小麦族植物单拷贝核Acc1和Pgk1基因序列的分子系统发育研究
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摘要
小麦族(Triticeae Dumortier)是禾本科(Poaceae)植物中一个十分重要的类群,约有350-450个种,广泛分布于北半球温带地区。小麦族植物包含重要的粮食作物如:小麦(Triticum aestivum L.)、大麦(Hordeum vulgare L.)、黑麦(Secale cereale L.),也包含许多有重要经济价值的牧草种类如:老芒麦(Elymus sibiricus L.)、羊草(Leymuschinensis(Trio.)Tzvelve)、冰草(Agropyron cristatum(L.)Gaerton)。因此,研究小麦族系统与进化历史,为麦类作物的改良和提高牧草品质提供良好的遗传资源;对草原的合理开发利用、草原生态系统平衡的维持、水土保持等方面有着重要的作用。
小麦族植物包括大量的二倍体和多倍体,二倍体通过不同天然杂交组合形成小麦族70-75%的多倍体植物。不同的二倍体和多倍体植物被禾草分类学家组合在不同的属中。按照基因组分类系统,小麦族普遍得到认可的二倍体属主要有:山羊草属(Aegilops)、冰草属(Agropyron)、澳冰草属(Australopyrum)、类大麦属(Crithopsis)、簇毛麦属(Dasypyrum)、旱麦草属(Eremopyrum)、亨氏草属(Henrardia)、异形花属(Heteranthelium)、大麦属(Hordeum)、新麦草草属(Psathyrostachys)、黑麦属(Secale)、拟鹅观草属(Pseudoroegneria)、带芒草属(Taeniatherum)、Festucopsis、Lophopyrum、Peridictyon和Thinopyrum等,多倍体属主要有:小麦属(Triticum)、披碱草属(Elymus)、偃麦草属(Elytrigia)、猬草属(Hystrix)、鹅观草属(Roegneria)、仲彬草属(Kengyilia)和赖草属(Leymus)等。其中,猬草属、鹅观草属和仲彬草属被包括在广义概念的披碱草属(广义披碱草属,Elymus sensu lato)中。小麦族二倍体属、广义披碱草属和赖草属含有的植物种类占整个小麦族物种数量的85%以上。理清它们的系统关系有助于把握小麦族的系统与进化历史,从而更好的应用到麦类作物和牧草品种遗传改良的实践中。目前,就二倍体属、广义披碱草属和赖草属植物的基因组系统关系、属间系统关系、属的系统地位及有效性、物种起源、基因组供体来源等存在较大的分歧。本研究基于编码质体乙酰-CoA羧化酶的单拷贝核Acc1基因和编码磷酸甘油酸激酶的单拷贝核Pgk1基因序列的分子系统发育分析,从二倍体属、广义披碱草属和赖草属的107个植物类群中分离获得158个Acc1基因单倍型序列和185个Pgk1基因单倍型序列,通过Acc1和Pgk1基因单倍型序列的遗传变异和直系同源比较,探讨小麦族二倍体属、广义披碱草属和赖草属植物的基因组系统关系、属间系统关系、属的系统地位、基因组供体来源、植物类群发生地理分化的生物学理论依据。主要结果如下:
1.基于Acc1和Pgk1基因序列对小麦族代表18个基因组的33个二倍体植物进行系统发育重建,探讨二倍体基因组的系统关系。系统发育分析显示部分植物类群在Acc1和Pgk1基因树间存在明显的系统冲突。独立基因以及联合基因的系统分析支持:(1)Triticum/Aegilops复合群为非单系起源,他们与Taeniatherum(Ta)和Thinopyrum(E~b)具有较近的亲缘关系;(2)Lophopyrum elongatum(E~e)和Thinopyrumbessarabicum(E~b)在进化上已经发生明显的分化;(3)Pseudoroegneria(St)、Lophopyrum(E~e)和Australopyrum(W)可能存在共同起源;(4)Peridictyon(Xp)和Dasypyrum(V)拥有较近的亲缘关系;(5)Eremopyrum(F)与Agropyron(P)可能存在共同起源。
