Phylogeny and taxonomy of the polyploidy species that contains St genome (Triticeae; Poaceae) based on four nuclear DNA and three chloroplast genes

doi:10.21203/rs.3.rs-4927682/v1

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Research Article

Phylogeny and taxonomy of the polyploidy species that contains St genome (Triticeae; Poaceae) based on four nuclear DNA and three chloroplast genes

https://doi.org/10.21203/rs.3.rs-4927682/v1

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Background

The genus Pseudoroegneria (Nevski) Á. Löve with the St genome accounts for more than 60% of perennial Triticeae speciation. However, the strong dominant character of the St genome results in challenging to distinguish each species even genus based on single or combined morphological traits, the phylogeny and taxonomy of the St-containing polyploid genera remain under controversy.

Results

In this study, we used nuclear and chloroplast DNA-based phylogenetic analyses to reveal the systematic relationships of the St-containing polyploidy species. The maximum likelihood (ML) tree based on nuclear ribosomal internal transcribed spacer region (nrITS) and three single-copy nuclear genes data (Acc1 + Pgk1 + DMC1) showed that St-containing polyploid species were separated into StStHH, StStYY, StStYYHH, StStYYPP, StStYYWW, StStPP, and StStEE genome types and polyploidy species in Caucasus, America and Australia have unique polyploidization events. The ML tree for the chloroplast DNA fragments (matK + rbcL + trnL-trnF) displayed that the P genome serves as a maternal donor of Kengyilia melanthera and K. dingqinensis from the Hengduan Mountains region, while the St or StY genome serves as the maternal donor of other St genome containing species. Herein, we reported the genome constitution of Kengyilia tibetica, K. changduensis, and K. dingqinensis with the StStYYPP genome for the first time.

Conclusions

The St-containing polyploid species should be treated as distinct genera according to different genome constitutions, St-containing polyploid species experienced independent allopolyploidization events in different distribution regions and the St-containing polyploid species had two relatively independent maternal origins from the P genome or St/StYgenome. Besides, the Xp genome may have contributed to the unknown Y genome formation.

St genome

polyploidy

Single–copy nuclear genes

nrITS

Chloroplast gene

Phylogeny

Molecular evolution

Triticeae Dumort includes economically important annual crops (such as wheat, barley, and rye) and crucial forage grasses (such as Elymus sibiricus L., Agropyron cristatum (L.) Gaertn., Leymus secalinus (Georgi) Tzvelev, etc.).

In Triticeae, 24 major basic genomes donated by diploid species have been designated (e.g.: A, S, D, Ns, Xm, E, St, Y, H, P, W), in various combinations (e.g.: AB, ABD, NsXm, StE, StH, StY, StYH, StYP, StEP, StYW, and StHNsXm) via hybridization constitute polyploids, which account for circa 75% of the Triticeae species [1–3]. Based on the taxonomic treatment of Löve, species with the same genome or same genome combinations were classified into one genus [1]. However, a large number of species, wide distribution, and complex and diverse habitats, lead to huge morphological variation, on the other hand, similar within and between genera.

Polyploidization, which involves the multiplication of genes and genomes, is intricately linked to the geographic distribution of plant species and the timing of their differentiation, and this process plays a crucial role in shaping plant evolution and speciation [4–5]. During the Miocene epoch, spanning from 23.8 to 5.3 million years ago, the climate in East-Central Asia transformed, embracing distinct seasonal patterns characterized by cold winters and hot summers, this climatic shift fostered the proliferation of diverse ecosystems, thereby unlocking new ecological niches [6]. The radiation of the Triticeae is presumed to have potentially been instigated by the climatic shifts during the late Miocene era [7]. After entering the 1.0–0.01 MYA, during the Pleistocene and Holocene epochs, due to multiple glacial and interglacial cycles, a large number of allopolyploidization phenomena occurred during this period, [8–11]. This has also led to the current distribution pattern of Triticeae, mainly distributed in temperate and cold regions [1].

