4.1 | Characterization of the reference genome ofPse. libanotica
In this study, we utilized assemble a highly contiguous reference genome sequence for Pse. libanotica with 2.99 Gb in size, by using Illumina sequencing, nanopore-based next-generation sequencing and chromosome-scale scaffolding by Hi-C. The St genome is smaller than other diploid Triticeae species reported at present, such as the D genome (4.3 Gb) of A. tauschii (Luo et al., 2017), the E genome (4.78 Gb) of Th. elongata (Wang et al., 2020), the R genome (7.74 Gb) of S. cereale (Li et al., 2021). Repeat sequences comprise 71.62% of the assembled Pse. libanotica genome which is lower than other Triticeae (with 80%~90% repeats in reported Triticeae species genome) even though it displayed no composition difference (Wang et al., 2022).
From a standpoint of germplasm innovation for breeding, clarifying the genome relationships in Triticeae can provide some useful strategies for obtaining the germplasm with the high level genetic diversity and fitness by artificial hybridization (Chen et al., 2020). In this study, we found that the St genome closely related to the A, B, and D genomes of wheat, offering the potential to transfer gene(s) from St genome to wheat. Furthermore, we observed that T. aestivum 4A was syntenic to Pse. libanotica chromosome 4St, 5St, and 7St, andT. urartu 4A was syntenic to Pse. libanotica chromosome 4St and 5St., which were related to the most significant overall re-arrangement of chromosome 4A in wheat (Devos et al., 1995; Miftahudin et al., 2004).
The St genome combines with other basic genomes and involve more than 60% perennial Triticeae speciation. Those St-containing species are excellent forages for feeding livestock and contain abundant resistant genes for crop breeding and improvement. The Pse. libanotica is an often-cross-pollination plant, the estimated genome size with 1.34% heterozygous. Cytogenetic researches revealed that 5St and 7St displayed high-level genetic heterogeneity among seven Pse. libanoticapopulations (Wu et al., 2022). The high genomic heterozygosity could frequently occur from open pollination plants, which not only spurs the establishment of fitness and abundant genetic diversity, but also contributes to the genetic advantage in terms of the richness of their polyploid offspring species in Triticeae. Many natural hybrids between various St-containing polyploid species have been reported (Zeng et al., 2012; Lu et al., 2019; Chen et al., 2022; Wu et al., 2023), further enlarging the richness of St-containing descendants.
The St genomic analysis revealed that unique gene families and expanded families displayed enrichment in cutin, suberine, and wax biosynthesis. Morphologically, the aerial parts of Pse. libanotica is covered by cuticular wax (Yen & Yang, 2011). It has been reported that plant cuticular wax, which acts as the first barrier against environmental threats, consistently serves a critical role in restricting nonstomatal water loss which were often related to drought resistance (Seo et al., 2011; Zhu & Xiong, 2013; Li et al., 2019; Lewandowska et al., 2020; Lee & Suh, 2022). Back to the origin of genus Pseudoroegneria , it diverged about 10.7 Mya during the middle and late Miocene. During that stage, the ice sheet growth, and the Tethyan Seaway went through gradually to completely closure leading to the low temperature and water deficit in Iranian Plateau (Sun et al., 2021). Thus, it is reasonable to speculated thatPse. libanotica diverged at during middle and late Miocene in Tran might develop cuticular wax resistance to cold and drought environment.