2.对猬草属及其近缘属Thinopyrum(E~b)、Lophopyrum(E~e)、拟鹅观草属(St)、新麦草属(Ns)、大麦属(H)、赖草属(NsXm)和披碱草属(StH)植物共23个类群的Acc1和Pgk1基因序列进行序列和系统发育分析,探讨猬草属及其近缘属植物的系统发育关系,猬草属的系统位置及有效性,猬草属植物基因组供体来源。序列分析显示Acc1基因序列在E.wawawaiensis中拥有一个182 bp的Stowaway转座插入,Pgk1基因序列在L.arenarius和Psa.juncea中有81 bp的Stowaway插入,Pgk1基因序列在Hy.duthiei、Hy.duthiei ssp.longearistata和L.akmolinensis中有29 bp的Copia反转座插入。系统发育分析表明:(1)猬草属模式种Hy.patula含有StH基因组,与披碱草属、拟鹅观草属和大麦属具有密切的亲缘关系;(2)猬草属的其他物种Hy.duthiei、Hy.duthiei ssp.longearistata、Hy.coreana和Hy.komarovii含有NsXm基因组,与新麦草属和赖草属植物亲缘关系密切。研究结果支持将础patula从猬草属组合到披碱草属中,而Hy.duthiei、Hy.duthiei ssp.logearistata、Hy.coreana和Hy.komarovii应组合到赖草属中。
3.从33个广义披碱草属植物中分离获得67个Acc1基因单倍型序列和59个Pgk1基因的单倍型序列。对这些单倍型序列与小麦族18个基因组的33-35个二倍体基因序列进行系统比较分析,探讨广义披碱草属系统关系、基因组供体来源及St基因组分化式样。结果表明:(1)广义披碱草属植物的St、H、P和W分别起源于拟鹅观草属、大麦属、冰草属和澳冰草属:(2)Y基因组与Peridictyon的Xp基因组和Dasypyrum的V基因组具有较近的亲缘关系;(3)广义披碱草属含StH基因组的植物存在北美与欧亚大陆的地理分化;(4)北美的Pse.spicata参与了北美StH基因组植物的物种形成,欧亚大陆广义披碱草属植物的St基因组存在多个来源,且可能经历了快速的遗传分化;(5)广义披碱草属植物存在多重起源;(6)披碱草属、鹅观草属和仲彬草属植物类群在系统发生上形成复杂的网状进化式样。
4.从广义披碱草属的仲彬草属植物类群的15个物种中分离到47个Pgk1基因单倍型序列。将这47个单倍型序列与4个拟鹅观草属物种和11个冰草属植物类群的Pgk1基因序列进行了序列与系统发育分析,探讨仲彬草属植物系统关系及地理分化。结果显示:(1) P基因组单倍型序列中,青藏高原的仲彬草属物种与来自内蒙古的Ag.cristatum及Ag.mongolicum在1251-1334bp处多了一个81bp插入,而中亚半荒漠-草原植被区的仲彬草属物种和中亚其他地区的Ag.cristatum没有发现81bp插入;(2)仲彬草属与拟鹅观草属和冰草属具有密切的亲缘关系;(3)拟鹅观草属可能没有直接作为St基因组供体来源参与仲彬草属物种形成;(4)中亚和青藏高原的仲彬草属物种可能为独立起源的两个支系,独立起源可能是导致仲彬草属存在中亚-青藏高原的地理分化格局的原因。
5.从27个赖草属物种分离获得代表不同基因组直系来源的50个Acc1基因的单倍型序列和42个Pgk1基因的单倍型序列。将这些单倍型序列与小麦族35个二倍体植物的Acc1和Pgk1基因序列进行了系统比较分析,探讨赖草属植物系统关系、基因组供体来源及地理分化。结果表明:(1)青藏高原赖草属植物在Acc1基因序列上比其他供试的赖草属植物多了一个33bp插入;(2)赖草属植物Acc1基因的Xm-copy序列与冰草属植物和Eremopyrum triticeum的Acc1基因序列比赖草属植物Ns-copy序列和新麦草属植物的Acc1基因序列多了一个TATA插入;(3)赖草属与新麦草属具有密切的亲缘关系,赖草属的Ns基因组起源于新麦草属;(4)赖草属Xm基因组的起源可能涉及到冰草属的P基因组、Ere.triticeum的F基因组和一个未知来源的基因组;(5)赖草属植物Ns基因组存在多个不同的起源;(6)赖草属植物存在北美-青藏高原-中亚的地理分化;(7)北美赖草可能由中亚的原始种通过白令陆桥迁徙而来,而青藏高原赖草由中亚的原始种演变而来。
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.
