Chloroplast Phylogenomic Analyses Resolve Multiple Origins of the Kengyilia Species (Poaceae: Triticeae) via Independent Polyploidization Events

Abstract Background Kengyilia is a group of allohexaploid species that arose from two hybridization events followed by genome doubling of three ancestral diploid species with different genomes St, Y and P in the wheat tribe. Estimating phylogenetic relationship in resolution of the maternal lineages has been difficult, owing to the extremely low rate of sequence divergence. Here, phylogenetic reconstructions based on the plastome sequences were used to explore the role of maternal progenitors in establishment of Kengyilia polyploid species.ResultsThe plastome sequences of 11 Kengyilia species were analyzed together with 11 tetraploid species (PP, StP, and StY) and 33 diploid taxa representing 20 basic genomes in the Triticeae. Phylogenomic analysis and genetic divergence patterns suggested that (1) Kengyilia is closely related to Roegneria, Pseudoroegneria, Agropyron, Lophopyrum, Thinopyrum, and Dasypyrum; (2) both the StY genome Roegneria tetraploids and the PP genome Agropyron tetraploids severed as the maternal donor during the speciation of Kengyilia species; (3) the different Kengyilia species derived their StY genome from different Roegneria species.ConclusionMultiple origins of species via independent polyploidization events have occurred in the genus Kengyilia, resulting in a maternal haplotype polymorphism. This helps explain the rich diversity and wide adaptation of polyploid species in the genus Kengyilia.

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Chloroplast phylogenomic analyses resolve multiple origins of the Kengyilia species via independent polyploidization events

10.21203/rs.2.22669/v1 ◽

2020 ◽

Author(s):

Shi-Yong Chen ◽

Hao Yan ◽

Li-Na Sha ◽

Ning Chen ◽

Yue Zhang ◽

...

Keyword(s):

Diploid Species ◽

Sequence Divergence ◽

Phylogenomic Analysis ◽

Polyploid Species ◽

Genome Doubling ◽

Multiple Origins ◽

Rich Diversity ◽

Wide Adaptation ◽

The Rich ◽

Phylogenomic Analyses

Abstract Background Kengyilia is a group of allohexaploid species that arose from two hybridization events followed by genome doubling of three ancestral diploid species with different genomes St, Y and P in the wheat tribe. Estimating phylogenetic relationship in resolution of the maternal lineages has been difficult, owing to the extremely low rate of sequence divergence. Here, phylogenetic reconstructions based on the plastome sequences were used to explore the role of maternal progenitors in establishment of Kengyilia polyploid species.ResultsThe plastome sequences of 11 Kengyilia species were analyzed together with 11 tetraploid species (PP, StP, and StY) and 33 diploid taxa representing 20 basic genomes in the Triticeae. Phylogenomic analysis and genetic divergence patterns suggested that (1) Kengyilia is closely related to Roegneria, Pseudoroegneria, Agropyron, Lophopyrum, Thinopyrum, and Dasypyrum; (2) both the StY genome Roegneria tetraploids and the PP genome Agropyron tetraploids severed as the maternal donor during the speciation of Kengyilia species; (3) the different Kengyilia species derived their StY genome from different Roegneria species.ConclusionMultiple origins of species via independent polyploidization events have occurred in the genus Kengyilia, resulting in a maternal haplotype polymorphism. This helps explain the rich diversity and wide adaptation of polyploid species in the genus Kengyilia.

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Chloroplast phylogenomics in Camelina (Brassicaceae) reveals multiple origins of polyploid species and the maternal lineage of C. sativa

Horticulture Research ◽

10.1093/hr/uhab050 ◽

2022 ◽

Vol 9 ◽

Author(s):

Jordan R Brock ◽

Terezie Mandáková ◽

Michael McKain ◽

Martin A Lysak ◽

Kenneth M Olsen

Keyword(s):

