The use of chloroplast genome sequences to solve phylogenetic incongruences inPolystachyaHook (Orchidaceae Juss)

The use of next generation sequencing to solve phylogenetic incongruences in Orchidaceae Juss

10.7287/peerj.preprints.26530v1 ◽

2018 ◽

Author(s):

Narjara Lopes de Abreu ◽

Ruy José Válka Alves ◽

Sérgio Ricardo Sodré Cardoso ◽

Yann JK Bertrand ◽

Filipe Sousa ◽

...

Keyword(s):

Next Generation Sequencing ◽

Chloroplast Genome ◽

Phylogenetic Trees ◽

Diploid Species ◽

Model Organisms ◽

Current Evidence ◽

Next Generation ◽

Coding Regions ◽

Phylogenetic Implications ◽

Generation Sequencing

Background. Current evidence suggests that for more robust estimates of species tree and divergence times, several unlinked genes are required. However, most phylogenetic trees for non-model organisms are based on single sequences or just a few regions, using traditional sequencing methods. Techniques for massive parallel sequencing or Next Generation Sequencing are an alternative to traditional methods that allow access to hundreds of DNA regions. Here we use this approach to resolve the phylogenetic incongruence found in Polystachya Hook. (Orchidaceae), a genus that stands out due to several interesting aspects, including cytological (polyploid and diploid species), evolutionary (reticulate evolution) and biogeographical (species widely distributed in the tropics and high endemism in Brazil). The genus has a notoriously complicated taxonomy, with several sections that are widely used but probably not monophyletic. Methods. We generated the complete chloroplast genome of 48 individuals from one clade within the genus. The method consisted in construction of genomic libraries, hybridization to RNA probes designed from available sequences of a related species, and subsequent sequencing of the product. We also tested how well a smaller sample of the chloroplast genome would perform in phylogenetic inference in two ways: by duplicating a fast region and analysing multiple copies of this dataset, and by sampling without replacement from all non-coding regions in our alignment. We further examined the phylogenetic implications of non-coding sequences that appear to have undergone hairpin inversions (reverse complemented sequences associated with small loops). Results. We retrieved 131,214 bp, including coding and non-coding regions of the chloroplast genome. The phylogeny was able to fully resolve the relationships among all species in the targeted clade with high support values. The first divergent species are represented by African accessions and the most recent ones are among Neotropical species. Discussion. Our results indicate that using the entire chloroplast is a better option than screening highly variable markers, especially when the expected tree is likely to contain many short branches. The phylogeny inferred is consistent with the proposed origin of the genus, showing a probable origin in Africa, with later dispersal into the Neotropics, as evidenced by a clade containing all Neotropical individuals. The multiple positions of Polystachya concreta (Jacq.) Garay & Sweet in the phylogeny are explained by allotetraploidy. Polystachya estrellensis Rchb.f. can be considered a genetically distinct species from P. concreta and P. foliosa (Lindl.) Rchb.f., but the delimitation of P. concreta remains uncertain. Our study shows that next generation sequencing provides a powerful tool for inferring relationships at low taxonomic levels, even in taxonomically challenging groups with short branches and intricate morphology.

The use of next generation sequencing to solve phylogenetic incongruences in Orchidaceae Juss

10.7287/peerj.preprints.26530 ◽

2018 ◽

Author(s):

Narjara Lopes de Abreu ◽

Ruy José Válka Alves ◽

Sérgio Ricardo Sodré Cardoso ◽

Yann JK Bertrand ◽

Filipe Sousa ◽

...

Keyword(s):

