polyploidization, different types of repeat sequence content, and the dynamics of long terminal repeat retrotransposons (LTRs). Surprisingly, we found that polyploidization shows no significant correlation with genome size, while LTR content demonstrates a significantly positive correlation. This may be due to genome instability after polyploidization, and since LTRs occupy most of the genome content, it may directly result in most of the genome variation. We found that the LTR insertion time is significantly negatively correlated with genome size, which may reflect the competition between insertion and deletion of LTRs in each genome, and that the old insertions are usually easy to recognize and eliminate. We also noticed that most of the LTR burst occurred within the last 3 million years, a timeframe consistent with the violent climate fluctuations in the Pleistocene. Our findings enhance our understanding of genome size evolution within angiosperms, and our methods offer immediate implications for corresponding research in other datasets. [ABSTRACT FROM AUTHOR]