The St was designed as the genome symbol of a perennial Triticeae genus Pseudoroegneria (Nevski) Á Löve [1]. It is diverged from the Triticeae tribe 14.4–14.7 million years ago (Myr), and earlier than the Triticum/Aegilops group (8.0–8.3 Myr) [12]. Diploid Pseudoroegneria species combined with other basic genomes usually serve as maternal donors during polyploidization [13]. The St-containing species, consisting of more than half of Triticeae species, are widely distributed in the Middle East and East-Central Asia, Ciscaucasica, North America, and even Australia has the existence of St-containing species [1, 14]. Most of the St-containing species are predominately cool-season grasses, and resistant to biotic (rust, powdery mildew, Fusarium head blight, etc.) and abiotic (drought, chilling, saline-alkali, etc.) stress, making them highly desirable for plant breeders [15–20].

The St-containing species display similarity in morphology characters regarding continued and minor differences in the palea and lemma, which lead to difficulty in the classification of species based on morphology [21–23]. Some taxonomists classified all St-containing species into one genus Elymus sensu lato. Later, cytogenetic research proved that St-containing species include diploid, tetraploid, hexaploid, and octaploid plants. According to the taxonomic treatment of Löve [1], St-containing species were classified as Pseudoroegneria (Nevski) Á. Löve (with StSt genome), Elymus L. sensu stricto (Elymus s.s., with StStHH genome), Roegneria C.Koch (StStYY), Campeiostachys Drobov (StStYYHH), Kengyilia C.Yen & J.L.Yang (StStYYPP), Anthosachne Steudel (StStYYWW), Douglasdeweya C.Yen, J.L.Yang & B.R.Baum (StStPP), Trichopyrum Á. Löve (StStEE) [3, 24–30]. Combined with morphology traits and cytogenetics results researchers classified the species of a new plant in the last century. Due to the extensive ecological distribution and during long times of reticulate evolution, the genomic constitution and taxonomic status of the new discovery species need more careful identification.

In this study, we collected three new Kengyilia species (Kengyilia tibetica Y. H. Zhou, C. B. Zhang, D. D. Wu & X. Y. Pan, Kengyilia changduensis Y. H. Zhou, C. B. Zhang, D. D. Wu & X. Y. Pan, and Kengyilia dingqinensis Y. H. Zhou, C. B. Zhang, D. D. Wu & X. Y. Pan) from Qamdo of Tibet Province in China and were classified primary according to morphology, such as a stunted apical spikelet, hairy lemma, and the glume has distinct ridges. However, they differed from each other and we described them as follows: Kengyilia tibetica and Kengyilia changduensis were similar to Kengyilia laxiflora (Keng) J.L.Yang, C.Yen et B.R.Baum in slightly curved spike, sparse spikelets, and Kengyilia dingqinensis is similar to Kengyilia hirsuta (Keng) J. L. Yang, C. Yen et B. R. Baum in spikelet densely upper and sparsely lower, and lemma has long awn. Whereas, in comparison to Kengyilia laxiflora, Kengyilia tibetica glume has 6mm awns, Kengyilia changduensis had 1-2mm awns, and Kengyilia laxiflora has no awns, and compared with Kengyilia hirsuta, Kengyilia dingqinensis lemma puberulent, glume has hair and awns, and awns are longer. Besides, Kengyilia laxiflora and Kengyilia hirsuta have not been found in Qamdo City, Tibet [30]. Thus, we speculate that these three materials are new species and need more molecular proof.

