Phylogenetic Analysis Of Triticeae Based On Single-copy Nuclear Acc1 And Pgk1 Sequences

The tribe Triticeae,including about 350-450 species distributed in the temperate and subtropical and tropic regions,is of enormous important group in Poaceae.Triticeae includes some of the world's most important cereal,wheat(Triticum aestivum L.),barley (Hordeum vulgare L.),and rye(Secale cereale L.),and a significant number of important forage grasses(e.g.,Elymus sibiricus L.,Leymus chinensis(Trio.) Tzvelve,and Agropyron cristatum(L.) Gaerton).The economic importance of the group makes relationships among its species of particular interest.A clear picture of phylogenetic relationships would point to wild taxa that may serve as sources of novel gene pool,focus efforts at conservation of germplasm,and help set priorities for preservation of grassland habitats.Triticeae consists of numerous diploids and polyploids,and polyploidy leads to the lineages of at least 70%of the species within Triticeae are polyploids.Different diploids and polyploids were included in different genera.According to the system of genome classifications,the main diploid genera includes Aegilops,Agropyron,Australopyrum, Crithopsis,Dasypyrum,Eremopyrum,Festucopsis,Henrardia,Heteranthelium,Hordeum, Lophopyrum,Peridictyon,Psathyrostachys,Secale,Pseudoroegneria,Taeniatherum and Thinopyrum,while the main polyploid genera includes Triticum,Elymus,Hystrix,Elytrigia, Roegneria,Kengyilia and Leymus.Hystrix,Elytrigia,Roegneria and Kengyilia were combined into Elymus sensu lato.The species of diploid genera,Elymus sensu lato,and Leymus are at least 85%of the species of Triticeae.The investigation of phylogenetic relationship among these genera can help understand the phylogeny and evolutionary history of Triticeae,thus making them guidance for the improvement of crop and forage. Despite decades of intensive efforts,there are still many unsolved questions to be answered, such as the phylogenetic relationships among genome and genera,the definition of genera, the origin of species,geographical differentiation,and the origin of unknown genome.In this study,we evaluated the phylogeny and geographical differentiation of diploid genera,Hystrix,Elymus sensu lato,and Leymus based on the haplotype of single-copy nuclear Acc1 and Pgk1 gene.One hundred and fifty-eight haplotypes of the Acc1 gene and 185 haplotypes of the Pgk1 gene were isolated from 107 plant taxa studied here.Sequence and phylogenetic analysis of haplotype of the Acc1 and Pgk1 gene showed as follows:1.To estimate phylogenetic relationships among the genome of Triticeae,the sequences of single-copy nuclear Acc1 and Pgk1 gene were isolated from 33 diploid taxa representing 18 basic genomes in Triticeae.Although phylogenetic analysis indicates conflicting Acc1 and Pgk1 gene trees,individul and combined data suggests that:(1) Triticum/Aegilops complex are non-monophyletic,and Triticum/Aegilops complex are closely related to Taeniatherum(Ta) and Thinopyrum(E~b);(2) Lophopyrum elongatum(E~e) and Thinopyrum bessarabicum(E~b) are evolutionary distinct;(3) there may be the same origin among Pseudoroegneria(St),Lophopyrum(E~e) and Australopyrum(W);(4) Peridictyon(Xp) is closely related to Dasypyrum(V);(5) the involvement of Eremopyrum (F) into Agropyron(P) may be a result of introgression.2.To evaluate the phylogenetic relationships between Hystrix and its related genera, sequences of the Acc1 and Pgk1 gene were analysed for five Hystrix taxa,together with three Pseudoroegneria(St) species,two Hordeum(H) species,two Psathyrostachys(Ns) species,four Elymus(StH) species,five Leymus(NsXm) species,Thinopyrum bessarabicum(E~b),and Lophopyrum elongatum(E~e).Sequence analyses indicated that an 182bp Stowaway insertion occurred in the Acc1 sequences of E.wawawaiensis,and an 81bp Stowaway insertion occurred in the Pgk1 sequences of L.arenarius and Psa.juncea, and a 29bp Copia