Phylogenetic Analyses ◽

Divergence Time ◽

Diploid Species ◽

Time Estimation ◽

Polyploid Species ◽

Chromosome Counts ◽

Diploid Parent ◽

Divergence Time Estimation ◽

Multiple Origins ◽

Chloroplast Genomes

Abstract The genus Camelina (Brassicaceae) comprises 7–8 diploid, tetraploid, and hexaploid species. Of particular agricultural interest is the biofuel crop, C. sativa (gold-of-pleasure or false flax), an allohexaploid domesticated from the widespread weed, C. microcarpa. Recent cytogenetics and genomics work has uncovered the identity of the parental diploid species involved in ancient polyploidization events in Camelina. However, little is known about the maternal subgenome ancestry of contemporary polyploid species. To determine the diploid maternal contributors of polyploid Camelina lineages, we sequenced and assembled 84 Camelina chloroplast genomes for phylogenetic analysis. Divergence time estimation was used to infer the timing of polyploidization events. Chromosome counts were also determined for 82 individuals to assess ploidy and cytotypic variation. Chloroplast genomes showed minimal divergence across the genus, with no observed gene-loss or structural variation. Phylogenetic analyses revealed C. hispida as a maternal diploid parent to the allotetraploid Camelina rumelica, and C. neglecta as the closest extant diploid contributor to the allohexaploids C. microcarpa and C. sativa. The tetraploid C. rumelica appears to have evolved through multiple independent hybridization events. Divergence times for polyploid lineages closely related to C. sativa were all inferred to be very recent, at only ~65 thousand years ago. Chromosome counts confirm that there are two distinct cytotypes within C. microcarpa (2n = 38 and 2n = 40). Based on these findings and other recent research, we propose a model of Camelina subgenome relationships representing our current understanding of the hybridization and polyploidization history of this recently-diverged genus.

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Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex

10.7287/peerj.preprints.243 ◽

2014 ◽

Author(s):

Aureliano Bombarely ◽

Jeremy E Coate ◽

Jeff J Doyle

Keyword(s):

Population Genomics ◽

Transcriptome Assembly ◽

Phylogenetic Analyses ◽

Diploid Species ◽

Complex Problem ◽

Common Mechanism ◽

Chromosome Loss ◽

Polyploid Species ◽

Multiple Origins ◽

Cultivated Soybean

Allopolyploidy combines two progenitor genomes in the same nucleus, and is a common mechanism for producing new species, especially in plants. Deciphering the origins of polyploid species is a complex problem, due to, among other things, extinct progenitors, multiple origins, gene flow between different polyploid populations, and loss of parental contributions through gene or chromosome loss. In this work, we studied three allopolyploid species in the genus Glycine, which includes the cultivated soybean (G. max). Previous work based on two nuclear sequences showed that these allopolyploids combine the genomes of extant diploid species in the G. tomentella complex. We use several phylogenetic and population genomics approaches to clarify the origin of these species using single nucleotide polymorphism data and a guided transcriptome assembly. The results support the hypothesis that each of the three polyploid species are fixed hybrids combining the homoeologous genomes of its two putative parents. Based on mapping to the soybean reference genome, there appear to be no large regions for which one homoeologous contribution is missing. Phylogenetic analyses of 27 selected transcripts using a coalescent approach also indicates multiple origins for G. tomentella polyploid species, and suggest that origins occurred within the last several hundred thousands years.

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Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex

10.7287/peerj.preprints.243v1 ◽

2014 ◽

Author(s):

Aureliano Bombarely ◽

Jeremy E Coate ◽

Jeff J Doyle

Keyword(s):

Population Genomics ◽

Transcriptome Assembly ◽

Phylogenetic Analyses ◽

Diploid Species ◽

Complex Problem ◽

Common Mechanism ◽

Chromosome Loss ◽

Polyploid Species ◽

Multiple Origins ◽

Cultivated Soybean

Allopolyploidy combines two progenitor genomes in the same nucleus, and is a common mechanism for producing new species, especially in plants. Deciphering the origins of polyploid species is a complex problem, due to, among other things, extinct progenitors, multiple origins, gene flow between different polyploid populations, and loss of parental contributions through gene or chromosome loss. In this work, we studied three allopolyploid species in the genus Glycine, which includes the cultivated soybean (G. max). Previous work based on two nuclear sequences showed that these allopolyploids combine the genomes of extant diploid species in the G. tomentella complex. We use several phylogenetic and population genomics approaches to clarify the origin of these species using single nucleotide polymorphism data and a guided transcriptome assembly. The results support the hypothesis that each of the three polyploid species are fixed hybrids combining the homoeologous genomes of its two putative parents. Based on mapping to the soybean reference genome, there appear to be no large regions for which one homoeologous contribution is missing. Phylogenetic analyses of 27 selected transcripts using a coalescent approach also indicates multiple origins for G. tomentella polyploid species, and suggest that origins occurred within the last several hundred thousands years.

