Phylogenetic analysis of Sorghum and related taxa using internal transcribed spacers of nuclear ribosomal DNA

The phylogenetic relationships of the genus Sorghum and related genera were studied by sequencing the nuclear ribosomal DNA (rDNA) internal transcribed spacer region (ITS). DNA was extracted from 15 Sorghum accessions, including one accession from each of the sections Chaetosorghum and Heterosorghum, four accessions from Parasorghum, two accessions from Stiposorghum, and seven representatives from three species of the section Sorghum (one accession from each of S. propinquum and S. halepense, and five races of S. bicolor). The maize (Zea mays) line, H95, and an accession from Cleistachne sorghoides were also included in the study. Variable nucleotides were used to construct a strict consensus phylogenetic tree. The analyses indicate that S. propinquum, S. halepense and S. bicolor subsp. arundinaceum race aethiopicum may be the closest wild relatives of cultivated sorghum; Sorghum nitidum may be the closest 2n=10 relative to S. bicolor, the sections Chaetosorghum and Heterosorghum appear closely related to each other and more closely related to the section Sorghum than Parasorghum; and the section Parasorghum is not monophyletic. The results also indicate that the genus Sorghum is a very ancient and diverse group.This research was partially supported by a Third Country Scholarship from Pioneer Hi-Bred International Incorporated Contribution 94-182-J from Kansas Agricultural Experiment Station     

The use of ribosomal ITS to determine phylogenetic relationships within Sorghum

 For the first time, a combined analysis of the ITS1 regions of all twenty-five Sorghum species has been undertaken. Parsimony analysis revealed a distinct lineage of Sorghum consisting of the cultivated species and their progenitors plus S. angustum, S. brachypodum, S. ecarinatum, S. macrospermum, S. laxiflorum and Saccharum officinarum. A second unsupported lineage consists of the Parasorghum and Stiposorghum species S. grande, S. leiocladum, S. nitidum, S. purpureosericeum, S. timorense, S. versicolor, S. amplum, S. bulbosum, S. interjectum, S. plumosum, S. stipoideum and the African grass Cleistachne sorghoides. Three Australian endemic species, S. angustum, S. brachypodum and S. ecarinatum, are closely related to S. bicolor, with S. angustum showing no difference to S. bicolor in ITS1 sequence. Sorghum macrospermum and S. laxiflorum form a strong clade within the Eusorghum branch indicating closer relationships to this group than to any of the Parasorghum or Stiposorghum species. Saccharum officinarum has shown closer relationships to Sorghum than to Zea mays, while the close relationship of Cleistachne sorghoides to Sorghum has been confirmed. These relationships between Sorghum species provide an important guide for plant breeders to exploit the wider Sorghum genepool through crosses between wild and cultivated species in an effort to improve sorghum production. Received April 30, 2001 Accepted July 10, 2001     

Sorghum resolved as a distinct genus based on combined ITS1, ndhF and Adh1 analyses

Recent studies on Sorghum have attempted to determine the genetic relationships between the 17 Australian native Sorghum species and the cultivated species, with several studies contradictory in their findings. To resolve these issues within Sorghum, a detailed investigation of the phylogenetic relationships was made. The alcohol dehydrogenase 1 gene (Adh1) from 25 Sorghum species and Cleistachne sorghoides was sequenced. Independent analyses of the Adh1 data, and combined analyses of the Adh1, ITS1 and ndhF data were carried out. All Sorghum species were resolved to a distinct clade with 100% support. Within Sorghum, the Eu-sorghum species were resolved to a strongly supported lineage that included the Australian native species S. macrospermum and S. laxiflorum. All other Australian species were resolved to a second strongly supported lineage. Sorghum laxiflorum and S. macrospermum have again been identified as the Australian species most closely related to cultivated sorghum. Analysis based on three genes has shown that the 25 Sorghum species form a distinct monophyletic group, and that there is little evidence to support the recent taxonomic revision of these species into three separate genera.     

