Evolutionary dynamics of the Pgk1 gene in the polyploid genus Kengyilia (Triticeae: Poaceae) and its diploid relatives

The level and pattern of nucleotide variation in duplicate gene provide important information on the evolutionary history of polyploids and divergent process between homoeologous loci within lineages. Kengyilia is a group of allohexaploid species with the StYP genomic constitutions in the wheat tribe. To investigate the evolutionary dynamics of the Pgk1 gene in Kengyilia and its diploid relatives, three copies of Pgk1 homoeologues were isolated from all sampled hexaploid Kengyilia species and analyzed with the Pgk1 sequences from 47 diploid taxa representing 18 basic genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1) Kengyilia species from the Central Asia and the Qinghai-Tibetan plateau have independent origins with geographically differentiated P genome donors and diverged levels of nucleotide diversity at Pgk1 locus; (2) a relatively long-time sweep event has allowed the Pgk1 gene within Agropyron to adapt to cold climate triggered by the recent uplifts of the Qinghai-Tibetan Plateau; (3) sweep event and population expansion might result in the difference in the d(N)/d(S) value of the Pgk1 gene in allopatric Agropyron populations, and this difference may be genetically transmitted to Kengyilia lineages via independent polyploidization events; (4) an 83 bp MITE element insertion has shaped the Pgk1 loci in the P genome lineage with different geographical regions; (5) the St and P genomes in Kengyilia were donated by Pseudoroegneria and Agropyron, respectively, and the Y genome is closely related to the Xp genome of Peridictyon sanctum. The interplay of evolutionary forces involving diverged natural selection, population expansion, and transposable events in geographically differentiated P genome donors could attribute to geographical differentiation of Kengyilia species via independent origins.     

Phylogeny and molecular evolution of the DMC1 gene within the StH genome species in Triticeae (Poaceae)

To estimate the phylogeny and molecular evolution of a single-copy nuclear disrupted meiotic cDNA (DMC1) gene within the StH genome species, two DMC1 homoeologous sequences were isolated from nearly all the sampled StH genome species and were analyzed with those from seven diploid taxa representing the St and H genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1) there is a close relationship among North American StH genome species; (2) the DMC1 gene sequences of the StH genome species from North America and Eurasia are evolutionarily distinct; (3) the StH genome polyploids have higher levels of sequence diversity in the St genome homoeolog than the H genome homoeolog; (4) the DMC1 sequence may evolve faster in the polyploid species than in the diploids; (5) high dN and dN/dS values in the St genome within polyploid species could be caused by low selective constraints or AT-biased mutation pressure. Our result provides some insight on evolutionary dynamics of duplicate DMC1 gene, the polyploidization events and phylogeny of the StH genome species.     

Phylogenetic relationships between Leymus (Poaceae,Triticeae) and related diploid Triticeae species based on isozyme and genome-specific random amplified polymorphic DNA (RAPD) markers

Abstract

To investigate the phylogenetic relationships between Leymus and related diploid species of the Triticeae tribe, the esterase isozyme (EST), superoxide dismutase (SOD) isozymes, and genome-specific random amplified polymorphic DNA (RAPD) markers were used to analyze for 14 Leymus species, together with two Psathyrostachys species (Ns), three Pseudoroegneria species (St), two Hordeum species (H), Lophopyrum elongatum (E^e), Australopyrum retrofractum (W), and Agropyron cristatum (P). The data were used to construct dendrograms by means of UPGMA in the NTSYS-pc computer program. The results suggested that (1) isozyme analysis can be used in the systematic studies of these perennial Triticeae; (2) there is a close relationship between Leymus, Psathyrostachys juncea, three Pseudoroegneria species, and Lophopyrum elongatum; (3) the Ns genome-specific RAPD marker was present in all 14 polyploid species of Leymus, while the E^e and P genome-specific RAPD markers were absent in 14 polyploid species of Leymus; the St, W and H genome-specific RAPD markers were present in some species of Leymus; (4) Leymus species have multiple origins, and different Leymus species derived their genomes from different donors.     

