Triticeae, an economically important tribe in the Poaceae family, includes three major cereals (wheat, Triticum aestivum; barley, Hordeum vulgare; rye, Secale cereale) and other agronomically important forage grasses (Löve, 1984; Wang and Lu, 2014). It is an excellent model group for studying taxonomy, cytogenetics, functional genomics, evolution, and speciation (Lu and Ellstrand, 2014; Al-Saghir, 2016). Approximately 69% of Triticeae species are polyploids and the other 31% are diploids (Eilam et al., 2007). The diploid Triticeae species often have a basic chromosome number of 7, and these chromosomes are proposed to have evolved from 12 protochromosomes of the ancestral grass genome after the ρ whole genome duplication event (Murat et al., 2017). Triticeae genomes are often very complex and large (e.g., rye, ∼8.0 Gb; barley and diploid einkorn wheat, ∼5.0 Gb; tetraploid emmer, >10 Gb; hexaploid wheat, ∼16 Gb), and more than 80% of each genome is composed of repetitive DNA sequences (Avni et al., 2017; Mascher et al., 2017; Appels et al., 2018; Ling et al., 2018; Maccaferri et al., 2019; Li et al., 2021; Rabanus-Wallace et al., 2021; Wang et al., 2022; Yang et al., 2023).

Chromosomal rearrangements (CRs) are known to cause genetic and epigenetic changes that can drive phenotypic variation and ecological diversity (Soltis et al., 2015; Wendel et al., 2016; Van de Peer et al., 2017; Alonge et al., 2020; Guo et al., 2020; Liu et al., 2020). The 1BL/1RS translocation took place during wheat breeding and led to substantial improvements of agronomic traits (Friebe et al., 1996; Kim et al., 2004; Zhao et al., 2012). The 7E1/7DL translocation event transferred the leaf rust resistance locus Lr19 to wheat (T. aestivum) from its relative Thinopyrum ponticum (Knott and Sharma 1966). The Pm21, an effective gene for powdery mildew resistance, was transferred from Haynaldia villosa into common wheat by the 6VS/6AL translocation (Chen et al., 1995). Several major CRs have been identified in Triticeae species using chromosome pairing, comparative genetic mapping, and comparative genomics. For example, CRs involving chromosomes 4, 5, and 7 have been found in wheat, rye, and Aegilops tauschii accession AY61 (Devos et al., 1993, 1995; Ma et al., 2013; Martis et al., 2013; Murat et al., 2014; Dvorak et al., 2018; Ruban and Badaeva, 2018; Walkowiak et al., 2020; Li et al., 2021; Zhou et al., 2021). However, the order of occurrence, timing, and breakpoints of these CRs remain ambiguous.

The 4L/5L reciprocal translocation (RT) has been found in several Triticeae species based on low-resolution genetic maps (Devos et al., 1993, 1995; King et al., 1994). This RT is proposed to have originated in the common ancestor of wheat and rye because they seem to share identical or similar breakpoints (Devos et al., 1993; Martis et al., 2013). However, this hypothesis contradicts the fact that many species in this clade, such as Thinopyrum elongatum and Ae. tauschii, do not have the 4L/5L translocation (King et al., 1994; Li et al., 2016; Chen et al., 2020; Wang et al., 2020; Zhou et al., 2021). Moreover, investigations using the recently available genome survey data for rye showed that the 5L breakpoint in rye is different from those in wheat (Li et al., 2016). An independent origin of the 4L/5L RT in Triticeae species has therefore been proposed in previous studies (Devos et al., 1995; Li et al., 2016).

In wheat, structural variations associated with the 4AL/7BS translocation event also remain uncertain. Based on chromosome pairing and other molecular and biochemical markers, it is generally accepted that a reciprocal translocation of 4AL/7BS occurred in tetraploid wheat (Anderson et al., 1992; Liu et al., 1992; Devos et al., 1995; Nelson et al., 1995). However, after genome sequencing of T. urartu, several studies suggested that the 4AL/7BS translocation was unidirectional from 7BS to 4AL. This is due to the absence of syntenic blocks between the T. urartu chromosome 4AL and the chromosome 7BS of the common wheat cultivar Chinese Spring (CS) (Ling et al., 2018; Chen et al., 2020). In addition, several CRs have caused the current compositions of chromosome 4A in different species and cultivars to be diversified and remain ambiguous (Devos et al., 1995; Miftahudin et al., 2004; Hernandez et al., 2012; Ma et al., 2013, 2014; Jorgensen et al., 2017; Dvorak et al., 2018). These uncertainties are largely due to prior studies conducting independent self-genomic comparisons or investigating a relatively small number of reference species. However, all modern species have evolved independently after speciation, and many species- or lineage-specific genomic variations/rearrangements may have occurred since. Therefore, to fully understand the CR history of Triticeae, it is necessary to systematically investigate structural variations and their high-resolution coordinates and carefully reconstruct the ancestral genomic state following the diversification of Triticeae.

Reconstruction of an ancestral genome facilitates the identification of genomic changes that specifically occurred at phylogenetic nodes, and can effectively distinguish between ancient and lineage-specific structural variations (Salse, 2012; Wang et al., 2015, 2017; Kim et al., 2017; Murat et al., 2017; Wu et al., 2017; Raymond et al., 2018; Perumal et al., 2020; He et al., 2021). For instance, the ancestral genome reconstruction for extant angiosperms, monocots, and eudicots led to the identification of 15 protochromosomes in the common ancestor of angiosperms, 10 fusions prior to the diversification of monocots, and 8 fusions before the diversification of eudicots (Murat et al., 2017). Recently, several high-quality Triticeae genomes have been assembled, including rye, barley, Th. elongatum, Ae. tauschii, T. urartu, and many polyploid wheats (Avni et al., 2017; Luo et al., 2017; Mascher et al., 2017, 2021; Zhao et al., 2017; Appels et al., 2018; Ling et al., 2018; Maccaferri et al., 2019; Monat et al., 2019; Walkowiak et al., 2020; Wang et al., 2020; Li et al., 2021, 2022; Rabanus-Wallace et al., 2021; Zhou et al., 2021; Navrátilová et al., 2022). These Triticeae genomes enabled us to employ ancestral genome reconstruction to investigate structural evolution following the origin and diversification of Triticeae and to clarify the structural uncertainties that presently exist. Construction of these ancestral genomes also provides a valuable resource for future identification and pinpointing of structural variations in other wheat species or cultivars.