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A new species of frog of the genus Abavorana Oliver, Prendini, Kraus & Raxworthy 2015 (Anura: Ranidae) from Gunung Jerai, Kedah, northwestern Peninsular Malaysia

Zootaxa ◽

10.11646/zootaxa.4320.2.4 ◽

2017 ◽

Vol 4320 (2) ◽

pp. 272 ◽

Cited By ~ 3

Author(s):

EVAN S.H. QUAH ◽

SHAHRULM.S. ANUAR ◽

L.L. GRISMER ◽

PERRY L. JR. WOOD ◽

SITI M.N. AZIZAH ◽

...

Keyword(s):

New Species ◽

Phylogenetic Analyses ◽

Sequence Divergence ◽

Peninsular Malaysia ◽

Colour Pattern ◽

Nominal Species ◽

Adult Males ◽

Rich Diversity ◽

The Rich ◽

A New Species

The recently erected ranid genus Abavorana is thought to contain one nominal species, A. luctuosa, that ranges from the Thai-Malay Peninsula to Borneo and Sumatra. A melanistic form from Gunung Jerai, Peninsular Malaysia previously thought to be the same species is new to science and herein described based on new specimens and data. Based on morphology, colour pattern, and phylogenetic analyses using the mitochondrial genes 16s, ND1 and three tRNAs (tRNA-leu, tRNA-lle, and tRNA-gln), we determine that this new species, Abavorana nazgul sp. nov., is the sister lineage to other populations of A. lucutosa from Peninsular Malaysia and one from Borneo. It differs from A. luctuosa by a minimum sequence divergence of 7.5% and the following combination of morphological and colour pattern characteristics: (1) SVL 42.1–50.0 mm in adult males; (2) prominent but small humeral glands in males (2.3–2.5 mm); (3) dorsolateral stripe continuous, orange to yellow in colour; (4) mid-dorsal region of dorsum black, with or without faint orange or yellow speckles; (5) flanks with distinct cream spots; (6) dorsal surfaces of limbs with cream spots–bar; and (7) venter grayish brown, with prominent light spots on throat and belly. The discovery of yet another endemic species from the upland regions of Peninsular Malaysia highlights the rich diversity of these habitats and the need for more studies in montane areas throughout the region.

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Comparative Analysis of Genetic and Morphological Variation within the Platanthera hyperborea Complex (Orchidaceae)

Systematic Botany ◽

10.1600/036364420x16033962925303 ◽

2020 ◽

Vol 45 (4) ◽

pp. 767-778

Author(s):

Eranga Wettewa ◽

Nick Bailey ◽

Lisa E. Wallace

Keyword(s):

North America ◽

Diploid Species ◽

Morphological Characters ◽

Evolutionary Patterns ◽

Founding Population ◽

Multiple Origins ◽

Geographic Structure ◽

Species Complexes ◽

Nuclear Its ◽

Cryptic Taxa

Abstract—Species complexes present considerable problems for a working taxonomy due to the presence of intraspecific variation, hybridization, polyploidy, and phenotypic plasticity. Understanding evolutionary patterns using molecular markers can allow for a more thorough assessment of evolutionary lineages than traditional morphological markers. In this study, we evaluated genetic diversity and phylogenetic patterns among taxa of the Platanthera hyperborea (Orchidaceae) complex, which includes diploid (Platanthera aquilonis) and polyploid (Platanthera hyperborea, P. huronensis, and P. convallariifolia) taxa spanning North America, Greenland, Iceland, and Asia. We found that three floral morphological characters overlap among the polyploid taxa, but the diploid species has smaller flowers. DNA sequence variation in a plastid (rpL16 intron) and a nuclear (ITS) marker indicated that at least three diploid species have contributed to the genomes of the polyploid taxa, suggesting all are of allopolyploid origin. Platanthera convallariifolia is most like P. dilatata and P. stricta, whereas P. huronensis and P. hyperborea appear to have originated from crosses of P. dilatata and P. aquilonis. Platanthera huronensis, which is found across North America, has multiple origins and reciprocal maternal parentage from the diploid species. By contrast, P. hyperborea, restricted to Greenland and Iceland, appears to have originated from a small founding population of hybrids in which P. dilatata was the maternal parent. Geographic structure was found among polyploid forms in North America. The area of Manitoba, Canada appears to be a contact zone among geographically diverse forms from eastern and western North America. Given the geographic and genetic variation found, we recommend continued recognition of four green-flowered species within this complex, but caution that there may be additional cryptic taxa within North America.