Phylogeny of Hystrix and related genera (Poaceae: Triticeae) based on nuclear rDNA ITS sequences

The taxonomic status of Hystrix and phylogenetic relationships among Hystrix and its related genera of Pseudoroegneria (St), Hordeum (H), Psathyrostachys (Ns), Elymus (StH), Leymus (NsXm), Thinopyrum bessarabicum (E(b)) and Lophopyrum elongatum (E(e)) were estimated from sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The type species of Hystrix, H. patula, clustered with species of Pseudoroegneria, Hordeum, Elymus, Th. bessarabicum and Lo. elongatum, while H. duthiei ssp. duthiei, H. duthiei ssp. longearistata, H. coreana and H. komarovii were grouped with Psathyrostachys and Leymus species. The results indicate that: (i) H. patula is distantly related to other species of Hystrix, but is closely related to Elymus species; (ii) H. duthiei ssp. duthiei, H. duthiei ssp. longearistata, H. coreana and H. komarovii have a close affinity with Psathyrostachys and Leymus species, and H. komarovii might contain the NsXm genome of Leymus; and (iii) the St, H and Ns genomes in Hystrix originate from Pseudoroegneria, Hordeum and Psathyrostachys, respectively, while the Xm in Hystrix and Leymus has a complex relationship with the E or St genomes. According to the genomic system of classification in Tiritceae, it is reasonable to treat Hystrix patula as Elymus hystrix L, and the other species of Hystrix as species of a section of Leymus, Leymus Sect. Hystrix.     

Phylogenetic relationships in Leymus (Triticeae; Poaceae): Evidence from chloroplast trnH-psbA and mitochondrial coxII intron sequences

Leymus Hochst. is a polyploid genus with a diverse array of morphology, cytology, ecology, and distribution in Triticeae. To investigate the phylogenetic relationships and maternal genome donor of polyploid Leymus, the chloroplast trnH-psbA region and mitochondrial coxII intron sequences of 33 Leymus taxa were analyzed with those of 36 diploid perennial species representing 19 basic genomes in Triticeae. The results showed that reticulate evolution occurred in Leymus species, with the cytoplasmic lineage of Leymus contributed by different progenitors. Interspecific relationships of Leymus were also elucidated on the basis of orthologous comparison. Our data suggested that: (i) due to incomplete lineage sorting and/or difference in the pattern of chloroplast and mitochondrial inheritance, the genealogical conflict between the two genealogical patterns suggest the contribution of Psathyrostachys Nevski, Agropyron J. Gaertn, Eremopyrum (Ledeb.) Jaub. & Spach, Pseudoroegneria (Nevski) Á. Löve, Thinopyrum Á. Löve, and Lophopyrum (Host) Á. Löve to the cytoplasmic lineage of Leymus; (ii) there is a close relationship among Leymus species from the same area or neighboring geographic regions; (iii) L. coreanus (Honda) K. B. Jensen & R. R.-C. Wang, L. duthiei (Stapf) Y. H. Zhou & H. Q. Zhang ex C. Yen, J. L. Yang & B. R. Baum, L. duthiei var. longearistatus (Hack.) Y. H. Zhou & H. Q. Zhang ex C. Yen, J. L. Yang & B. R. Baum, and L. komarovii(Roshev.) C. Yen, J. L. Yang & B. R. Baum are closely related to other Leymus species, and it is reasonable to transfer these species from the genus Hystrix Moench to Leymus; (iv) Leymus species from North America are closely related to L. coreanus from the Russian Far East and L. komarovii from northeast China but are evolutionarily distinct from Leymus species from Central Asia and the Qinghai–Tibet Plateau. The occurrence of multiple origin and introgression could account for the rich diversity and ecological adaptation of Leymus species.     

