Introduction
Whole-genome duplication (WGD) or polyploidization has been suggested to
be prevalent throughout the evolutionary history of plants, acting as an
important evolutionary force promoting diversification, speciation, and
adaptation to new environments (Jiao et al., 2011; Levin, 1983; Soltis
& Soltis, 2016; Wood et al., 2009). Neofunctionalization or
subfunctionalization of duplicated genes post-WGD, as well as
species-specific gene retention and loss, lead to expansion and
contraction of gene families, resulting in the generation of
morphological and adaptive diversity (Force et al., 1999; Ren et al.,
2022; Van de Peer et al., 2017). However, the process of species
differentiation after ancient WGD is often accompanied by the occurrence
of genome rearrangement events, resulting in the generation of new genes
or changes in the expression and regulation mode of existing genes,
which may result in the emergence of new traits and promote speciation
(Estep et al., 2014; Hu et al., 2021). Based on the origin and level of
ploidy, polyploidy can be divided into two types, autopolyploidy and
allopolyploidy. The former involves duplication of the diploid genome in
a single species; whereas the latter is formed by a genomic combination
between two or more distant species (Soltis & Soltis, 2016; Stebbins,
1947). Although the relative proportion of the two types are comparable,
allopolyploids are generally expected to have higher evolutionary
advantages due to the pairing of chromosomes from each parent, which
often results in more chromosomal structural variations, novel gene
interactions, and morphological innovations (Soltis & Soltis, 2016;
Taylor & Larson, 2019). In general, polyploid plants exhibit greater
vigor, stronger resistance, wider environmental adaptability, and higher
biomass and economic yield than their diploid relatives (Barker et al.,
2016; Ding et al., 2018; Estep et al., 2014; Taylor & Larson, 2019).
However, the underlying genomic basis of ecological adaptation and
subsequent diversification remain poorly understood in most polyploid
species.
Chloridoideae, containing approximately 124 genera and 1,602 species, is
the fourth largest subfamily of the grass family (Gramineae; Soreng et
al., 2017). Most species of this subfamily use the C4 photosynthetic
pathway, and the first evolutionary transition from C3 to
C4 photosynthesis was found in this subfamily about 32–25 million years
ago (Ma; Christin et al. 2008). Species of this subfamily possess strong
tolerance to arid environments (Soreng et al. 2017), such asOropetium thomaeum and Cleistogenes songorica (VanBuren et
al., 2015; Zhang et al., 2021a). With a base chromosome number of x =
10, it is suggested that more than 90% of species within this subfamily
are polyploids, including the staple grain crop teff in Ethiopia and
many turfgrass and forage species (Roodt & Spies, 2003). Ancient WGD
events should have contributed to the stress tolerance, emergence of
valuable traits and diversification of these grasses (Roodt and Spies,
2003; Zhang et al., 2021a). Thus, this subfamily may serve as a valuable
system for investigating potential impacts of WGD, subsequent subgenome
divergence, functional innovations, genome rearrangement, and
diversification in polyploid plants. Recent advances in sequencing
technologies have facilitated genome assemblies for polyploid species.
To date, 16 reference genomes of this subfamily have been reported, 13
of which are polyploid. Five genomes were used for comparative
examination of desiccation tolerance and sensitivity (Chávez Montes et
al., 2021; Pardo et al., 2020). Whereas the rest mainly focused on the
genomes themselves and investigated the divergence between subgenomes or
the genomic basis of adaptation to extreme environments (e.g.,VanBuren et al., 2015; VanBuren et al., 2021; Wang et al., 2022; Zhang
et al., 2021a). Among these studies, however, few have focused
specifically on evolutionary divergence after polyploidization. Thus, a
comprehensive understanding of how subsequent speciation and
diversification occurs in these polyploid genomes remains unknown (Hu et
al., 2021).
We focus on a newly named subtribe, Orininae, belonging to the tribe
Cynodonteae, Chloridoideae (Peterson et al., 2016; Soreng et al., 2017).
This subtribe includes two genera, Orinus (3 species) andCleistogenes (17 species), which are often difficult to separate
morphologically. For example, Hao (1938) has treated one Orinusspecies, Orinus kokonorica (K.S. Hao) Tzvelev, as aCleistogenes . However, there are two distinct morphological
differences between the two genera. Cleistogenes has hidden
cleistogamous spikelets concealed within the upper sheaths, which is not
found in Orinus ; and Orinus has elongated rhizomes covered
with leathery and glossy scales, while Cleistogenes has a
cespitose
habit or very short rhizomes (Chen et al., 2006). Cleistogenes
songorica is an allotetraploid species (2n = 4x = 40) and possesses a
genomic basis for its dimorphic flower differentiation and drought
adaptation (Zhang et al., 2021a). Our karyotyping also revealed a
chromosome number of 40 for O. kokonorica (Figure 1A), indicating
that this species is a tetraploid plant. However, there is no reference
genome for Orinus , which significantly limits our understanding
of its evolutionary history and genomic divergence between these two
genera. Here, we selected O. kokonorica as a case study and
performed comparative genomics between O. kokonorica and C.
songorica to investigate genomic basis of adaptive evolution and
diversification after polyploidization.
Orinus kokonorica is mainly distributed in the northeastern
Qinghai-Tibet Plateau (QTP) at elevations between 2400 and 4200 m (Su et
al., 2015), whereas C. songorica widely occurs in semi-arid and
desert areas in central Asia at relatively low altitude (Chen et al.,
2006). Both species are important forage resources with good
palatability and high nutritious value for local livestock in arid
regions. The two species display differences mainly in flower and
rhizome morphology and in altitudinal distributions. In addition, with
elongated rhizomes, O. kokonorica has developed a strong
underground root system (Figure 1A), which helps to improve sand
fixation and water conservation in arid areas. In this study, we first
performed genome assembly and RNA-seq-based transcriptomics under
different stress treatments for O. kokonorica . Then, using
publicly available genomic and transcriptomic data for C.
songorica , we conducted comparative genomic and transcriptomic analyses
to elucidate the evolutionary history of the two species and the genomic
basis of their subsequent divergence.