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Conclusion

10.23943/princeton/9780691167787.003.0008 ◽

2018 ◽

Author(s):

Stefan Winter

Keyword(s):

Middle Eastern ◽

Rich Diversity ◽

The Social ◽

Local Contexts ◽

History Of ◽

Religious Oppression ◽

The Rich ◽

To Come

This concluding chapter summarizes key themes and presents some final thoughts. The book has shown that the multiplicity of lived ʻAlawi experiences cannot be reduced to the sole question of religion or framed within a monolithic narrative of persecution; that the very attempt to outline a single coherent history of “the ʻAlawis” may indeed be misguided. The sources on which this study has drawn are considerably more accessible, and the social and administrative realities they reflect consistently more mundane and disjointed, than the discourse of the ʻAlawis' supposed exceptionalism would lead one to believe. Therefore, the challenge for historians of ʻAlawi society in Syria and elsewhere is not to use the specific events and structures these sources detail to merely add to the already existing metanarratives of religious oppression, Ottoman misrule, and national resistance but rather to come to a newer and more intricate understanding of that community, and its place in wider Middle Eastern society, by investigating the lives of individual ʻAlawi (and other) actors within the rich diversity of local contexts these sources reveal.

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PSYCHOLOGICAL FEATURES OF EDUCATION AND TOLERANCE IN STUDENTS

Main Issues Of Pedagogy And Psychology ◽

10.24234/miopap.v16i1.329 ◽

2018 ◽

Vol 16 (1) ◽

pp. 112-119

Author(s):

VLADIMIR GLEB NAYDONOV

Keyword(s):

Statistical Analysis ◽

Training Program ◽

Rich Diversity ◽

Interethnic Differences ◽

The World ◽

The Rich ◽

Correct Understanding ◽

Psychological Features ◽

Different Levels

The article considers the students’ tolerance as a spectrum of personal manifestations of respect, acceptance and correct understanding of the rich diversity of cultures of the world, values of others’ personality. The purpose of the study is to investgate education and the formation of tolerance among the students. We have compiled a training program to improve the level of tolerance for interethnic differences. Based on the statistical analysis of the data obtained, the most important values that are significant for different levels of tolerance were identified.

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Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing

The ISME Journal ◽

10.1038/s41396-021-01052-3 ◽

2021 ◽

Author(s):

Valentin Waschulin ◽

Chiara Borsetto ◽

Robert James ◽

Kevin K. Newsham ◽

Stefano Donadio ◽

...

Keyword(s):

Genome Mining ◽

Gene Clusters ◽

Biosynthetic Gene Cluster ◽

Full Length ◽

Metagenomic Sequencing ◽

Short Read ◽

Short Read Sequencing ◽

Rich Diversity ◽

Long Read ◽

The Rich

AbstractThe growing problem of antibiotic resistance has led to the exploration of uncultured bacteria as potential sources of new antimicrobials. PCR amplicon analyses and short-read sequencing studies of samples from different environments have reported evidence of high biosynthetic gene cluster (BGC) diversity in metagenomes, indicating their potential for producing novel and useful compounds. However, recovering full-length BGC sequences from uncultivated bacteria remains a challenge due to the technological restraints of short-read sequencing, thus making assessment of BGC diversity difficult. Here, long-read sequencing and genome mining were used to recover >1400 mostly full-length BGCs that demonstrate the rich diversity of BGCs from uncultivated lineages present in soil from Mars Oasis, Antarctica. A large number of highly divergent BGCs were not only found in the phyla Acidobacteriota, Verrucomicrobiota and Gemmatimonadota but also in the actinobacterial classes Acidimicrobiia and Thermoleophilia and the gammaproteobacterial order UBA7966. The latter furthermore contained a potential novel family of RiPPs. Our findings underline the biosynthetic potential of underexplored phyla as well as unexplored lineages within seemingly well-studied producer phyla. They also showcase long-read metagenomic sequencing as a promising way to access the untapped genetic reservoir of specialised metabolite gene clusters of the uncultured majority of microbes.

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