Next Generation Sequencing ◽

Chloroplast Genome ◽

Phylogenetic Trees ◽

Diploid Species ◽

Model Organisms ◽

Current Evidence ◽

Next Generation ◽

Coding Regions ◽

Phylogenetic Implications ◽

Generation Sequencing

Background. Current evidence suggests that for more robust estimates of species tree and divergence times, several unlinked genes are required. However, most phylogenetic trees for non-model organisms are based on single sequences or just a few regions, using traditional sequencing methods. Techniques for massive parallel sequencing or Next Generation Sequencing are an alternative to traditional methods that allow access to hundreds of DNA regions. Here we use this approach to resolve the phylogenetic incongruence found in Polystachya Hook. (Orchidaceae), a genus that stands out due to several interesting aspects, including cytological (polyploid and diploid species), evolutionary (reticulate evolution) and biogeographical (species widely distributed in the tropics and high endemism in Brazil). The genus has a notoriously complicated taxonomy, with several sections that are widely used but probably not monophyletic. Methods. We generated the complete chloroplast genome of 48 individuals from one clade within the genus. The method consisted in construction of genomic libraries, hybridization to RNA probes designed from available sequences of a related species, and subsequent sequencing of the product. We also tested how well a smaller sample of the chloroplast genome would perform in phylogenetic inference in two ways: by duplicating a fast region and analysing multiple copies of this dataset, and by sampling without replacement from all non-coding regions in our alignment. We further examined the phylogenetic implications of non-coding sequences that appear to have undergone hairpin inversions (reverse complemented sequences associated with small loops). Results. We retrieved 131,214 bp, including coding and non-coding regions of the chloroplast genome. The phylogeny was able to fully resolve the relationships among all species in the targeted clade with high support values. The first divergent species are represented by African accessions and the most recent ones are among Neotropical species. Discussion. Our results indicate that using the entire chloroplast is a better option than screening highly variable markers, especially when the expected tree is likely to contain many short branches. The phylogeny inferred is consistent with the proposed origin of the genus, showing a probable origin in Africa, with later dispersal into the Neotropics, as evidenced by a clade containing all Neotropical individuals. The multiple positions of Polystachya concreta (Jacq.) Garay & Sweet in the phylogeny are explained by allotetraploidy. Polystachya estrellensis Rchb.f. can be considered a genetically distinct species from P. concreta and P. foliosa (Lindl.) Rchb.f., but the delimitation of P. concreta remains uncertain. Our study shows that next generation sequencing provides a powerful tool for inferring relationships at low taxonomic levels, even in taxonomically challenging groups with short branches and intricate morphology.

Disentangling Reticulate Evolution of North Temperate Haplostemonous Ludwigia (Onagraceae)

Annals of the Missouri Botanical Garden ◽

10.3417/2020479 ◽

2020 ◽

Vol 105 (2) ◽

pp. 163-182

Author(s):

Shih-Hui Liu ◽

Hsun-An Yang ◽

Yoshiko Kono ◽

Peter C. Hoch ◽

Janet C. Barber ◽

...

Keyword(s):

Phylogenetic Trees ◽

Diploid Species ◽

Single Copy ◽

Reticulate Evolution ◽

Plant Evolution ◽

Hybrid Origin ◽

Ploidy Levels ◽

The North ◽

Molecular Phylogenetic ◽

Ancestral Area Reconstruction

While it is known that whole genome duplication (WGD) and reticulate evolution play important roles in plant evolution, the origins and evolutionary histories of most polyploid and reticulate groups are still poorly known. The North Temperate haplostemonous (NTH) Ludwigia L. (sections Isnardia (L.) W. L. Wagner & Hoch, Ludwigia, Microcarpium Munz, and Miquelia P. H. Raven) group, characterized by having 4-merous and haplostemonous flowers, pluriseriate and free seeds, glabrous and convex nectaries, and a north-temperate distribution, is a polyploid complex (2×, 4×, 6×, and 8×) of 24 species with frequent reports of inter- and intrasectional hybridization. Although earlier biosystematics studies postulated some evolutionary scenarios and recent molecular phylogenetic studies have partially tested these propositions, the full history of their reticulate evolution remains puzzling. In this study, we sequenced four chloroplast regions (rpL16, rpoB-trnC, trnL-trnF, and ycf6-psbM) and conducted extensive molecular cloning of the biparentally inherited single-copy nuclear PgiC gene (376 clones in total), sampling 23 of the 24 NTH Ludwigia species whose chromosome numbers and ploidy levels were confirmed. Both the chloroplast and PgiC trees include strongly supported sister clades of section Ludwigia (four diploid species) and the “Microcarpium complex” (composed of sections Isnardia, Microcarpium, and Miquelia), which together are sister to the rest of Ludwigia. In the PgiC tree, eight clades are identified within the Microcarpium complex, with four clades including no extant diploid species. Neither sections Isnardia nor Microcarpium are monophyletic, while the monospecific section Miquelia has a hybrid origin. By integrating our phylogenetic trees with previous cytological hypotheses, the reticulate evolution of NTH Ludwigia is disentangled and four to eight extinct diploid species are inferred. Ancestral area reconstruction supports a North American origin of L. ovalis whose current East Asian distribution reflects a relict of the Arcto-Tertiary Geoflora. Based on our results, we propose to synonymize sections Microcarpium and Miquelia under the expanded section Isnardia.