高粱属植物的地理分布

为探讨高粱属(Sorghum Moench)的系统发育关系,通过野外调查及查阅标本和文献资料,对高粱属植物的地理分布进行了整理和研究。高粱属植物约有29种,分布于全世界热带到温带地区,其中澳大利亚22种,亚洲15种,非洲9种,欧洲3种,地中海2种,美洲6种。中国有5种,分布在东北、西南到华南各省(区)。高粱属有5亚属,仅高粱亚属(subgen.Sorghum)延伸至新世界,其他亚属均分布在旧世界,高粱亚属覆盖非洲并扩散到全世界热带到温带地区;拟高粱亚属(subgen.Parasorghum)分布在非洲、亚洲、澳大利亚;有柄高粱亚属(subgen.Stiposorghum)主要分布在澳大利亚,个别种分布到亚洲;多毛高粱亚属(subgen.Chaetosorghum)分布在澳大利亚;异高粱亚属(subgen.Heterosorghum)分布在澳大利亚和亚洲。这表明澳大利亚东北部是高粱属的现代分布中心和多样化中心,非洲东北部和热带亚洲是否是高粱属的起源地尚需确证。     

Allotetraploid origin and divergence in Eleusine (Chloridoideae, Poaceae): evidence from low-copy nuclear gene phylogenies and a plastid gene chronogram

Background and Aims Eleusine

(Poaceae) is a small genus of the subfamily Chloridoideae exhibiting considerable morphological and ecological diversity in East Africa and the Americas. The interspecific phylogenetic relationships of Eleusine are investigated in order to identify its allotetraploid origin, and a chronogram is estimated to infer temporal relationships between palaeoenvironment changes and divergence of Eleusine in East Africa.

Methods

Two low-copy nuclear (LCN) markers, Pepc4 and EF-1α, were analysed using parsimony, likelihood and Bayesian approaches. A chronogram of Eleusine was inferred from a combined data set of six plastid DNA markers (ndhA intron, ndhF, rps16-trnK, rps16 intron, rps3, and rpl32-trnL) using the Bayesian dating method.

Key Results

The monophyly of Eleusine is strongly supported by sequence data from two LCN markers. In the cpDNA phylogeny, three tetraploid species (E. africana, E. coracana and E. kigeziensis) share a common ancestor with the E. indica–E. tristachya clade, which is considered a source of maternal parents for allotetraploids. Two homoeologous loci are isolated from three tetraploid species in the Pepc4 phylogeny, and the maternal parents receive further support. The A-type EF-1α sequences possess three characters, i.e. a large number of variations of intron 2; clade E-A distantly diverged from clade E-B and other diploid species; and seven deletions in intron 2, implying a possible derivation through a gene duplication event. The crown age of Eleusine and the allotetraploid lineage are 3·89 million years ago (mya) and 1·40 mya, respectively.

Conclusions

The molecular data support independent allotetraploid origins for E. kigeziensis and the E. africana–E. coracana clade. Both events may have involved diploids E. indica and E. tristachya as the maternal parents, but the paternal parents remain unidentified. The habitat-specific hypothesis is proposed to explain the divergence of Eleusine and its allotetraploid lineage.     

Giants and dwarfs: molecular phylogenies reveal multiple origins of annual spurges within Euphorbia subg. Esula

Euphorbia (Euphorbiaceae) comprises over 2150 species and is thus the second-largest genus of flowering plants. In Europe, it is represented by more than 100 species with highest diversity in the Mediterranean area; the majority of taxa belong to subgenus Esula Pers., including about 500 taxa. The few available phylogenetic studies yielded contrasting results regarding the monophyly of subg. Esula, and the phylogenetic relationships among its constituents remain poorly understood. We have sampled DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) and the plastid trnT-trnF region from about 100, predominantly European taxa of subg. Esula in order to infer its phylogenetic history. The plastid data support monophyly of subg. Esula whereas the ITS phylogeny, which is generally less resolved, is indecisive in this respect. Although some major clades have partly incongruent positions in the ITS and plastid phylogenies, the taxonomic content of the major terminal clades is congruent in both trees. As traditional sectional delimitations are largely not corroborated, an improved classification is proposed. Character state reconstruction illustrates that the annual life form developed independently several times in different clades of subgenus Esula from perennial ancestors, and that several morphological traits used in previous classifications of Euphorbia developed in parallel in different lineages.     