小麦族植物包括大量的二倍体和多倍体,二倍体通过不同天然杂交组合形成小麦族70-75%的多倍体植物。不同的二倍体和多倍体植物被禾草分类学家组合在不同的属中。按照基因组分类系统,小麦族普遍得到认可的二倍体属主要有:山羊草属(Aegilops)、冰草属(Agropyron)、澳冰草属(Australopyrum)、类大麦属(Crithopsis)、簇毛麦属(Dasypyrum)、旱麦草属(Eremopyrum)、亨氏草属(Henrardia)、异形花属(Heteranthelium)、大麦属(Hordeum)、新麦草草属(Psathyrostachys)、黑麦属(Secale)、拟鹅观草属(Pseudoroegneria)、带芒草属(Taeniatherum)、Festucopsis、Lophopyrum、Peridictyon和Thinopyrum等,多倍体属主要有:小麦属(Triticum)、披碱草属(Elymus)、偃麦草属(Elytrigia)、猬草属(Hystrix)、鹅观草属(Roegneria)、仲彬草属(Kengyilia)和赖草属(Leymus)等。其中,猬草属、鹅观草属和仲彬草属被包括在广义概念的披碱草属(广义披碱草属,Elymus sensu lato)中。小麦族二倍体属、广义披碱草属和赖草属含有的植物种类占整个小麦族物种数量的85%以上。理清它们的系统关系有助于把握小麦族的系统与进化历史,从而更好的应用到麦类作物和牧草品种遗传改良的实践中。目前,就二倍体属、广义披碱草属和赖草属植物的基因组系统关系、属间系统关系、属的系统地位及有效性、物种起源、基因组供体来源等存在较大的分歧。本研究基于编码质体乙酰-CoA羧化酶的单拷贝核Acc1基因和编码磷酸甘油酸激酶的单拷贝核Pgk1基因序列的分子系统发育分析,从二倍体属、广义披碱草属和赖草属的107个植物类群中分离获得158个Acc1基因单倍型序列和185个Pgk1基因单倍型序列,通过Acc1和Pgk1基因单倍型序列的遗传变异和直系同源比较,探讨小麦族二倍体属、广义披碱草属和赖草属植物的基因组系统关系、属间系统关系、属的系统地位、基因组供体来源、植物类群发生地理分化的生物学理论依据。主要结果如下:
1.基于Acc1和Pgk1基因序列对小麦族代表18个基因组的33个二倍体植物进行系统发育重建,探讨二倍体基因组的系统关系。系统发育分析显示部分植物类群在Acc1和Pgk1基因树间存在明显的系统冲突。独立基因以及联合基因的系统分析支持:(1)Triticum/Aegilops复合群为非单系起源,他们与Taeniatherum(Ta)和Thinopyrum(E~b)具有较近的亲缘关系;(2)Lophopyrum elongatum(E~e)和Thinopyrumbessarabicum(E~b)在进化上已经发生明显的分化;(3)Pseudoroegneria(St)、Lophopyrum(E~e)和Australopyrum(W)可能存在共同起源;(4)Peridictyon(Xp)和Dasypyrum(V)拥有较近的亲缘关系;(5)Eremopyrum(F)与Agropyron(P)可能存在共同起源。
2.对猬草属及其近缘属Thinopyrum(E~b)、Lophopyrum(E~e)、拟鹅观草属(St)、新麦草属(Ns)、大麦属(H)、赖草属(NsXm)和披碱草属(StH)植物共23个类群的Acc1和Pgk1基因序列进行序列和系统发育分析,探讨猬草属及其近缘属植物的系统发育关系,猬草属的系统位置及有效性,猬草属植物基因组供体来源。序列分析显示Acc1基因序列在E.wawawaiensis中拥有一个182 bp的Stowaway转座插入,Pgk1基因序列在L.arenarius和Psa.juncea中有81 bp的Stowaway插入,Pgk1基因序列在Hy.duthiei、Hy.duthiei ssp.longearistata和L.akmolinensis中有29 bp的Copia反转座插入。