Analysis of random and specific sequences of nuclear and cytoplasmic DNA in diploid and tetraploid American wild rice species (Oryza spp.)

Genome ◽

10.1139/g01-019 ◽

2001 ◽

Vol 44 (3) ◽

pp. 476-494 ◽

Cited By ~ 20

Author(s):

Glaucia Salles Cortopassi Buso ◽

Paulo Hideo Nakano Rangel ◽

Márcio Elias Ferreira

Keyword(s):

Flow Cytometry ◽

Wild Rice ◽

Phylogenetic Trees ◽

Rapd Markers ◽

Diploid Species ◽

Distinct Species ◽

Individual Species ◽

Genome Species ◽

Wild Rice Species ◽

Cladistic Analyses

A sample of American wild rice and other accessions of the genus Oryza were studied at polymorphic regions of nuclear, mitochondrial, and chloroplastic genomes. First, flow cytometry, genome-specific RAPD markers, and chromosome counting were utilized to verify the original ploidy and classification of 230 accessions studied. Based on these methods, 8% of the accessions were considered to be misclassified either taxonomically or as a result of contamination. Second, a fine resolution analysis was conducted at genomic regions sampled at random by RAPD markers and at specific sites of the chloroplast and mitochondrial DNA by cleaved amplified polymorphic sequence (CAPS) analysis. Phylogenetic trees resulting from phenetic and cladistic analyses of RAPD, cpDNA, and mtDNA polymorphisms were obtained. The results indicated that the American diploid species O. glumaepatula should be considered an individual species, distinct from O. rufipogon, and confirmed that the American tetraploid species (O. alta, O. grandiglumis, and O. latifolia) belong to the O. officinalis complex. The data indicate that these species should still be treated as a group rather than as three distinct species and that their closest relative is a CC-genome species. It was estimated that the diploid and tetraploid American species diverged from O. sativa O. nivara (AA genome) and CC- and BBCC-genome species, respectively, 20 million years ago.Key words: RAPD, cleaved amplified polymorphic sequences, flow cytometry, Oryza glumaepatula, rice evolution.

Uncovering dynamic evolution in the plastid genome of seven Ligusticum species provides insights into species discrimination and phylogenetic implications

Scientific Reports ◽

10.1038/s41598-020-80225-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Can Yuan ◽

Xiufen Sha ◽

Miao Xiong ◽

Wenjuan Zhong ◽

Yu Wei ◽

...

Keyword(s):

Plastid Genome ◽

Species Discrimination ◽

Chloroplast Genomes ◽

Genomic Arrangement ◽

Phylogenetic Implications ◽

Solid Foundation ◽

Conserved Gene ◽

Fine Resolution ◽

Genome Scale ◽

First Time

AbstractLigusticum L., one of the largest members in Apiaceae, encompasses medicinally important plants, the taxonomic statuses of which have been proved to be difficult to resolve. In the current study, the complete chloroplast genomes of seven crucial plants of the best-known herbs in Ligusticum were presented. The seven genomes ranged from 148,275 to 148,564 bp in length with a highly conserved gene content, gene order and genomic arrangement. A shared dramatic decrease in genome size resulted from a lineage-specific inverted repeat (IR) contraction, which could potentially be a promising diagnostic character for taxonomic investigation of Ligusticum, was discovered, without affecting the synonymous rate. Although a higher variability was uncovered in hotspot divergence regions that were unevenly distributed across the chloroplast genome, a concatenated strategy for rapid species identification was proposed because separate fragments inadequately provided variation for fine resolution. Phylogenetic inference using plastid genome-scale data produced a concordant topology receiving a robust support value, which revealed that L. chuanxiong had a closer relationship with L. jeholense than L. sinense, and L. sinense cv. Fuxiong had a closer relationship to L. sinense than L. chuanxiong, for the first time. Our results not only furnish concrete evidence for clarifying Ligusticum taxonomy but also provide a solid foundation for further pharmaphylogenetic investigation.