Allozyme variation among the spontaneous species of Sorghum section Sorghum (Poaceae)

Summary A survey of allozyme variation among the spontaneous taxa of Sorghum section Sorghum was undertaken. Eight plants each of 90 accessions representing the diploid S. bicolor (ssp. arundinaceum and drummondii) and the tetraploids S. almum and S. halepense were analyzed for 17 enzyme systems encoded by 30 loci. Low levels of variation were found within and among accessions, although there was more variation than is typical of inbreeding species. We found an average of 3.2 alleles per locus in ssp. arundinaceum, with a mean expected heterozygosity for the accessions of 0.034 and total panmictic heterozygosity of 0.154. An analysis of the apportionment of genetic variation among accessions of ssp. arundinaceum indicated that 26% of the variation occurs within accessions and 74% among accessions. Cultivated sorghum contains far less allozymic variation than ssp. arundinaceum, its presumed progenitor. This is consistent with the prediction that cultivated sorghum experienced a loss of genetic variation during domestication. For the most part, cultivated sorghum contains a subset of the allozymes found in ssp. arundinaceum. Principal component analysis revealed continuous variation among the accessions and geographic regions, with accessions failing to segregate into discrete clusters. However, accessions of race virgatum of ssp. arundinaceum occupied one end of the continuum and were, in that sense, distinguished from the other accessions. Similarly, most accessions of S. halepense and S. almum occupied the central portion of the continuum. The allozymic data presented here are consistent with the hypothesized origin of S. halepense via autopolyploidy or segmental allopolyploidy.     

Phylogenetic analysis of the genus Sorghum based on combined sequence data from cpDNA regions and ITS generate well-supported trees with two major lineages

Background and Aims

Wild Sorghum species provide novel traits for both biotic and abiotic stress resistance and yield for the improvement of cultivated sorghum. A better understanding of the phylogeny in the genus Sorghum will enhance use of the valuable agronomic traits found in wild sorghum.

Methods

Four regions of chloroplast DNA (cpDNA; psbZ-trnG, trnY-trnD, trnY-psbM and trnT-trnL) and the internal transcribed spacer (ITS) of nuclear ribosomal DNA were used to analyse the phylogeny of sorghum based on maximum-parsimony analyses.

Key Results

Parsimony analyses of the ITS and cpDNA regions as separate or combined sequence datasets formed trees with strong bootstrap support with two lineages: the Eu-sorghum species S. laxiflorum and S. macrospermum in one and Stiposorghum and Para-sorghum in the other. Within Eu-sorghum, S. bicolor-3, -11 and -14 originating from southern Africa form a distinct clade. S. bicolor-2, originally from Yemen, is distantly related to other S. bicolor accessions.

Conclusions

Eu-sorghum species are more closely related to S. macrospermum and S. laxiflorum than to any other Australian wild Sorghum species. S. macrospermum and S. laxiflorum are so closely related that it is inappropriate to classify them in separate sections. S. almum is closely associated with S. bicolor, suggesting that the latter is the maternal parent of the former given that cpDNA is maternally inherited in angiosperms. S. bicolor-3, -11 and -14, from southern Africa, are closely related to each other but distantly related to S. bicolor-2.     

Retrodihydrochalcones in Sorghum species: Key intermediates in the biosynthesis of 3-deoxyanthocyanidins?

Two new open chain flavonoids were isolated from the butanediol/ethanol extract of Sorghum bicolor (L.) Moench leaf sheaths by fractionation and purification processes. This work led to the structural characterization of the 3-(2,4,6-trihydroxyphenyl)-1-(4-hydroxyphenyl)-propan-1-one (or 2,4,4′,6-tetrahydroxydihydrochalcone) 1, and 3-(2,6-dihydrox-4-methoxyphenyl)-1-(4-hydroxyphenyl)-propan-1-one (or 2,4′,6-trihydroxy-4-methoxydihydro-chalcone) 2. The structures of these flavonoids were determined by extensive spectroscopic analyses, including UV, ESIMS, HRESIMS, 1D and 2D NMR. The chemical properties of 1 were similar to those earlier described in literature for apiforol, never fully characterized. These results led us to re-question the real structure of this flavan-4-ol, which is often described to be present in Sorghum and has even been considered as a key intermediate in the formation of Sorghum 3-deoxyanthocyanidins.     

