Comparative Plastomes and Phylogenetic Analysis of Cleistogenes and Closely Related Genera (Poaceae)

Cleistogenes (Orininae, Cynodonteae, Chloridoideae, Poaceae) is an ecologically important genus. The phylogenetic placement of Cleistogenes and phylogenetic relationships among Cleistogenes taxa remain controversial for a long time. To resolve the intra- and inter-generic relationships of Cleistogenes, the plastomes of 12 Cleistogenes taxa (including 8 species and 4 varieties), one Orinus species, 15 Triodia species, two Tripogon species, and two Aeluropus species were included in the present study. All the taxa showed a similar pattern in plastome structure, gene order, gene content, and IR boundaries. The number of simple sequence repeats ranged from 145 (O. kokonorica) to 161 (T. plurinervata and T. schinzii). Moreover, 1,687 repeats were identified in these taxa, including 1,012 forward, 650 palindromic, 24 reverse, and one complement. Codon usage analysis revealed that these plastomes contained 16,633 (T. stipoides) to 16,678 (T. tomentosa) codons. Sequence divergence analysis among Cleistogenes and closely related genera identified five non-coding regions (trnS-UGA-psbZ, rpl32-trnL-UAG, trnQ-UUG-psbK, trnD-GUC-psbM, trnT-GGU-trnE-UUC). Phylogenetic analysis of complete plastomes indicated that Cleistogenes is sister to a clade composed of Orinus and Triodia, whereas it did not support the sister relationship between the recently proposed subtribe Orininae (Cleistogenes and Orinus) and Triodia. The subtribe Orininae was not supported by our complete plastome data. The split between Cleistogenes and Orinus-Triodia clade go back to 14.01 Ma. Besides, our findings suggested that C. squarrosa and C. songorica are the successive early diverging groups in the phylogenetic analysis. The other 10 taxa are divided into two groups: a monophyletic group composed of Cleistogenes sp. nov. and C. caespitosa var. ramosa is sister to other eight Cleistogenes taxa. Cleistogenes was estimated to have experienced rapid divergence within a short period, which could be a major obstacle in resolving phylogenetic relationships within Cleistogenes. Collectively, our results provided valuable insights into the phylogenetic study of grass species.

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Molecular phylogenetic analysis of Dendrobium (Orchidaceae), with emphasis on the Australian section Dendrocoryne, and implications for generic classification

Australian Systematic Botany ◽

10.1071/sb07038 ◽

2008 ◽

Vol 21 (1) ◽

pp. 1 ◽

Cited By ~ 25

Author(s):

Jacinta M. Burke ◽

Michael J. Bayly ◽

Peter B. Adams ◽

Pauline Y. Ladiges

Keyword(s):

Phylogenetic Analysis ◽

Sequence Divergence ◽

Its Region ◽

Sister Group ◽

Main Group ◽

Internal Transcribed Spacers ◽

Nuclear Rdna ◽

Sister Relationship ◽

Asian Clade ◽

Molecular Phylogenetic

Sequences of the internal transcribed spacers (ITS) of nuclear rDNA were obtained for a broad range of dendrobium orchids for phylogenetic analysis using parsimony. A progressive approach was used to identify functional outgroups for analysis of all taxa in Dendrobium sect. Dendrocoryne. Our first, broadest analysis confirmed the results of other workers that Dendrobium sensu lato includes a major Australasian clade and a sister Asian clade. In the Australasian clade, the New Zealand species D. cunninghamii (=gen. Winika, Clements et al. 1997) was identified as the sister group to a well supported clade that includes the genera Cadetia, Diplocaulobium and Flickingeria, and Dendrobium sects Grastidium, Latouria, Spatulata, Australorchis (=gen. Australorchis), Rhizobium (= gen. Dockrillia) and Dendrocoryne. Sect. Dendrocoryne is probably polyphyletic, with two species, D. aemulum and D. callitrophilum (=gen. Tropilis), outside the main group and sect. Rhizobium (= gen. Dockrillia) nested within it. Sect. Australorchis (= gen. Australorchis) is possibly the sister group to the clade of Rhizobium plus the main group of Dendrocoryne. Thelychiton (a genus reinstated for several species in Dendrocoryne) is polyphyletic, given that Tetrabaculum (=D. tetragonum complex) and Dockrillia fall within the same clade. The splitting of the Australasian dendrobiums into various genera by other authors is excessive and unnecessary, and alternative taxonomic treatments are offered here for debate. Our study included accessions for all varieties in the following three widespread eastern Australian species: D. speciosum, D. kingianum and D. tetragonum. Each of these species showed significant sequence divergence between particular geographic regions, but some varieties had identical sequences. The splitting of D. speciosum into 11 species is not supported. We identified pseudogenes in the ITS region for D. fleckeri and D. finniganense, which appear to have evolved before these two species diverged, but support their sister relationship. Sequences for D. callitrophilum and D. (Grastidium) baileyi (the latter from GenBank) also appear to be pseudogenes, and these taxa need further study.