Whole Chloroplast Genomes reveals the uniqueness of Bolivian native cacao (Theobroma cacao) from the northern part of Bolivia

10.1101/2021.04.16.440153 ◽

2021 ◽

Author(s):

Marcia Gumiel ◽

Oscar M Rollano-Penaloza ◽

Carmelo Peralta-Rivero ◽

Leslie Tejeda ◽

Valeria D. Palma Encinas ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Next Generation Sequencing ◽

Theobroma Cacao ◽

Phylogenetic Trees ◽

Plastid Genome ◽

Next Generation ◽

Center Of Origin ◽

Chloroplast Genomes ◽

Geographical Locations ◽

Generation Sequencing

We report the complete chloroplast sequences of two varieties of Theobroma cacao collected in the Bolivian Amazonia using Next-Generation Sequencing. Comparisons made between these two chloroplast genomes and the Belizean reference plastid genome identified 19 and 22 nucleotide variants. The phylogenetic analysis reported three main T. cacao clades belonging to the Forastero, Criollo and Trinitario groups. The Bolivian Native Cacao varieties were located inside the Trinitario group forming their unique branch. The Bolivian Native Cacao branch reveals a possible new subpopulation different from the well-characterized T. cacao subpopulations. The phylogenetic trees showed that the relationships among the T. cacao varieties were consistent with their geographical locations placing the Cacao Center of Origin in Western Amazon. The data presented here will contribute to the usage of ultrabarcoding to distinguish different T. cacao varieties and to identify native cacaos from introduced cacaos. Thus helping in the conservation of local native varieties of T. cacao.

Sperm ultrastructure of Pochazia shantungensis (Chou & Lu) and Ricania speculum (Walker) (Hemiptera, Ricaniidae) with phylogenetic implications

ZooKeys ◽

10.3897/zookeys.880.32810 ◽

2019 ◽

Vol 880 ◽

pp. 43-59

Author(s):

Zhen Jiang ◽

Jianing Liu ◽

Daozheng Qin

Keyword(s):

Neck Region ◽

Mature Spermatozoon ◽

Current Evidence ◽

Sperm Ultrastructure ◽

Transmission Electron ◽

Phylogenetic Implications ◽

Dense Substance ◽

The Individual ◽

Relationship Of ◽

Centriole Adjunct

The sperm ultrastructure of two ricaniid species, Pochazia shantungensis (Chou & Lu) and Ricania speculum (Walker), was investigated using light and transmission electron microscopy. Both species have monoflagellate sperm, the shape and ultrastructure of the mature spermatozoon of these two species are similar in morphology, and 128 spermatozoa are organized into sperm bundles with their heads embedded in a homogenous matrix forming the spermatodesmata. The individual sperm is filiform and includes the head, neck and flagellum. The head is needle-like, with a bilayer acrosome and an inferior elongated nucleus which is formed of homogeneously compact and electron-dense chromatin. The neck region is indistinct and is comprised of the centriole and centriole adjunct with a homogeneous dense substance. The long flagellum has the typical 9 + 9 + 2 axoneme microtubule pattern and two symmetrical mitochondrial derivatives with an orderly array of cristae flanking both sides, and a pair of well-developed fishhook-shaped accessory bodies. Current evidence shows that ricaniid species have D-shaped mitochondrial derivatives in cross-section and a serrated electron-dense region. The phylogenetic relationship of Fulgoroidea with other superfamilies in Auchenorrhyncha is briefly discussed.

