Dataset Information

Genetic Diversity and Phylogenetic Relationships of Annual and Perennial Glycine Species.

ABSTRACT: We have estimated the average genetic diversity of two Glycine annual and six perennial species based upon 76 orthologous gene sets and performed phylogenetic analysis, divergence analysis and tests for departure from neutrality of the eight species using 52 orthologous gene sets. In addition, 367 orthologous gene sets were used to estimate the relationships of 11 G. canescens accessions. Among the perennials, G. canescens showed the highest nucleotide diversity. The other perennials, except for G. tomentella, had higher nucleotide diversity than the two annuals. Phylogenetic analysis of the Glycine showed a similar genome grouping with the previous report except for G. cyrtoloba and G. stenophita which formed a sister clade in the study. Divergence analysis supported the phylogenetic relationships that G. falcata was the most divergent from G. max, followed by G. cyrtoloba, G. syndetika, G. tomentella D3, G. stenophita and G. canescens Most genic sequences were homogeneous in the levels of polymorphism and divergence between G. max and other Glycine species based on the HKA test, thus, Glycine perennials may have experienced a very similar evolution as inferred by trans-specific mutation analysis. The greater genetic diversity of most perennial Glycine species and their origins from the warmer and drier climates of Australia suggests the perennials maybe a potential source of heat and drought resistance that will be of value in the face of climate change.

SUBMITTER: Hwang EY

PROVIDER: S-EPMC6643897 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Genetic Diversity and Phylogenetic Relationships of Annual and Perennial Glycine Species.

Hwang Eun-Young EY Wei He H Schroeder Steven G SG Fickus Edward W EW Quigley Charles V CV Elia Patrick P Araya Susan S Dong Faming F Costa Larissa L Ferreira Marcio Elias ME Cregan Perry B PB Song Qijian Q

G3 (Bethesda, Md.) 20190709 7

We have estimated the average genetic diversity of two Glycine annual and six perennial species based upon 76 orthologous gene sets and performed phylogenetic analysis, divergence analysis and tests for departure from neutrality of the eight species using 52 orthologous gene sets. In addition, 367 orthologous gene sets were used to estimate the relationships of 11 G. canescens accessions. Among the perennials, G. canescens showed the highest nucleotide diversity. The other p ...[more]

PMID: 31097479

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Project description:BackgroundThe perennial, Oryza rufipogon distributed from Asia to Australia and the annual O. meridionalis indigenous to Australia are AA genome species in the Oryza. However, recent research has demonstrated that the Australian AA genome perennial populations have maternal genomes more closely related to those of O. meridionalis than to those found in Asian populations of O. rufipogon suggesting that the Australian perennials may represent a new distinct gene pool for rice.ResultsAnalysis of an Oryza core collection covering AA genome species from Asia to Oceania revealed that some Oceania perennials had organellar genomes closely related to that of O meridionalis (meridionalis-type). O. rufipogon accessions from New Guinea carried either the meridionalis-type or rufirpogon-type (like O. rufipogon) organellar genomes. Australian perennials carried only the meridionalis-type organellar genomes when accompanied by the rufipogon-type nuclear genome. New accessions were collected to better characterize the Australian perennials, and their life histories (annual or perennial) were confirmed by field observations. All of the material collected carried only meridionalis-type organellar genomes. However, there were two distinct perennial groups. One of them carried an rufipogon-type nuclear genome similar to the Australian O. rufipogon in the core collection and the other carried an meridionalis-type nuclear genome not represented in the existing collection. Morphologically the rufipogon-type shared similarity with Asian O. rufipogon. The meridionalis-type showed some similarities to O. meridionalis such as the short anthers usually characteristic of annual populations. However, the meridionalis-type perennial was readily distinguished from O. meridionalis by the presence of a larger lemma and higher number of spikelets.ConclusionAnalysis of current accessions clearly indicated that there are two distinct types of Australian perennials. Both of them differed genetically from Asian O. rufipogon. One lineage is closely related to O. meridionalis and another to Asian O. rufipogon. The first was presumed to have evolved by divergence from O. meridionalis becoming differentiated as a perennial species in Australia indicating that it represents a new gene pool. The second, apparently derived from Asian O. rufipogon, possibly arrived in Australia later.