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Comparative morphology and phylogenetic systematics of the families Cheilodactylidae and Latridae (Perciformes: Cirrhitoidea), and proposal of a new classification

Zootaxa ◽

10.11646/zootaxa.4536.1.1 ◽

2018 ◽

Vol 4536 (1) ◽

pp. 1

Author(s):

KATSUYA KIMURA ◽

HISASHI IMAMURA ◽

TOSHIO KAWAI

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Comparative Morphology ◽

Monophyletic Group ◽

Phylogenetic Systematics ◽

New Classification ◽

Sister Relationship ◽

Transformation Series

The phylogenetic relationships of the families Cheilodactylidae and Latridae, plus related taxa, are examined from a detailed osteological perspective. The monophyly of each family is re-evaluated and a new classification is proposed on the basis of phylogenetic relationships. A phylogenetic analysis of characters in 67 transformation series showed Latridae to comprise a monophyletic group nested within cheilodactylids. Cheilodactylidae was non-monophyletic, but rather was formed by a clade including Cheilodactylus fasciatus and C. pixi having a sister relationship with a second clade comprising remaining cheilodactylids and latrids. A new classification is proposed, Cheilodactylidae, including only genus Cheilodactylus, and Latridae, including six genera (Latris, Nemadactylus, Mendosoma, Goniistius, Latridopsis and Dactylophora).

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Phylogenetic relationships in Neonectria species having Cylindrocarpon anamorphs inferred from mitochondrial ribosomal DNA sequences

Canadian Journal of Botany ◽

10.1139/b01-002 ◽

2001 ◽

Vol 79 (3) ◽

pp. 334-340 ◽

Cited By ~ 15

Author(s):

Feky R Mantiri ◽

Gary J Samuels ◽

James E Rahe ◽

Barry M Honda

Keyword(s):

Phylogenetic Analysis ◽

Dna Sequence ◽

Ribosomal Dna ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Sequence Divergence ◽

Small Subunit ◽

New Combinations ◽

Rdna Sequences ◽

Informal Groups

Mitochondrial small subunit (mtSSU) rDNA sequences elucidated phylogenetic relationships in Neonectria Wollenw. (anamorphs = Cylindrocarpon Wollenw.; Ascomycetes, Hypocreales). Twelve isolates representing seven species in five taxonomically informal groups of Neonectria were subjected to phylogenetic analysis. Fusarium inflexum R. Schneid. (teleomorph: Gibberella) and Nectria cinnabarina (Fr.) Fr. (= Nectria s.str.) were outgroups. All of the Neonectria species formed a strongly supported clade with respect to the outgroups, indicating a single ascomycete genus for the holomorphs of Cylindrocarpon. Within the Neonectria clade there were three well-supported subclades that only partially corresponded to phenotype-defined groups. DNA sequence divergence among the twelve Neonectria isolates, 2.3-7.4%, was sufficient to resolve them. The results suggest that the mtSSU rDNA region is appropriate for phylogenetic analysis of Neonectria and Cylindrocarpon. The following new combinations are proposed: Neonectria coronata, Neonectria discophora, Neonectria neomacrospora, Neonectria radicicola, Neonectria rugulosa, Neonectria veuillotiana.Key words: Ascomycetes, Hypocreales, Nectria, systematics, tree pathogens.