Abstract 2722: Large Scale Mutation Discovery Screen Identifies Functionally Variant UGDH Alleles in Patients with Atrioventricular Valve Defects

Circulation ◽

10.1161/circ.116.suppl_16.ii_604 ◽

2007 ◽

Vol 116 (suppl_16) ◽

Author(s):

Jeroen Bakkers ◽

Sonja Chocron ◽

Victor Gouriev ◽

Kelly Smith ◽

Ronald Lekanne dit Deprez ◽

...

Keyword(s):

Candidate Genes ◽

Congenital Heart Defects ◽

Congenital Heart ◽

Large Scale ◽

Heart Defects ◽

Glucose Dehydrogenase ◽

Model Organisms ◽

Missense Mutations ◽

Coding Regions

Background: Congenital heart defects are the most common birth defects. Although genetic dispositions are believed to cause CHDs, only few genes have been identified that harbour mutations causing such defects. Studies in model organisms have identified many essential genes for cardiac development. UDP-glucose dehydrogenase (UGDH) enzymatic activity is required for the signal transduction of FGF and Wnt ligands and zebrafish jekyll/ugdh mutations lack AV valves. Methods and Results: From literature candidate genes were selected that are essential for AV canal-, septum-, and valve formation. By large scale sequencing we analysed the coding regions of 36 candidate genes in 192 patients with reported AVSDs. As a result we identified 457 genetic variations of which 207 variants are in flanking non-coding regions, 156 variants are in coding regions but silent and 94 variants are non-synonymous variants that alter the protein sequence. Comparison with the available databases such as HapMap and screening 350 control individuals resulted in the validation of 49 non-synonomous missense mutations in 23 genes only present in the patient group. These included novel GATA4 missense mutations (R285C and M224V) located in the highly conserved DNA binding domains, which by in vitro analysis significantly reduce transcriptional activity of the protein. Three patients with mitral valvar prolapse and mitral regurgitation were identified with novel missense mutations in the UDP-glucose dehydrogenase (UGDH) gene (R141C and E416D). In vitro experiments demonstrated a negative affect on enzyme activity and stability by a change in protein conformation. Furthermore, experiments in zebrafish jekyll/ugdh mutants showed that UGDH R141C and UGDH E416D couldn’t rescue the defects in AV formation demonstrating an inactivating effect of these missense mutations in vivo. Conclusions: A model organism based candidate gene screen in CHD patients resulted in the identification of novel functional missense mutations in the UGDH gene not previously implicated in congenital heart defects.

The Dogma of Dingoes—Taxonomic status of the dingo: A reply to Smith et al.

Zootaxa ◽

10.11646/zootaxa.4564.1.7 ◽

2019 ◽

Vol 4564 (1) ◽

pp. 198 ◽

Cited By ~ 3

Author(s):

STEPHEN M. JACKSON ◽

PETER J.S. FLEMING ◽

MARK D.B. ELDRIDGE ◽

SANDY INGLEBY ◽

TIM FLANNERY ◽

...

Keyword(s):