Project description:The water dropworts Oenanthe linearis Wall. ex DC. and O. javanica (Blume) DC. are aquatic perennial herbs that have been used in China as vegetables and traditional medicines. However, their phylogenetic relationships and genetic diversity are poorly understood. Here, we presented the phenotypic traits and genome-wide DNA marker-based analysis of 158 water dropwort accessions representing both species. The analysis revealed that Oenanthe linearis was readily segregated into linear-leaf and deep-cleft leaf water dropworts according to their leaf shapes at flowering. Oenanthe javanica was classified by clustering analysis into two clusters based mainly on the morphological characteristics of their ultimate segments (leaflets). A set of 11 493 high-quality single-nucleotide polymorphisms was identified and used to construct a phylogenetic tree. There was strong discrimination between O. linearis and O. javanica, which was consistent with their phenotype diversification. The population structure and phylogenetic tree analyses suggested that the O. linearis accessions formed two major groups, corresponding to the linear-leaf and deep-cleft leaf types. The most obvious phenotypic differences between them were fully expressed at the reproductive growth stage. A single-nucleotide polymorphism-based analysis revealed that the O. javanica accessions could be categorized into groups I andII. However, this finding did not entirely align with the clusters revealed by morphological classification. Landraces were clustered into one group along with the remaining wild accessions. Hence, water dropwort domestication was short in duration. The level of genetic diversity for O. linearis (π = 0.1902) was slightly lower than that which was estimated for O. javanica (π = 0.2174). There was a low level of genetic differentiation between O. linearis and O. javanica (Fst = 0.0471). The mean genetic diversity among accessions ranged from 0.1818 for the linear-leaf types to 0.2318 for the groupII accessions. The phenotypic traits and the single-nucleotide polymorphism markers identified here lay empirical foundation for future genomic studies on water dropwort.

Project description:Background and aimsTheory predicts that outcrossing should be more prevalent among perennials than annuals, a pattern confirmed by comparative evidence from diverse angiosperm families. However, intraspecific comparisons between annual and perennial populations are few because such variation is uncommon among flowering plants. Here, we test the hypothesis that perennial populations outcross more than annual populations by investigating Incarvillea sinensis, a wide-ranging insect-pollinated herb native to China. The occurrence of both allopatric and sympatric populations allows us to examine the stability of mating system differences between life histories under varying ecological conditions.MethodsWe estimated outcrossing rates and biparental inbreeding in 16 allopatric and five sympatric populations in which both life histories coexisted using 20 microsatellite loci. In each population we measured height, branch number, corolla size, tube length and herkogamy for ~30 individuals. In a sympatric population, we recorded daily flower number, pollinator visitation and the fruit and seed set of annual and perennial plants.Key resultsAs predicted, outcrossing rates (t) were considerably higher in perennial (mean = 0.76) than annual (mean = 0.09) populations. This difference in mating system was also maintained at sympatric sites where plants grew intermixed. In both allopatric and sympatric populations the degree of herkogamy was consistently larger in outcrossing than selfing plants. Perennials were more branched, with more and larger flowers than in annuals. In a sympatric population, annuals had a significantly higher fruit and seed set than perennials.ConclusionsGenetically based differences in herkogamy between annuals and perennials appear to play a key role in governing outcrossing rates in populations, regardless of variation in local ecological conditions. The maintenance of mating system and life history trait differentiation between perennial and annual populations of I. sinensis probably results from correlated evolution in response to local environmental conditions.

Dataset Information

Genetic Diversity and Phylogenetic Relationships of Annual and Perennial Glycine Species.

Publications

Genetic Diversity and Phylogenetic Relationships of Annual and Perennial <i>Glycine</i> Species.

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