Synopsis of Leymus Hochst. (Triticeae: Poaceae)

Leymus is a genus in the Triticeae tribe, Poaceae. The taxa of this genus are allopolyploid species which possess the Ns and Xm genomes. According to cytological, cytogenetic and molecular genetic analyses, some species of Hystrix and Elymus ought to be transferred to this genus. A world revision of the genus Leymus is needed. In this paper we summarize experimental results, provide a key to sections, species and varieties, and list all the taxa we recognize in Leymus with their synonyms. This synopsis is a new taxonomic system to be used for the revision of Leymus.     

Phylogeny and molecular evolution of the Acc1 gene within the StH genome species in Triticeae (Poaceae)

To estimate the phylogeny and molecular evolution of a single-copy gene encoding plastid acetyl-CoA carboxylase (Acc1) within the StH genome species, two Acc1 homoeologous sequences were isolated from nearly all the sampled StH genome species and were analyzed with those from 35 diploid taxa representing 19 basic genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1) the StH genome species from the same areas or neighboring geographic regions are closely related to each other; (2) the Acc1 gene sequences of the StH genome species from North America and Eurasia are evolutionarily distinct; (3) Dasypyrum has contributed to the nuclear genome of Elymus repens and Elymus mutabilis; (4) the StH genome polyploids have higher levels of sequence diversity in the H genome homoeolog than the St genome homoeolog; and (5) the Acc1 sequence may evolve faster in the polyploid species than in the diploids. Our result provides some insight on evolutionary dynamics of duplicate Acc1 gene, the polyploidy speciation and phylogeny of the StH genome species.     

Phylogeny and molecular evolution of the rbcL gene of St genome in Elymus sensu lato (Poaceae: Triticeae)

Analysis of the patterns and levels of diversity in duplicate gene not only traces evolutionary history of polyploids, but also provides insight into how the evolutionary process differs between lineages and between homoeologous loci within lineages. Elymus sensu lato is a group of allopolyploid species, which share a common St genome and with the different combinations of H, Y, P, and W genomes. To estimate the evolutionary process of the rbcL gene in species of Elymus s. l. and its putative dioploid relatives, 74 sequences were obtained from 21 species of Elymus s. l. together with 24 diploid taxa representing 19 basic genomes in Triticeae. Phylogeny and sequence diversity pattern analysis suggested that (1) species of Pseudoroegneria (Nevski) Á. Löve might serve as the maternal donor of the species of Elymus s. l; (2) differentiation of St genome were shown in the species of Elymus s. l. following polyploidy event; (3) divergences within the species might associate with geographic diversity and morphological variability; (4) differences in the levels and patterns of nucleotide diversity of the rbcL gene implied that the St genome lineages in the species of Elymus s. l. have differently evolutionary potentials.     

国产赖草属的分类修订

通过标本研究和野外考察,对中国赖草属（Leymus Hochst.）进行了分类修订。结果在中国共确认了3组、33种、7变种赖草属植物,其中多穗组包含4种,少穗组包含24种、7变种,单穗组包含5种,新报道的3个种和新修订的4个类群（即3个新组合和1个新名称）皆隶于少穗组。同时对赖草属的研究简史、属的形态特征和一些类群的地理分布也分别作了简要介绍。     

Genome organization and polyploid evolution in the genus Eleusine (Poaceae)

 Eleusine (Poaceae) includes six diploid and three polyploid species and has three basic chromosome numbers, x=8, 9 and 10. The species are annual as well as perennial and all are wild except E. coracana, which is cultivated for grain and fodder in Africa and the Indian subcontinent. Eleusine coracana and E. africana have the same genome and chromosome number (2n=36). Eleusine indica and E. floccifolia are identified as two genome donors to these polyploid species. Eleusine kigeziensis is the third polyploid species of the genus with 2n=38. Its genome may have come from E. jaegeri and from one of the species with x=9, most probably from E. indica. Eleusine indica, E. tristachya, E. floccifolia and E. intermedia with x=9 and two polyploid species, E. coracana and E. africana, are closely related and there is free genetic flow between them. Eleusine multiflora with x=8 is significantly different in morphology and at genomic level from other species. Eleusine jaegeri with x=10 is morphologically similar to E. indica, however, more information is needed to ascertain its position in the genus. Eleusine coracana, which is commonly called finger millet, is a potential and nutritious crop for the increasing population of the world, particularly in arid and semi-arid regions. It can also serve as a gene pool for various important characters and disease resistant genes. Received February 11, 2002; accepted May 27, 2002 Published online: October 14, 2002 Addresses of the authors: Madho Singh Bisht and Yasuhiko Mukai (e-mail: ymukai@cc.osaka-kyoiku.ac.jp), Laboratory of Plant Molecular Genetics, Division of Natural Science, Osaka Kyoiku University, 4-698-1 Asahigaoka, Kashiwara, Osaka 582-8582, Japan.     