系统发育分析表明:(1)猬草属模式种Hy.patula含有StH基因组,与披碱草属、拟鹅观草属和大麦属具有密切的亲缘关系;(2)猬草属的其他物种Hy.duthiei、Hy.duthiei ssp.longearistata、Hy.coreana和Hy.komarovii含有NsXm基因组,与新麦草属和赖草属植物亲缘关系密切。研究结果支持将础patula从猬草属组合到披碱草属中,而Hy.duthiei、Hy.duthiei ssp.logearistata、Hy.coreana和Hy.komarovii应组合到赖草属中。
3.从33个广义披碱草属植物中分离获得67个Acc1基因单倍型序列和59个Pgk1基因的单倍型序列。对这些单倍型序列与小麦族18个基因组的33-35个二倍体基因序列进行系统比较分析,探讨广义披碱草属系统关系、基因组供体来源及St基因组分化式样。结果表明:(1)广义披碱草属植物的St、H、P和W分别起源于拟鹅观草属、大麦属、冰草属和澳冰草属:(2)Y基因组与Peridictyon的Xp基因组和Dasypyrum的V基因组具有较近的亲缘关系;(3)广义披碱草属含StH基因组的植物存在北美与欧亚大陆的地理分化;(4)北美的Pse.spicata参与了北美StH基因组植物的物种形成,欧亚大陆广义披碱草属植物的St基因组存在多个来源,且可能经历了快速的遗传分化;(5)广义披碱草属植物存在多重起源;(6)披碱草属、鹅观草属和仲彬草属植物类群在系统发生上形成复杂的网状进化式样。
4.从广义披碱草属的仲彬草属植物类群的15个物种中分离到47个Pgk1基因单倍型序列。将这47个单倍型序列与4个拟鹅观草属物种和11个冰草属植物类群的Pgk1基因序列进行了序列与系统发育分析,探讨仲彬草属植物系统关系及地理分化。结果显示:(1) P基因组单倍型序列中,青藏高原的仲彬草属物种与来自内蒙古的Ag.cristatum及Ag.mongolicum在1251-1334bp处多了一个81bp插入,而中亚半荒漠-草原植被区的仲彬草属物种和中亚其他地区的Ag.cristatum没有发现81bp插入;(2)仲彬草属与拟鹅观草属和冰草属具有密切的亲缘关系;(3)拟鹅观草属可能没有直接作为St基因组供体来源参与仲彬草属物种形成;(4)中亚和青藏高原的仲彬草属物种可能为独立起源的两个支系,独立起源可能是导致仲彬草属存在中亚-青藏高原的地理分化格局的原因。
5.从27个赖草属物种分离获得代表不同基因组直系来源的50个Acc1基因的单倍型序列和42个Pgk1基因的单倍型序列。将这些单倍型序列与小麦族35个二倍体植物的Acc1和Pgk1基因序列进行了系统比较分析,探讨赖草属植物系统关系、基因组供体来源及地理分化。结果表明:(1)青藏高原赖草属植物在Acc1基因序列上比其他供试的赖草属植物多了一个33bp插入;(2)赖草属植物Acc1基因的Xm-copy序列与冰草属植物和Eremopyrum triticeum的Acc1基因序列比赖草属植物Ns-copy序列和新麦草属植物的Acc1基因序列多了一个TATA插入;(3)赖草属与新麦草属具有密切的亲缘关系,赖草属的Ns基因组起源于新麦草属;(4)赖草属Xm基因组的起源可能涉及到冰草属的P基因组、Ere.triticeum的F基因组和一个未知来源的基因组;(5)赖草属植物Ns基因组存在多个不同的起源;(6)赖草属植物存在北美-青藏高原-中亚的地理分化;(7)北美赖草可能由中亚的原始种通过白令陆桥迁徙而来,而青藏高原赖草由中亚的原始种演变而来。
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.
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