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.