Genomic organization of the ribosomal DNA of sorghum and its close relatives

Summary The structure and organization of the ribosomal DNA (rDNA) of sorghum (Sorghum bicolor) and several closely related grasses were determined by gel blot hybridization to cloned maize rDNA. Monocots of the genus Sorghum (sorghum, shattercane, Sudangrass, and Johnsongrass) and the genus Saccharum (sugarcane species) were observed to organize their rDNA as direct tandem repeats of several thousand rDNA monomer units. For the eight restriction enzymes and 14 cleavage sites examined, no variations were seen within all of the S. bicolor races and other Sorghum species investigated. Sorghum, maize, and sugarcane were observed to have very similar rDNA monomer sizes and restriction maps, befitting their close common ancestry. The restriction site variability seen between these three genera demonstrated that sorghum and sugarcane are more closely related to each other than either is to maize. Variation in rDNA monomer lengths were observed frequently within the Sorghum genus. These size variations were localized to the intergenic spacer region of the rDNA monomer. Unlike many maize inbreds, all inbred Sorghum diploids were found to contain only one rDNA monomer size in an individual plant. These results are discussed in light of the comparative timing, rates, and modes of evolutionary events in Sorghum and other grasses. Spacer size variation was found to provide a highly sensitive assay for the genetic contribution of different S. bicolor races and other Sorghum species to a Sorghum population.     

基于ITS序列探讨杜鹃属的亚属和组间系统关系

首次报道了 15种杜鹃属 (Rhododendron)植物、1种杜香属 (Ledum)植物和Cassiopefastigiata的内转录间隔区(ITS) (包括 5 .8S)序列。加上从GenBank下载的 13种杜鹃属植物和Bajiariaracemosa的ITS序列 ,以C .fastigiata和B .racemosa为外类群 ,用最大简约法对杜鹃属的亚属和组间的系统关系进行了分析。结果表明 :1)杜鹃属是一个单系类群 ,叶状苞亚属为杜鹃属的基部类群 ;2 )杜香属确应归并到杜鹃属中 ,且与有鳞杜鹃亚属有较近的亲缘关系 ;3)有鳞杜鹃亚属和杜香构成一个单系分支 ,该分支是其余无鳞杜鹃花的姐妹群 ;4 )由无鳞杜鹃花组成的一个分支的内部支持率较低 ,其中常绿杜鹃亚属和映山红亚属均为内部支持率很高的单系类群 ,而羊踯躅亚属和马银花亚属均为多系类群 ;5 )在马银花亚属中 ,长蕊杜鹃组和马银花组均分别得到强烈支持 ,马银花组与异蕊杜鹃亚属可能构成姐妹群关系 ,异蕊杜鹃亚属和马银花组组成的一个分支可能与映山红亚属构成姐妹群关系。     

基于ITS序列探讨杜鹃属的亚属和组间系统关系

首次报道了15种杜鹃属(Rhododendron)植物、1种杜香属(Ledum)植物和Cassiope fastigiata的内转录间隔区(ITS) (包括5.8S)序列.加上从GenBank下载的13种杜鹃属植物和Bajiaria racemosa的ITS序列,以C. fastigiata和B. racemosa为外类群,用最大简约法对杜鹃属的亚属和组间的系统关系进行了分析.结果表明: 1)杜鹃属是一个单系类群,叶状苞亚属为杜鹃属的基部类群; 2)杜香属确应归并到杜鹃属中,且与有鳞杜鹃亚属有较近的亲缘关系; 3)有鳞杜鹃亚属和杜香构成一个单系分支,该分支是其余无鳞杜鹃花的姐妹群; 4)由无鳞杜鹃花组成的一个分支的内部支持率较低,其中常绿杜鹃亚属和映山红亚属均为内部支持率很高的单系类群,而羊踯躅亚属和马银花亚属均为多系类群; 5)在马银花亚属中,长蕊杜鹃组和马银花组均分别得到强烈支持,马银花组与异蕊杜鹃亚属可能构成姐妹群关系,异蕊杜鹃亚属和马银花组组成的一个分支可能与映山红亚属构成姐妹群关系.     