Genome composition and origin of the polyploid Aegean grass Avenula agropyroides (Poaceae)

Aim The Aegean is a hotspot of plant biodiversity, with its island biota harbouring a large number of endemic taxa. To investigate the relationship between biogeography, polyploid speciation and genomics in the Aegean we used the biogeographically isolated highly polyploid eastern Mediterranean grass species Avenula agropyroides (2n = 70) as an example of complicated polyploid origin. Location Mediterranean, Aegean. Methods To clarify the origin of A. agropyroides, we conducted chromosome studies using repetitive DNAs as hybridization probes in fluorescent in situ hybridization experiments, chromosome banding methods and DNA sequence analyses of plasmid‐cloned nuclear ribosomal (nr) ITS1–5.8S–ITS2 DNA. Results Decaploid A. agropyroides had near‐autopolyploid karyotype structure and contained characteristic sequence motifs of nrDNA repeats not encountered in any of the diploids studied. Special repeat types found in one of its accessions (Crete) showed that A. agropyroides originated from a diploid species with a hybrid background. One of the genomes involved was close to both that of extant species (Avenula aetolica, Avenula compressa, Avenula hookeri, Avenula schelliana, Avenula versicolor) distributed mostly in the eastern Mediterranean to Asia and North America and also to the west Mediterranean (Avenula bromoides). The other resembled that of exclusively western Mediterranean species (Avenula albinervis, Avenula levis, Avenula marginata, Avenula sulcata). Main conclusions Avenula agropyroides represents a remarkable polyploid in the eastern Mediterranean, conserving the genome structure of a diploid species that no longer exists. This highlights how the Aegean has been less affected than other Eurasian regions by the repeated shifts of climatic zones and vegetation belts since the Late Tertiary.     

Morphological,cytological, and molecular evidences for natural hybridization between Roegneria stricta and Roegneria turczaninovii (Triticeae: Poaceae)

Some plants with low fertility are morphologically intermediate between Roegneria stricta and Roegneria turczaninovii, and were suspected to be natural hybrids between these species. In this study, karyotype analysis showed that natural hybrids and their putative parents were tetraploids (2n = 4x = 28). Meiotic pairing in natural hybrids is more irregular than its putative parents. Results of genomic in situ hybridization and fluorescence in situ hybridization indicate that natural hybrids contain the same genome as their putative parents. The nuclear gene DNA meiotic recombinase 1 (DMC1) and the chloroplast gene rps16 of natural hybrids and their putative parents were analyzed for evidence of hybridization. The results from molecular data supported by morphology and cytology demonstrated that the plants represent natural hybrids between R. stricta and R. turczaninovii. The study is important for understanding species evolution in the genus since it demonstrates for the first time the existence of populations of natural homoploid hybrids in Roegneria. The study also reports for the first time that the composition of the genomic formula of R. turczaninovii is StY, confirming that the current taxonomic status is correct.     