insertion occurred in the Pgk1 sequences of Hy.duthiei,Hy.duthiei ssp. longearistata and L.akmolinensis.Phylogenetic analyses indicated that:(1) Hy.patula was closely related to Pseudoroegneria,Hordeum and Elymus;(2) Hy.duthiei,Hy.duthiei ssp. longearistata,Hy.coreana and Hy.komarovii were closely related to Psathyrostachys and Leymus.Based on these results,it is reasonable to transfer Hy.patula from Hystrix to Elymus,and to combine Hy.duthiei,Hy.duthiei ssp.longearistata,Hy.coreana and Hy. komarovii into Leymus.3.Using the sequences of two single-copy nuclear gene(Acc1 and Pgk1), phylogenetic analysis was performed on 33 accessions of the genus Elymus L.sensu lato in the tribe Triticeae and 33-35 diploid species representing 18 genome.Sixty-seven haplotypes of Acc1 sequence and 59 haplotypes of Pgk1 sequence were obtained from these 35 taxa used here.Phylogenetic analysis of haplotype suggests that:(1) the St,H,P, and W genomes in polyploid Elymus sensu lato were donated by Pseudoroegneria, Hordeum,Agropyron,and Australopyrum,respectively;(2) the Y genome is closely related to the V genome of Dasypyrum and Xp genome of Peridictyon;(3) tetraploid StH species is in good agreement their geographical origin-Eurasian and North American distinction;(4) North America Pse.spicata may sever as the St genome donor during the speciation of tetraploid StH species from North America,while the St genome of Elymus sensu lato in Eurasian might have been derived from more than one Pseudoroegneria species/populations;(5) multiple origin might occurred in some species of Elymus sensu lato;(6) there is a pattern of network evolution in Elymus,Roegneria and Kengyilia.4.Forty-seven haplotyps of the Pgk1 gene were isolated from 15 polyploid Kengyilia. These haplotypes were analysis together with the haplotypes from 4 Pseudoroegneria and 11 Agropyron taxa.Sequence analysis indicats that the P-copy sequences of the Kengyilia species from Qinghai-Tibetan Plateau and two Agropyron species(Ag.cristatum and Ag. mongolicum) from Nei-monglia of China shared an 81 bp insertion at position 1251-1334 bp,while this insertion were not found in other St-copy,Y-copy sequences,even though the P-copy sequences of the Kengyilia species and Agropyron species from central region. Phylogenetic analysis suggests that:(1) Kengyilia is closely related to Pseudoroegneria and Agropyron;(2) there may no hybridization events involving hexaploid Kengyilia species;(3) the central Asia and Qinghai-Tibetan Plateau Kengyilia species have independent alloploid origins with different P-genome donors,which may result in the geographical distinction of central Asia-Qinghai-Tibetan Plateau.5.Fifty haplotypes of the Acc1 gene and forty-two haplotypes of the Pgk1 gene were isolated from 27 Leymus species.These haplotype were analysed with the haplotype from 35 diploid taxa representing 18 basic genomes in Triticeae.Sequence analysis indicates that:(1) Ns-copy sequence of Acc1 gene of Leymus species from Qinghai-Tibetan Plateau has a 33bp insertion compared to the species distributed in other regions;(2) the Xm-copy sequences of Acc1 gene of Leymus species and the sequences of Agropyron species and Eremopyrum triticeum share a 4-bp TATA insertion in the intron region compared to the Ns-copy sequences.Phylogenetic analysis suggests that:(1) the Ns genome of Leymus is donated by Psathyrostachys;(2) the Xm genome in Leymus might originate from the P genome of Agropyron and the F genome of Ere.triticeum and an unknown origin;(3) the Ns genome of Leymus might have been derived from more than one Psathyrostachys species/populations;(4) Leymus species is in good agreement the geographical pattern of North America-Qinghai-Tibetan Plateau-central Asia;(5) North America Leymus species might originate from colonization of East Asia via the Bering land bridge,and the Leymus species from Qinghai-Tibetan Plateau might originate from central Asia.