Diversification history of Adesmia ser. psoraleoides (Leguminosae): Evolutionary processes and the colonization of the southern Brazilian highland grasslands

A molecular phylogeny is used to analyze the diversification history of Adesmia ser. psoraleoides, and its implications for understanding the historical assembly of the grasslands in the highlands of southern Brazil. All species of A. ser. psoraleoides were sampled, including multiple accessions for each species, plus representative species of the rest of Adesmia covering its geographic distribution. Phylogenetic analyses were based on nuclear and plastid DNA sequences, and a plastid matK phylogeny was dated. A. ser. psoraleoides is a well-supported monophyletic group, nested within the series bicolores, muricatae, subnudae, longisetae and candidae. The stem of A. ser. psoraleoides is c. 11 Mya, but most extant species diversified c. 3–5 Mya, suggesting that the flora of the subtropical grasslands of southern Brazil was assembled recently, co-incident with the expansion of other tropical grassland systems globally.     

Microbody enzymes and carboxylases in sequential extracts from c(4) and c(3) leaves

A seven-step sequential grinding procedure was applied to leaves of Atriplex rosea, Sorghum sudanense, and Spinacia oleracea to study the distribution of carboxylases and microbody enzymes. In the extracts from C₄ species there were 7- to 10-fold reciprocal changes in specific activities of ribulose-1, 5-diphosphate carboxylase and phosphoenolpyruvate carboxylase. No such changes occurred in sequential extracts from spinach. No inhibitors of ribulose-1, 5-diphosphate carboxylase were detected when the mesophyll extracts of Sorghum were assayed together with spinach extracts. These results reaffirm the conclusion of others that phosphoenolpyruvate carboxylase is largely confined to the mesophyll in these species and ribulose-1, 5-diphosphate carboxylase to the bundle sheath. The specific activities of glycolate oxidase and hydroxypyruvate reductase in bundle sheath extracts were two to three times those in mesophyll fractions. Catalase behaved similarly in Atriplex rosea but in Sorghum the specific activity was virtually the same in all fractions. From the relative amounts of these enzymes present, and comparison with the data obtained from spinach, it is concluded that typical leaf peroxisomes are present in the bundle sheaths of both C₄ species and in the mesophyll of Atriplex rosea. The relative enzyme activities in the mesophyll of Sorghum suggest that the microbodies there are of the non-specialized type found in many nongreen tissues. The activities of the microbody enzymes in the bundle sheath of Sorghum seem quite inadequate to support photorespiration.     

四种栎属青冈亚属植物叶绿体基因组特征及系统发育研究

栎属青冈亚属植物的系统发育地位长期存在着争议，部分种的种间关系不明确。为揭示宁冈青冈(Quercus ningangensis)、曼青冈(Q.oxyodon)、毛曼青冈(Q.gambleana)、竹叶青冈(Q.neglecta)的叶绿体基因组特征及系统发育关系，该研究选择以上4种栎属青冈亚属植物的成熟叶片进行二代测序，对其叶绿体基因组结构和特征进行分析，并结合相关类群进行系统发育研究。结果表明：(1)宁冈青冈、曼青冈、毛曼青冈、竹叶青冈的叶绿体基因组序列长度分别为160 906、160 883、160 832、160 784 bp,均编码133个基因，包括88个蛋白质编码基因、37个tRNA基因、8个rRNA基因。(2)4种栎属青冈亚属植物偏好以A/T结尾的密码子，质体基因组变异区域主要存在于非编码序列。(3)通过IR边界分析得出，4种栎属青冈亚属植物存在ycf1假基因且在IRb/SSC区域发生扩张。(4)系统发育分析显示，在壳斗科中，水青冈属(Fagus)和轮叶三棱栎属(Trigonobalanus)较早分化出来，栎亚属(subg.Quercus)未形成一个单系群，叶绿体基因组建树结...     