Molecular phylogenetic trees based on several genes or intergenic regions are widely applied to infer the evolutionary history and predict the phylogenetic relationships between species or genera [31–33]. Single- or low-copy nuclear genes, such as acetyl-CoA carboxylase (Acc1), disrupted meiotic cDNA 1 (DMC1) and phosphoglycerate kinase (Pgk1) genes, which are less susceptible to concerted evolution, can potentially serve as useful markers for phylogenetic reconstruction for polyploids, have been used to examine phylogenetic relationships, hybridization events and the donor species of different genomes [33–36]. Noncoding DNA sequences such as nuclear internal transcribed spacer (nrITS) DNA sequences, which have a faster rate of mutation, have been used to study phylogenetic and genomic relationships at lower taxonomic levels [32, 37–39]. The chloroplast DNA (cpDNA) sequences, including coding and non–coding regions such as the rbcL gene, matK gene, and the intron of the intergenic spacer of trnL-trnF, due to its maternally inherited characteristics, are also valuable sources of markers for identifying the maternal donors of polyploids with additional capacity to reveal phylogenetic relationships of related species [31–32, 36, 40]. In previous studies, these sequences have been used to study the status of genus and species levels to identify genome donors, demonstrate hybridization events or introgression, and reveal the evolutionary history and origin of its species [41–43]. Multigene conjoint analyses are often preferred, as their phylogenetic signal quality tends to be more accurate. In addition, phylogenetic reconstruction from rapidly and slowly evolving genes may reduce incongruence and resolve relationships at different levels in phylogeny [12].

In this study, we analyzed 32 diploid species with St, P, W, V, K, O, R, Q, H, I, E, Xp mono genome, and 46 allotetraploids containing St genome based on the conjoint analyses of three single-copy nuclear genes (Acc1, DMC1, and Pgk1), one nrDNA ITS, and the combined chloroplast sequences (matK, rbcL, and trnL-trnF). We aim to: (1) discuss the phylogeny and taxonomy status of Triticeae polyploid species that contain the St genome; (2) investigate the origin of species of Triticeae polyploid species that contain St genome; (3) explore the possible origin of the Y genome in Triticeae, and (4) clarify the genomic constitution of three newly Kengyilia species, Kengyilia tibetica, Kengyilia changduensis, and Kengyilia dingqinensis.

Phylogenetic analyses of Acc1 + Pgk1 + DMC1 sequences

To discuss the taxonomic status of the St-containing species, we constructed the ML tree based on the combined Acc1 + Pgk1 + DMC1 sequences using TVM + I + G model (Fig. 1). The assumed nucleotide frequencies were A: 0.2496; C: 0.2016; G: 0.2096; T: 0.3392, the proportion of invariable sites and gamma shape parameter were equaled to none and 0.6470, respectively. We obtained St, Y, E, H, and P haplotypes from St-containing species based on Acc1 + Pgk1 + DMC1 conjoint data (Fig. 1). The St clade included the St genome diploid Pseudoroegneria spp. and St-containing polyploid genera, such as tetraploid Elymus s.s. (StStHH genome), tetraploid Roegneria (StStYY genome), Douglasdeweya (StStPP genome), hexaploid Campeiostachys (StStYYHH genome), hexaploid Kengyilia (StStYYPP genome), hexaploid Anthosachne (StStYYWW genome), and hexaploid Trichopyrum (StStEEEE genome). The H clade consisted of three diploid Hordeum L. (HH/II genome) and the H-containing polyploid Elymus s.s. and Campeiostachys. The P clade contained P genome diploid Agropyron (PP genome), P-containing polyploid Douglasdeweya (StStPP genome), and Kengyilia (StStYYPP genome), including Eremopyrum (Ledeb.) Jaub. & Spach species (XeXe/FF genome). There was no W clade according to the conjoint Acc1 + Pgk1 + DMC1 sequences tree, but single gene Acc1 and Pgk1 trees displayed clear W clade (Figure S1-S3). Trichopyrum intermedium (Host) Barkworth & D.R.Dewey (StStEEEE genome) was clustered with diploid Lophopyrum bassarabicum (Savul. & Rayss) C. Yen & J. L. Yang (E^bE^b genome).

In summary, our results clearly show that the genus Elymus s.s contained St and H sub-genomes, Roegneria contained St and Y sub-genomes; Campeiostachys contained St, Y, and H sub-genomes; Kengyilia contained St, Y, and P sub-genomes included three Kengyilia species Kengyilia tibetica, K. changduensis, and K. dingqinensis; Anthosachne contained St, Y, and W sub-genomes; Douglasdeweya contained St and P sub-genomes, and Trichopyrum intermedium contained St and two-copy E sub-genomes.