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Phylogenetic relationships of 'Polyalthia' in Fiji

PhytoKeys ◽

10.3897/phytokeys.165.57094 ◽

2020 ◽

Vol 165 ◽

pp. 99-113

Author(s):

Bine Xue ◽

Yanwen Chen ◽

Richard M. K. Saunders

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Strong Support ◽

The Other ◽

Molecular Phylogenetic Analysis ◽

Phylogenetic Study ◽

Herbarium Specimens ◽

Molecular Phylogenetic ◽

Taxonomic Changes

The genus Polyalthia (Annonaceae) has undergone dramatic taxonomic changes in recent years. Nine Polyalthia species have historically been recognized in Fiji, all of which have subsequently been transferred to three different genera, viz. Goniothalamus, Huberantha and Meiogyne. The transfer of six of these species has received strong molecular phylogenetic support, although the other three species, Polyalthia amoena, P. capillata and P. loriformis [all transferred to Huberantha], have never previously been sampled in a phylogenetic study. We address this shortfall by sampling available herbarium specimens of all three species and integrating the data in a molecular phylogenetic analysis. The resultant phylogeny provides strong support for the transfer of these species to Huberantha. The taxonomic realignment of all nine Fijian species formerly classified in Polyalthia is also clearly demonstrated and supported by the resultant phylogeny. The updated taxonomic treatments of the nine species, a key to the three genera and a key to the Fijian Huberantha species are provided.

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Comparative Chloroplast Genomes of Sorghum Species: Sequence Divergence and Phylogenetic Relationships

BioMed Research International ◽

10.1155/2019/5046958 ◽

2019 ◽

Vol 2019 ◽

pp. 1-11 ◽

Cited By ~ 5

Author(s):

Yun Song ◽

Yan Chen ◽

Jizhou Lv ◽

Jin Xu ◽

Shuifang Zhu ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Molecular Markers ◽

Species Identification ◽

Dna Markers ◽

Phylogenetic Relationships ◽

Sequence Divergence ◽

Monophyletic Group ◽

Ecological Diversity ◽

Chloroplast Genomes ◽

Gc Contents

Sorghum comprises 31 species that exhibit considerable morphological and ecological diversity. The phylogenetic relationships among Sorghum species still remain unresolved due to lower information on the traditional DNA markers, which provides a limited resolution for identifying Sorghum species. In this study, we sequenced the complete chloroplast genomes of Sorghum sudanense and S. propinquum and analyzed the published chloroplast genomes of S. bicolor and S. timorense to retrieve valuable chloroplast molecular resources for Sorghum. The chloroplast genomes ranged in length from 140,629 to 140,755 bp, and their gene contents, gene orders, and GC contents were similar to those for other Poaceae species but were slightly different in the number of SSRs. Comparative analyses among the four chloroplast genomes revealed 651 variable sites, 137 indels, and nine small inversions. Four highly divergent DNA regions (rps16-trnQ, trnG-trnM, rbcL-psaI, and rps15-ndhF), which were suitable for phylogenetic and species identification, were detected in the Sorghum chloroplast genomes. A phylogenetic analysis strongly supported that Sorghum is a monophyletic group in the tribe Andropogoneae. Overall, the genomic resources in this study could provide potential molecular markers for phylogeny and species identification in Sorghum.