Molecular evidence for the origin and evolutionary history of the rare American desert monotypic family Setchellanthaceae

Setchellanthus caeruleus, which has disjunct populations in the north of the Chihuahuan Desert and in the Tehuacán-Cuicatlán valley, was selected to understand the evolutionary history of plants in this desert and its southerly relicts. This species constitutes the monotypic family Setchellanthaceae, which forms part of a group of plants that produce mustard-oil glucosides or glucosinolates. Molecular phylogenetic analyses based on DNA plastid sequences of plants of S. caeruleus from both areas, including representative taxa of the order Brassicales, were carried out to estimate the time of origin of the family (based on matK?+?rcbL) and divergence of populations (based on psbI-K, trnh-psbA, trnL-trnF). In addition, comparative ecological niche modelling was performed to detect if climate variables vary significantly in northern and southern populations. Analyses revealed that Setchellanthaceae is an ancient lineage that originated between 78 and 112 Mya during the mid-late Cretaceous—much earlier than the formation of the Chihuahuan Desert. The molecular data matrix displayed a few indel events as the only differences of plastid DNA sequences between northern and southern populations. It is suggested that due to climate changes in this desert in the Pliocene, populations of Setchellanthus remained in the Sierra de Jimulco and in Cuicatlán, in climatically stable locations. Ecological niche models of northern populations predict niches of southern populations and identity niche tests indicate that there are no differences in their ecological niches.     

Functional Exploration of Chaperonin (HSP60/10) Family Genes and their Abiotic Stress-induced Expression Patterns in Sorghum bicolor

Background Sorghum, the C4 dry-land cereal, important for food, fodder, feed and fuel, is a model crop for abiotic stress tolerance with smaller genome size, genetic diversity, and bio-energy traits. The heat shock proteins/chaperonin 60s (HSP60/Cpn60s) assist the plastid proteins, and participate in the folding and aggregation of proteins. However, the functions of HSP60s in abiotic stress tolerance in Sorghum remain unclear.MethodsGenome-wide screening and in silico characterization of SbHSP60s were carried out along with tissue and stress-specific expression analysis.ResultsA total of 36 HSP60 genes were identified in Sorghum bicolor. They were subdivided into 2 groups, the HSP60 and HSP10 co-chaperonins encoded by 30 and 6 genes, respectively. The genes are distributed on all the chromosomes, chromosome 1 being the hot spot with 9 genes. All the HSP60s were found hydrophilic and highly unstable. The HSP60 genes showed a large number of introns, the majority of them with more than 10. Among the 12 paralogs, only 1 was tandem and the remaining 11 segmental, indicating their role in the expansion of SbHSP60s. Majority of the SbHSP60 genes expressed uniformly in leaf while a moderate expression was observed in the root tissues, with the highest expression displayed by SbHSP60-1. From expression analysis, SbHSP60-3 for drought, SbHSP60-9 for salt, SbHSP60-9 and 24 for heat and SbHSP60-3, 9 and SbHSP10-2 have been found implicated for cold stress tolerance and appeared as the key regulatory genes.ConclusionThis work paves the way for the utilization of chaperonin family genes for achieving abiotic stress tolerance in plants.     

Phylogenetic relationships among Southeast Asian climbing bamboos (Poaceae: Bambusoideae) and the Bambusa complex

A phylogenetic analysis of Bambusa and allies based on the plastid DNA non-coding regions rps16-trnQ, trnC-rpoB, trnH-psbA and trnD-T, and a partial nuclear GBSSI gene, was carried out. This included representatives from all four Bambusa subgenera (including type species), a group of segregate Southeast Asian genera distinctive by their climbing–scrambling culms (Dinochloa, Holttumochloa, Kinabaluchloa, Maclurochloa, Soejatmia, Sphaerobambos), and two other Bambusinae genera (Dendrocalamus, Gigantochloa). The results do not support the present subgeneric classification of Bambusa. The climbing Southeast Asian genera, all of which include species previously placed in Bambusa, are distinct from the “core Bambusa group” (type species and alliance) and the Bambusa complex generally.