Phylogenetic analyses of matK + rbcL + TrnL-F sequences

To further investigate the maternal donor of the St-containing species, we constructed the ML tree based on the conjoint of the chloroplast matK + rbcL + TrnL-F sequence data using the best-fit model TPM3uf + I + G (Fig. 2). The assumed nucleotide frequencies were A: 0.3100; C: 0.1716; G: 0.1665; T: 0.3519, the gamma shape parameter equals to 0.4130. The result showed that the chloroplast DNA sequences of St-containing species were split into two clades. The clade I included Pseudoroegneria species with the St genome, Lophopyrum elongatum and Lophopyrum bessarabicum with E genome, Dasypyrum villosum (K. Koch) Nevski with the V genome, and other polyploid forty-one species with the St subgenome. The clade II consisted of the diploid Agropyron cristatus (L.) Gaertn and Agropyron mongolicum Keng with the P genome, Eremopyrum triticeum (Gaertn.) Nevski with the Xe genome, Eremopyrum distans (K. Koch) Nevski with the F genome, and two polyploid Kengyilia melanthera (Keng) J. L. Yang, C. Yen & B. R. Baum and Kengyilia dingqinensis with the P subgenome. Thus, Kengyilia melanthera and Kengyilia dingqinensis showed different maternal donors compared with other St-containing species in this study.

Phylogenetic analyses of nrITS sequences

To explore the species differentiation characteristics of St-containing species, we performed a phylogenetic analysis of the nrITS sequences using the SYM + G4 model (Fig. 3). The nrITS data yielded a single phylogenetic tree, the proportion of invariable sites equals to none, gamma shape parameter = 0.5253. We obtained three clades (clade I-III) of nrITS sequences from St-containing species in this research. The clade I included diploid Pseudoroegneria with the St genome, and polyploids with the St subgenome, such as Elymus s.s. (StStHH), Roegneria (StStYY), Campeiostachys (StStYYHH), Kengyilia (StStYYPP), Anthosachne (StStYYWW), and Trichopyrum (StStEE/StStEEEE), diploid Lophopyrum elongatum and Lophopyrum bessarabicum with the E genome, and Dasypyrum villosum (K. Koch) Nevski with the V genome. The clade II consisted of the diploid Hordeum bogdanii Wilensky with the H genome, polyploid Elymus s.s., and Campeiostachys. The clade III was grouped by diploid Agropyron cristatus (L.) Gaertn with the P genome, Douglasdeweya (StStPP), polyploid species in genera Kengyilia (StStYYPP) and three new Kengyilia species. It is worth noting that the clade I was divided into three subclades (subclade I-III). Subclades I and III were the St clades. The diploid St genome species Pseudoroegneria strigosa (M. Bieb.) and Pseudoroegneria libanotica (Hackel) D. R. Dewey, distributed in Central Asia and the Middle East, were grouped in the subclade III. The subclade I contained diploid St genome species Pseudoroegneria stipifolia (Czern. ex Nevski), Pseudoroegneria spicata (Pursh) Á. Löve, dispersed in the Caucasus and North America regions respectively), and all autotetraploid Pseudoroegneria species located in Central Asia (Fig. 4).

Phylogenetic relationships among the polyploidy species that contain the St genome

The St-genome species consists of a large number of allopolyploids which are widely distributed and include some endemic species [13]. The dominant effect of the St genome makes abundant St-containing polyploid species that share similar morphological characteristics, such as tufted plants, similar spikelets, lemma lanceolate-oblong, and five‐seven veined [2, 22, 44]. Morphology similarity and different genome constitutions lead to the difficulty in the classification of St-containing species. In this study, conjoint analyses of Acc1 + Pgk1 + DMC1, matK + rbcL + trnL-trnF, and nrITS sequences collected from a wide range of St-containing polyploid species and basic diploid genera to shed light on their phylogenetic relationships, ancestral donors and the polyploidization events in the speciation processes based on orthologous comparison. The Elymus s.s., Roegneria, Campeiostachys, Kengyilia, Anthosachne, Douglasdeweya, and Trichopyrum species contained StH, StY, StYH, StYP, StYW, StP, and StE genome symbols and should be treated as independent genera according to different genome constitution [20, 23–24].