Phylogeny and evolutionary history of Leymus (Triticeae; Poaceae) based on a single-copy nuclear gene encoding plastid acetyl-CoA carboxylase

Background  

Single- and low- copy genes are less likely subject to concerted evolution, thus making themselves ideal tools for studying the origin and evolution of polyploid taxa. Leymus is a polyploid genus with a diverse array of morphology, ecology and distribution in Triticeae. The genomic constitution of Leymus was assigned as NsXm, where Ns was presumed to be originated from Psathyrostachys, while Xm represented a genome of unknown origin. In addition, little is known about the evolutionary history of Leymus. Here, we investigate the phylogenetic relationship, genome donor, and evolutionary history of Leymus based on a single-copy nuclear Acc1 gene.     

Genome origins in Leymus (Poaceae: Triticeae): evidence of maternal and paternal progenitors and implications for reticulate evolution

The polyploid Leymus species have the Ns nuclear genomes evolved from Psathyrostachys and the Xm nuclear genomes from unknown origins. Currently, little is known about the cytoplasmic genomes of Leymus, and the species of Psathyrostachys that transferred the Ns genome to Leymus remain elusive. To determine the origins of the plastid and nuclear genome for Leymus species, sequences of two chloroplast genes, rpoA and rbcL, and partial sequences of the nuclear gene DMC1 of 15 Leymus species were phylogenetically analyzed with those of 71 accessions belonging to 19 monogenomic genera in Triticeae. Both rpoA and rbcL sequences revealed that Psathyrostachys juncea, P. lanuginosa, and P. stoloniformis had close phylogenetic relationships with the Eurasian and one North American Leymus accessions, L. cinereus. Three American Leymus species, L. erianthus, L. triticoides, and L. innovatus had different maternal origins from Eurasian Leymus species. DMC1 sequences of Leymus were grouped into several phylogenetically distant clades indicating that either Ns or Xm originated from different lineages. These results suggest multiple contributions to the chloroplast as well as nuclear genomes in Leymus species. The comprehensive data indicate reticulate evolution in polyploid Leymus.     

Cytogenetic and phylogenetic studies of diploid and polyploid members of tribe Anemoninae (Ranunculaceae)

The ancestry, phylogenetic differentiation and systematic classification of the worldwide-distributed genus Anemone have been debated for many years. In this paper 11 Anemone, three Pulsatilla species and Hepatica nobilis were subjected to detailed karyotype analysis with the aim of obtaining new cytogenetic data that will contribute to karyotype evolutionary studies of the tribe Anemoninae. The results are interpreted in a phylogenetic context, established from the intergenic nontranscribed spacer (NTS) of 5S rDNA and internal transcribed spacer (ITS) of 35S rDNA. One to three 35S and one to three 5S rDNA loci are present in diploid and polyploid taxa. The 35S rDNA loci are located terminally on the short arm of acrocentric chromosomes, while for 5S rDNA there is no preferential chromosomal position as it exhibits terminal, subterminal, interstitial or pericentromeric positions, and is located either on acrocentric or metacentric chromosomes. The karyotype of hexaploid A. baldensis (2n = 6x = 48) is presented for the first time, and A. sylvestris is proposed as one of its putative parental species. Chromosome fusion/translocation is proposed as the key mechanism involved in reduction of the basic chromosome number from 8 in the Anemone subgenus to 7 in the Anemonidium subgenus. The cytogenetic data obtained are mainly supported by ITS and NTS phylogeny. Diversification of the genus Anemone was accompanied by a large reduction of heterochromatin, from the Mediterranean anemones that have large amounts of heterochromatin to the New World anemones without any detectable heterochromatic blocks.     

A new multiflorous species of Leymus (Poaceae: Triticeae) from western China

A new species of Leymus section Racemosus, L. pluriflorus L.B.Cai & T.L.Zhang, is described and illustrated. It grows in the eastern part of Qinghai Province and the southern part of Gansu Province, China. It most closely resembles L. crassiusculus L.B.Cai, from which it differs in having longer rachis internodes, some pedicellate spikelets, more florets per spikelet, glabrous lemmas, shorter paleas and shorter anthers. It differs from all other Chinese species taxa in Leymus with regard to the large number (8–12) of florets in its spikelets, and from all species of Leymus in adjacent countries in having three to four spikelets per node. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 343–348.     