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Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽

10.3390/insects12080668 ◽

2021 ◽

Vol 12 (8) ◽

pp. 668

Author(s):

Tinghao Yu ◽

Yalin Zhang

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Strong Support ◽

Intergenic Spacer ◽

Taxonomic Status ◽

Start Codon ◽

Gene Arrangement ◽

Mitochondrial Genomes ◽

Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

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Morphological, Ecological, and Molecular Divergence of Conogethes pinicolalis from C. punctiferalis (Lepidoptera: Crambidae)

Insects ◽

10.3390/insects12050455 ◽

2021 ◽

Vol 12 (5) ◽

pp. 455

Author(s):

Na Ra Jeong ◽

Min Jee Kim ◽

Sung-Soo Kim ◽

Sei-Woong Choi ◽

Iksoo Kim

Keyword(s):

Phylogenetic Analysis ◽

First Generation ◽

Incomplete Lineage Sorting ◽

Divergence Time ◽

Sequence Divergence ◽

Lineage Sorting ◽

Mitochondrial Coi ◽

Feeding Type ◽

Pine Trees ◽

Yellow Peach Moth

Conogethes pinicolalis has long been considered as a Pinaceae-feeding type of the yellow peach moth, C. punctiferalis, in Korea. In this study, the divergence of C. pinicolalis from the fruit-feeding moth C. punctiferalis was analyzed in terms of morphology, ecology, and genetics. C. pinicolalis differs from C. punctiferalis in several morphological features. Through field observation, we confirmed that pine trees are the host plants for the first generation of C. pinicolalis larvae, in contrast to fruit-feeding C. punctiferalis larvae. We successfully reared C. pinicolalis larvae to adults by providing them pine needles as a diet. From a genetic perspective, the sequences of mitochondrial COI of these two species substantially diverged by an average of 5.46%; moreover, phylogenetic analysis clearly assigned each species to an independent clade. On the other hand, nuclear EF1α showed a lower sequence divergence (2.10%) than COI. Overall, EF1α-based phylogenetic analysis confirmed each species as an independent clade, but a few haplotypes of EF1α indicated incomplete lineage sorting between these two species. In conclusion, our results demonstrate that C. pinicolalis is an independent species according to general taxonomic criteria; however, analysis of the EF1α sequence revealed a short divergence time.

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Diversity of pathogenic Pseudomonas isolated from citrus in Tunisia

AMB Express ◽

10.1186/s13568-020-01134-z ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Maroua Oueslati ◽

Magdalena Mulet ◽

Mohamed Zouaoui ◽

Charlotte Chandeysson ◽

Jorge Lalucat ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Pseudomonas Syringae ◽

Ice Nucleation ◽

Phylogenetic Study ◽

Future Studies ◽

Citrus Orchards ◽

First Time ◽

New Cultivars

Abstract The damages observed in Tunisian citrus orchards have prompted studies on the Pseudomonas spp. responsible for blast and black pit. Prospective orchards between 2015 and 2017 showed that the diseases rapidly spread geographically and to new cultivars. A screening of Pseudomonas spp. isolated from symptomatic trees revealed their wide diversity according to phylogenetic analysis of their housekeeping rpoD and cts genes. The majority of strains were affiliated to Pseudomonas syringae pv. syringae (Phylogroup PG02b), previously described in Tunisia. However, they exhibited various BOX-PCR fingerprints and were not clonal. This work demonstrated, for the first time in Tunisia, the involvement of Pseudomonas cerasi (PG02a) and Pseudomonas congelans (PG02c). The latter did not show significant pathogenicity on citrus, but was pathogenic on cantaloupe and active for ice nucleation that could play a role in the disease. A comparative phylogenetic study of citrus pathogens from Iran, Montenegro and Tunisia revealed that P. syringae (PG02b) strains are closely related but again not clonal. Interestingly P. cerasi (PG02a) was isolated in two countries and seems to outspread. However, its role in the diseases is not fully understood and it should be monitored in future studies. The diversity of pathogenic Pseudomonas spp. and the extension of the diseases highlight that they have become complex and synergistic. It opens questions about which factors favor diseases and how to fight against them efficiently and with sustainable means.