Geography and maternal origins of the St-containing polyploid species

Previously, cytogenetical studies reveal that diploid Pseudoroegneria, Hordeum, Australopyrum, Agropyron, and Lophopyrum species have been served as the St, H, W, P, and E genome donors, respectively, during the polyploid speciation of St-containing polyploid species [36, 45]. It is interesting to discriminate which type are the origin and parental genome donors of those polyploid species since the diploid donors displayed multiple species and abundant genetic diversity among ecological types. In the present study, conjoint analysis of nuclear gene fragment Acc1, DMC1, and Pgk1 and chloroplast matK, rbcL, and TrnL-F sequence datasets revealed that genome donors of the St and H genomes and maternal donors of Kengyilia in St-containing polyploidy species have different origins and are associated with geographical distribution.

In this study, the St-containing polyploid species distributed in North America and Eurasia were clustered with sympatric diploid St genome donor Pseudoroegneria species respectively based on the AccI and nrITS, indicating the geographically different origins. The result is similar to the research proposed by Sun et al. [46] that Elymus s.s. species distributed in Eurasian and American have independent origins. Previous studies have suggested that species exchange between the Eurasian and the Americas is related to the formation of the Pleistocene Bering Strait land bridge, and during this period recurrent cycles of glaciation caused sea levels to fall by 100-135m and resulted in the reformed of the Bering Strait land bridge, it promoted the spread of species between the Eurasian and American, and formation of numerous polyploids in the Triticeae were occurred during this period based on previous studies by molecular clocks [12, 47–50]. The same situation also exists in Asia and Australia terrestrial connections, due to geological activity, leading to species exchange, and all of Anthosachne species were clustered together in the subclade I [51]. Therefore, we speculate that during the Pleistocene period, ancestors of diploid St genome species migrated from the Eurasian continent across the Bering Strait land bridge to North America, hybridized with the local H genome species through allopolyploidization, and subsequently formed the Elymus s.s. species in North America and species with the StY genome may spread to Australia through allopolyploidy hybridization with the W genome species to form the Anthosachne species (Fig. 5). The above evidence indicates that St-containing polyploid species have undergone independent heteropolyploidy hybridization events, resulting in different St genome origins of different St-containing polyploidy species.

According to the results of matK + rbcL + TrnL-F, except for Kengyilia melanthera and Kengyilia changduensis, St-containing species were clustered together in the St clade indicating the maternal donor was St and/or StY genome. As standpoint by Chen et al. [13], the diploid Pseudoroegneria species is the maternal donor of the allo-tetraploid species in the genera Elymus s.s., Roegneria, Douglasdeweya, and Trichopyrum, subsequently, the tetraploid Roegneria species with StY genome are served as the maternal donors of the allo-hexaploidy species in genera Campeiostachys, Anthosachne, and part of Kengyilia respectively, through the second hybridization and whole genome duplication events. Previous analysis revealed that the diploid species in genus Agropyron with P genome served as the maternal donor of Kengyilia melanthera with StYP genome, collected in the western Sichuan, in the Hengduan Mountains region [52]. In the research, we presented that Kengyilia dingqinensis, collected in the Qamdo, also in the Hengduan Mountains region, also took the P genome as the Kengyilia maternal donor, which differed from other species in Kengyilia. Therefore, except for the St genome, the P genome also served as a maternal donor during Kengyilia speciation, and interestingly, those species are distributed in the Hengduan Mountains region based on our and previous research findings [13, 26]. The molecular mechanisms behind the geographical region preference speciation need to expand the sample size and deepen exploration.