Taxonomic Status ◽

Distinct Species ◽

Domestic Dogs ◽

Current Evidence ◽

Morphological Evidence ◽

Evolutionary Divergence ◽

Gray Wolf ◽

Separate Species ◽

Gray Wolves ◽

Narrow Scope

Adopting the name Canis dingo for the Dingo to explicitly denote a species-level taxon separate from other canids was suggested by Crowther et al. (2014) as a means to eliminate taxonomic instability and contention. However, Jackson et al. (2017), using standard taxonomic and nomenclatural approaches and principles, called instead for continued use of the nomen C. familiaris for all domestic dogs and their derivatives, including the Dingo. (This name, C. familiaris, is applied to all dogs that derive from the domesticated version of the Gray Wolf, Canis lupus, based on nomenclatural convention.) The primary reasons for this call by Jackson et al. (2017) were: (1) a lack of evidence to show that recognizing multiple species amongst the dog, including the Dingo and New Guinea Singing Dog, was necessary taxonomically, and (2) the principle of nomenclatural priority (the name familiaris Linnaeus, 1758, antedates dingo Meyer, 1793). Overwhelming current evidence from archaeology and genomics indicates that the Dingo is of recent origin in Australia and shares immediate ancestry with other domestic dogs as evidenced by patterns of genetic and morphological variation. Accordingly, for Smith et al. (2019) to recognise Canis dingo as a distinct species, the onus was on them to overturn current interpretations of available archaeological, genomic, and morphological datasets and instead show that Dingoes have a deeply divergent evolutionary history that distinguishes them from other named forms of Canis (including C. lupus and its domesticated version, C. familiaris). A recent paper by Koepfli et al. (2015) demonstrates exactly how this can be done in a compelling way within the genus Canis—by demonstrating deep evolutionary divergence between taxa, on the order of hundreds of thousands of years, using data from multiple genetic systems. Smith et al. (2019) have not done this; instead they have misrepresented the content and conclusions of Jackson et al. (2017), and contributed extraneous arguments that are not relevant to taxonomic decisions. Here we dissect Smith et al. (2019), identifying misrepresentations, to show that ecological, behavioural and morphological evidence is insufficient to recognise Dingoes as a separate species from other domestic dogs. We reiterate: the correct binomial name for the taxon derived from Gray Wolves (C. lupus) by passive and active domestication, including Dingoes and other domestic dogs, is Canis familiaris. We are strongly sympathetic to arguments about the historical, ecological, cultural, or other significance of the Dingo, but these are issues that will have to be considered outside of the more narrow scope of taxonomy and nomenclature.

A genomic perspective on the taxonomy of the subtribe Carcharodina (Lepidoptera: Hesperiidae: Carcharodini)

Zootaxa ◽

10.11646/zootaxa.4748.1.10 ◽

2020 ◽

Vol 4748 (1) ◽

pp. 182-194 ◽

Cited By ~ 1

Author(s):

JING ZHANG ◽

ERNST BROCKMANN ◽

QIAN CONG ◽

JINHUI SHEN ◽

NICK V. GRISHIN

Keyword(s):

Dna Sequences ◽

Type Species ◽

Phylogenetic Trees ◽

Type Specimens ◽

African Species ◽

Protein Coding ◽

Coding Regions ◽

As Species ◽

Close Relatives ◽

Genomic Regions

We obtained whole genome shotgun sequences and phylogenetically analyzed protein-coding regions of representative skipper butterflies from the genus Carcharodus Hübner, [1819] and its close relatives. Type species of all available genus-group names were sequenced. We find that species attributed to four exclusively Old World genera (Spialia Swinhoe, 1912, Gomalia Moore, 1879, Carcharodus Hübner, [1819] and Muschampia Tutt, 1906) form a monophyletic group that we call a subtribe Carcharodina Verity, 1940. In the phylogenetic trees built from various genomic regions, these species form 7 (not 4) groups that we treat as genera. We find that Muschampia Tutt, 1906 is not monophyletic, and the 5th group is formed by currently monotypic genus Favria Tutt, 1906 new status (type species Hesperia cribrellum Eversmann, 1841), which is sister to Gomalia. The 6th and 7th groups are composed of mostly African species presently placed in Spialia. These groups do not have names and are described here as Ernsta Grishin, gen. n. (type species Pyrgus colotes Druce, 1875) and Agyllia Grishin, gen. n. (type species Pyrgus agylla Trimen, 1889). Two subgroups are recognized in Ernsta: the nominal subgenus and a new one: Delaga Grishin, subgen. n. (type species Pyrgus delagoae Trimen, 1898). Next, we observe that Carcharodus is not monophyletic, and species formerly placed in subgenera Reverdinus Ragusa, 1919 and Lavatheria Verity, 1940 are here transferred to Muschampia. Furthermore, due to differences in male genitalia or DNA sequences, we reinstate Gomalia albofasciata Moore, 1879 and Gomalia jeanneli (Picard, 1949) as species, not subspecies or synonyms of Gomalia elma (Trimen, 1862), and Spialia bifida (Higgins, 1924) as a species, not subspecies of Spialia zebra (Butler, 1888). Sequencing of the type specimens reveals 2.2-3.2% difference in COI barcodes, the evidence that combined with wing pattern differences suggests a new status of a species for Spialia lugens (Staudinger, 1886) and Spialia carnea (Reverdin, 1927), formerly subspecies of Spialia orbifer (Hübner, [1823]).