Karyotype evolution and phylogenetic analyses in the genus Cardiospermum L. (Paullinieae,Sapindaceae)

Cardiospermum L. belongs to the Paullinieae tribe (Sapindaceae) and comprises 16 species. Of these, 12 species are present in South America and all occur in Brazil. Cardiospermum shows the most variable chromosome number of the tribe. Phylogenetic relationships within the genus Cardiospermum, especially with other species of the tribe, are poorly understood. This research focuses on characterisation of the karyotypic features of Cardiospermum using conventional cytogenetic methods, CMA/DAPI chromosome banding and fluorescence in situ hybridisation (FISH). To elucidate the phylogeny of the genus, the nuclear markers ITS1 and ITS2 were sequenced and analysed using maximum parsimony and Bayesian inference. Cardiospermum shows important diversity in basic numbers, with x = 7, 9, 10, 11 and 12. All species studied have metacentric and submetacentric chromosomes, some species have subtelocentric chromosomes, while telocentric chromosomes are absent. The interphase nuclei differentiate the Cardiospermum species into two groups. The CMA₃/DAPI chromosome banding revealed the presence of an AT‐rich terminal region in C. corindum, C. grandiflorum and C. urvilleoides, whereas GC‐rich regions were found in C. grandiflorum, C. halicacabum var. halicacabum, C. halicacabum var. microcarpum, C. heringeri and C. integerrimum. FISH revealed syntenic and non‐syntenic distribution of the 18‐5.8‐26S and 5S rDNA. The syntenic distribution always occurred in the short arms of the same chromosome in all of the species. The phylogenetic relationships reveal, in part, the taxonomic arrangement of the genus Cardiospermum.     

Phylogenetic relationships among Leymus and related diploid genera (Triticeae: Poaceae) based on chloroplast trnQ–rps16 sequences

To investigate the phylogenetic relationships among Leymus and related diploid genera, the genome donor of Leymus, and the evolutionary history of polyploid Leymus species, chloroplast trnQ–rps16 sequences were analyzed for 36 accessions of Leymus representing 25 species, together with 11 diploid taxa from six monogenomic genera. The phylogenetic analyses (Neighbor‐Joining and MJ network) supported three major clades (Ns, St and Xm). Sequence diversity and genealogical analysis suggested that 1) Leymus species from the same areas or neighboring geographic regions are closely related; 2) most of the Eurasian Leymus species are closely related to Psathyrostachys: P. juncea might serve as the Ns genome donor of polyploid Eurasian Leymus species; 3) the Xm genome may originate from ancestral lineages of Pseudoroegneria (St), Lophopyrum (E^e), Australopyrum (W) and Agropyron (P); 4) the trnQ–rps16 sequences of Leymus are evolutionarily distinct, and may clarify parental lineages and phylogenetic relationships in Leymus.     

赖草属的地理分布及其起源散布

为了探讨赖草属（Leymus Hochst.）植物的地理分布及起源散布,通过野外调查、标本查阅和文献搜集,同时结合地史、气候及类群演化关系的综合分析,对其地理分布及起源散布进行了整理和研究。结果显示,赖草属植物有3组53种（含变种）,主要分布于欧亚大陆和北美地区;中国有3组40种（含变种）,主要分布于西北、华北、东北以及西南地区,也是该属种类最为集中的区域;尤其是新疆北部的阿尔泰地区及青藏高原东北部的唐古特地区又是中国该属分布相对密集之地,有3组22种,并且其间不同等级、不同系统演化水平的类群均有分布,是该属的现代分布中心。同时,阿尔泰地区多汇集赖草属不同等级的原始类群和外类群,故该地区极有可能是该属的起源地,起源时间大约在第三纪渐新世。赖草属起源后,在渐新世末期青藏高原不断隆升、气候与环境发生巨变,其在中国境内地质活动较为剧烈的区域得到进一步发展和分化,主要通过两个阶段和三条路径扩散成现今的地理分布格局。