Possible reasons for conflicts in different gene analysis

In this study, we observed phylogenetic tree conflicts between single gene and conjoint gene analyses. For example, two single genes (Acc1 and Pgk1) phylogenetic trees displayed that Anthosachne was closely related to Pseudoroegneria (St genome) and Australopyrum (W genome), whereas, conjoint analysis of Acc1 + DMC1 + Pgk1 formed a single diploid Australopyrum with W genome group. The reason for this phenomenon may be the result of introgression between different genomes during allopolyploidy, incomplete lineage sorting, and other processes such as horizontal gene transfer and is generated by the different rates of evolution of different genes and the deletion or replacement of individual genes between different groups, which leads to phylogenetic tree conflicts [53–54]. It is noteworthy that the H genome of Campeiostachys purpuraristata and Y genome of Campeiostachys tangutorum were not tightly clustered together from H and Y clade, previous research has reported that the H genome of Campeiostachys purpuraristata and Y genome of Campeiostachys tangutorum had translocation with the other genomes based on in situ hybridization results [55–56]. In addition, previous studies have found that the chromosome pairing analysis of Lophopyrum elongatum and Lophopyrum bassarabicum showed that these two species contained the same genome, but the results of fluorescence in situ hybridization and phylogeny of PepC and Pgk1 showed that the variation between them is relatively large [57, 58]. In summary, for phylogenetic systematic analyses, different types of genes should be selected according to different evolution rates, and it may reflect the genome constitution and classification to some extent, more precise genetic relationships, ancestral donors, and the polyploidization events of Triticeae species should be investigated compromised proves including morphological, cytological, and appropriate molecular phylogenetic analyses.

Possible origin of the Y genome

The Y genome is an important basic genome among perennial Triticeae species, and those species mainly distributed in Asia, such as genera Roegneria (StStYY, StStStStYY), Campeiostachys (StStYYHH), Anthosachne (StStYYWW), Kengyilia (StStYYPP) [21, 24, 26–28, 30, 59, 60]. However, the donor of the Y genome has not been identified previously, and the origin of the Y genome remains unknown [3, 29–30, 44]. Dewey [45] speculated that the donor of the Y genome might have once been distributed in central Asia or the Himalayan area but now may be extinct. Based on the study of ITS sequences, some researchers found that the St and Y genomes shared some similarities and further speculated that St and Y genomes might originate from a common ancestor [38, 61–64]. Other authors have suggested that St and Y genomes have their donors and that the Y genome has an even closer relationship to W, P, V, or Xp genomes than the St genomes [32, 65–67]. Our result is similar to Fan et al. [67], the Y genome was closely related to the Xp genomes and the Y genome has a different origin from the St genome. In Triticeae, many polyploids are produced by the natural introgression of chromosomes and chromosome fragments during polyploidization and hybridization [42]. Thus, the Xp genome may have participated in Y genome formation and evolution.

From this study, based on phylogenetic analysis of sequence data for three nuclear DNA regions (Acc1, DMC1, and Pgk1) and nrITS, three chloroplast DNA regions (matK, rbcL, and trnL-trnF), the most important conclusions are as follows:

(1) The Triticeae polyploidy species that consisted of different genome types should be treated as a distinct genus.

(2) Some St-genome polyploidy species experienced independent allopolyploidization events in different distribution regions.

(3) The Kengyilia have two relatively independent origins.

(4) The Y genome originated from a Y diploid species which is closely related to Peridictyon sanctum.

(5) Kengyilia tibetica, Kengyilia changduensis, and Kengyilia dingqinensis are hexaploid species with the StStYYPP genomic constitution and should be classified under Kengyilia.

Materials

In this study, Triticeae polyploid species that contain the St genome were included in this study and were analyzed together with thirty diploid taxa representing twelve basic genomes in the tribe Triticeae (Table S1). Bromus inermis Leyss was used as an outgroup of phylogenetic trees. Three new Kengyilia species were collected from Qamdo of Tibet Province in China and were classified primarily according to morphology needs molecular proof ,and numbered ZCB1483, ZCB1498 and ZCB1459 respectively. No permissions were necessary to collect seed samples. Yonghong Zhou identifed the three plant materials. They were nominated as Kengyilia tibetica, Kengyilia changduensis, and Kengyilia dingqinensis. The plants and voucher specimens were deposited at the Herbarium of Triticeae Research Institute, Sichuan Agricultural University, China (SAUTI).