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Use of tall fescue EST-SSR markers in phylogenetic analysis of cool-season forage grasses

Genome ◽

10.1139/g05-029 ◽

2005 ◽

Vol 48 (4) ◽

pp. 637-647 ◽

Cited By ~ 64

Author(s):

M A. Rouf Mian ◽

Malay C Saha ◽

Andrew A Hopkins ◽

Zeng-Yu Wang

Keyword(s):

Phylogenetic Analysis ◽

Ssr Markers ◽

Tall Fescue ◽

Related Species ◽

Grass Species ◽

Forage Grass ◽

Forage Grasses ◽

Cool Season ◽

Phylogenetic Relations ◽

Wide Range

Microsatellites or simple sequence repeats (SSRs) are highly useful molecular markers for plant improvement. Expressed sequence tag (EST)-SSR markers have a higher rate of transferability across species than genomic SSR markers and are thus well suited for application in cross-species phylogenetic studies. Our objectives were to examine the amplification of tall fescue EST-SSR markers in 12 grass species representing 8 genera of 4 tribes from 2 subfamilies of Poaceae and the applicability of these markers for phylogenetic analysis of grass species. About 43% of the 145 EST-SSR primer pairs produced PCR bands in all 12 grass species and had high levels of polymorphism in all forage grasses studied. Thus, these markers will be useful in a variety of forage grass species, including the ones tested in this study. SSR marker data were useful in grouping genotypes within each species. Lolium temulentum, a potential model species for cool-season forage grasses, showed a close relation with the major Festuca–Lolium species in the study. Tall wheatgrass was found to be closely related to hexaploid wheat, thereby confirming the known taxonomic relations between these species. While clustering of closely related species was found, the effectiveness of such data in evaluating distantly related species needs further investigations. The phylogenetic trees based on DNA sequences of selected SSR bands were in agreement with the phylogenetic relations based on length polymorphism of SSRs markers. Tall fescue EST-SSR markers depicted phylogenetic relations among a wide range of cool-season forage grass species and thus are an important resource for researchers working with such grass species.Key words: phylogeny, EST-SSR, forage grasses, tall fescue.

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Bulinus species on Madagascar: molecular evolution, genetic markers and compatibility with Schistosoma haematobium

Parasitology ◽

10.1017/s003118200100806x ◽

2001 ◽

Vol 123 (7) ◽

pp. 261-275 ◽

Cited By ~ 22

Author(s):

J. R. STOTHARD ◽

P. BRÉMOND ◽

L. ANDRIAMARO ◽

B. SELLIN ◽

E. SELLIN ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Ribosomal Subunit ◽

Population Genetic Analysis ◽

Basal Node ◽

Pcr Rflp ◽

Dna Sequence Variation ◽

Long Time ◽

Laboratory Infection ◽

Species Groups ◽

Nucleotide Divergence

Of the four species of Bulinus found on Madagascar, three species: B. obtusispira, B. liratus and B. bavayi are endemic while the fourth, B. forskalii, is probably a recent introduction from the African mainland. The evolutionary relationships of these species with Bulinus species from Africa were studied by phylogenetic analysis of DNA sequence variation at two mitochondrial loci: cytochrome oxidase subunit I (COI) and large ribosomal subunit (LSU) or 16S. The observed levels of nucleotide divergence within Bulinus were substantial but may underestimate the true levels as there was evidence of ‘saturation' of transitional substitutions at both loci. A putative secondary structure model for the sequenced segment of the 16S was developed. Subsequent phylogenetic analysis using transversional changes only for both loci, showed that there were contrasting levels of divergence within the four species groups. B. obtusispira was consistently placed within the B. africanus group, appearing ancestral to this group and was closest to the basal node within Bulinus. Together with B. bavayi, the two species appear to have been isolated on Madagascar for a long time, contrasting with both B. liratus and B. forskalii that appear more recent colonisers; however, estimate of exact times of divergence is problematic. A PCR-RFLP assay was developed to enable identification and discrimination of B. obtusispira and B. liratus using discriminatory variation within the COI. To enable population genetic analysis within B. obtusispira, microsatellite markers were developed using an enrichment method and 8 primer pairs are reported. Laboratory infection experiments using Madasgacan S. haematobium from the Mahabo area showed that certain populations of B. obtusispira, B. liratus and B. bavayi were compatible.

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