DNA amplification and sequencing

The CTAB (Cetyltrimethyl Ammonium Bromide) procedure was used to isolate the total genomic DNA [65]. The nuclear Acc1, Pgk1, DMC1, and nrITS sequences, chloroplast matK, rbcL, and TrnL-F sequences were amplified with primers listed in Table S2. PCR amplification of the DNA was carried out in a 25 µL reaction mixture, containing 10× ExTaq polymerase buffer, 200 µM of dNTP, 1 µM of each primer, 1.5 U ExTaq (TaKaRa, Dalian, China), and about 50 ng of template DNA. Amplifications were performed on the Veriti 96 Well Thermal Cycler (Thermo Fisher Scientific, USA). The PCR products were visualized on 1.0% agarose gels, purified by a FastPure Gel DNA Extraction Mini Kit (Vazyme, Nanjing, China), and then cloned into pMD19–T vector (TaKaRa, Dalian, China) according to the manufacturer’s instructions. At least 15 random clones per haploid were chosen to sequence. All clones were sequenced in both directions in Sangon Biotech (Shanghai) Co., Ltd.

Phylogenetic analysis

Multiple sequence alignments were conducted using MAFFT v7.490, with additional manual adjustment [68]. Phylogenetic analyses were performed using Maximum likelihood (ML). The determined best-fit evolutionary model and phylogenetic analyses were conducted using the ML method in IQ-TREE v2.0.7 [69]. The stochastic models of nucleotide sequence changed due to different nucleotide substitution, insertion, and deletion rates [67]. The optimal model was TPM3uf + I + G for three chloroplast data, TVM + I + G for three nuclear DNA, and SYM + G4 for nrITS data. Maximum likelihood heuristic searches were performed with 100 random addition sequence replications and a Tree Bisection-Reconnection (TBR) branch-swapping algorithm. To infer the robustness of clades, bootstrap support (BS) values were calculated with 1000 replications [70].

Maximum likelihood

Acc1

Acetyl-CoA carboxylase

DMC1

Disrupted meiotic cDNA

Pgk1

phosphoglycerate kinase

nrITS

Nuclear ribosomal internal transcribed spacer

CTAB

Cetyltrimethyl ammonium bromide

Bootstrap support

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Funding

This work was supported by the National Natural Science Foundation of China (No. 32200180), the Science and Technology Department of Sichuan Province (2023NSFSC1995, 2024NSFSC1327), and the Special Projects of the Central Government in Guidance of Local Science and Technology Development (2023ZYD0088).

Author Contribution

YHZ and DDW designed the study, participated in the design of the experiments, and revised the manuscript. XYP conducted the experiment, wrote the manuscript, and carried out data analyses; XYP, TTZ, and YXZ carried out part of the experiments; HYK and HQZ participated in its design and coordination and helped to draft the manuscript. XF, LNS, and WZ collected seed materials; YW, YRC, YHL, and LLX gave good suggestions in the experiments and manuscript; All authors read and approved the final manuscript.

Acknowledgement

The authors are thankful to the National Natural Science Foundation of China (No. 32200180), the Science and Technology Department of Sichuan Province (2023NSFSC1995, 2024NSFSC1327), and the Special Projects of the Central Government in Guidance of Local Science and Technology Development (2023ZYD0088) for the financial support. We also thank anonymous reviewers for their very useful comments on this manuscript. In addition, the authors are thankful to the American National Plant Germplasm System for kindly providing some seeds for this study.

Data Availability

Data is provided within the manuscript or supplementary information files

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Phylogeny and taxonomy of the polyploidy species that contains St genome (Triticeae; Poaceae) based on four nuclear DNA and three chloroplast genes

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Abstract

Background

Results

Conclusions

Figures

Background

Results

Phylogenetic analyses of nrITS sequences

Discussion

Phylogenetic relationships among the polyploidy species that contain the St genome

Geography and maternal origins of the St-containing polyploid species

Possible reasons for conflicts in different gene analysis

Possible origin of the Y genome

Conclusion

Material and Methods

Materials

DNA amplification and sequencing

Phylogenetic analysis

Abbreviations

Declarations

Funding

Author Contribution

Acknowledgement

Data Availability

References

Additional Declarations

Supplementary Files

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Version 1