Resolving generic limits in Cyperaceae tribe Abildgaardieae using targeted sequencing

2021 ◽  
Author(s):  
Isabel Larridon ◽  
Alexandre R Zuntini ◽  
Russell L Barrett ◽  
Karen L Wilson ◽  
Jeremy J Bruhl ◽  
...  
Keyword(s):  
Sanger Sequencing ◽  
Democratic Republic Of Congo ◽  
Targeted Sequencing ◽  
Morphological Data ◽  
Phylogenetic Hypothesis ◽  
Sequencing Data ◽  
African Species ◽  
Limited Sampling ◽  
Molecular Phylogenetic ◽  
Large Genus

Abstract Morphological characterizations of genera in Cyperaceae tribe Abildgaardieae have been highly problematic and the subject of much debate. Earlier molecular phylogenetic studies based on Sanger sequencing and a limited sampling have indicated that several generic circumscriptions are not monophyletic. Here, we provide the first phylogenetic hypothesis for Abildgaardieae using targeted sequencing data obtained with the Angiosperms353 enrichment panel for 50 species. We test whether recent taxonomic decisions made based on Sanger sequencing data are validated by our targeted sequencing data. Our results support subsuming the small African genus Nemum into the large genus Bulbostylis and subsuming the monotypic genus Crosslandia into the diverse genus Fimbristylis. Also, our results support the recent publication of the new genus Zulustylis for two African species previously placed in Fimbristylis. Furthermore, we investigate the phylogenetic placement of recently described tropical Australian endemic species of Actinoschoenus, which are recognized here as the new morphologically cryptic genus Scleroschoenus. Based on our phylogenetic hypothesis and supported by morphological data, we recognize the genus Abildgaardia. The placement in Abildgaardieae of two monotypic genera Nelmesia and Trichoschoenus, only known from the type collections from the Democratic Republic of Congo and Madagascar, respectively, are also discussed. New combinations and lectotypifications are made in Abildgaardia, Actinoschoenus, Arthrostylis and Scleroschoenus.

scholarly journals Genetic investigation of 211 Chinese families expands the mutational and phenotypical spectra of hereditary retinopathy genes through targeted sequencing technology

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Zhouxian Bai ◽  
Yanchuan Xie ◽  
Lina Liu ◽  
Jingzhi Shao ◽  
Yuying Liu ◽  
...  
Keyword(s):  
Sanger Sequencing ◽  
Molecular Genetic ◽  
Gene Mutations ◽  
Central China ◽  
Targeted Sequencing ◽  
Sequencing Data ◽  
Targeted Next Generation Sequencing ◽  
Pathogenic Variants ◽  
Number Of Patients ◽  
Ophthalmologic Examination

Abstract Background Hereditary retinopathy is a significant cause of blindness worldwide. Despite the discovery of many mutations in various retinopathies, a large number of patients remain genetically undiagnosed. Targeted next-generation sequencing of the human genome is a suitable approach for the molecular diagnosis of retinopathy. Methods We describe a cohort of 211 families from central China with various forms of retinopathy; 95 patients were investigated using multigene panel sequencing, and the other 116 with suspected Leber hereditary optic neuropathy (LHON) were tested by Sanger sequencing. The detected variation of targeted sequencing was verified by PCR-based Sanger sequencing. We performed a comprehensive analysis of the cases using sequencing data and ophthalmologic examination information. Results Potential causal mutations were identified in the majority of families with retinopathy (57.9% of 95 families) and suspected LHON (21.6% of 116 families). There were 68 variants of a certain significance distributed in 31 known disease-causing genes in the 95 families; 37 of the variants are novel and have not been reported to be related to hereditary retinopathy. The NGS panel solution provided a 45.3% potential diagnostic rate for retinopathy families, with candidate gene mutations of undefined pathogenicity revealed in another 12.6%of the families. Conclusion Our study uncovered novel mutations and phenotypic aspects of retinopathy and demonstrated the genetic and clinical heterogeneity of related conditions. The findings show the detection rate of pathogenic variants in patients with hereditary retinopathy in central China as well as the diversity and gene distribution of these variants. The significance of molecular genetic testing for patients with hereditary retinopathy is also highlighted.

A novel approach to detect large indels from targeted sequencing data in clinical cancer setting.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e13002-e13002 ◽  
Author(s):  
Lijuan Chen ◽  
Caiping Chen ◽  
Dongling Chen ◽  
Qiuyi Zou ◽  
Gungwei Qin ◽  
...  
Keyword(s):  
Sanger Sequencing ◽  
Break Point ◽  
Accurate Method ◽  
Targeted Sequencing ◽  
Sequencing Data ◽  
Illumina Platform ◽  
Cancer Treatments ◽  
Clinical Cancer ◽  
Large Indels ◽  
Cancer Setting

e13002 Background: Next generation sequencing (NGS) technologies have already shown numerous advances to revolutionize our understanding of cancer genomic profiling and improve cancer treatments. There have been many NGS data analysis tools available for identification of different genomic alternations including short insertion and deletion (short indel, < 25 bp in general). However, detection of > 100 bp large indel (L-indel) from short reads (generally < 200 bp) remains a huge challenge. L-indels identified in genes like MET and FLT3 have proven a critical implication in cancer treatments. Moreover, there is an urgent need for an algorithm to validate L-indels generated by genomic modification systems like ZFN, TALENs and CRISPR/Cas9. Methods: A novel algorithm was developed for calling L-indels in targeted sequencing data as following: raw reads were first filtered by selecting high-quality ones and correcting wrong bases; a chunk of contig (unitig) was then assembled and aligned to reference genome; lastly, break point information was collected and L-indels were calculated. The algorithm was applied on the reads generated from NA12878 cell line and FFPE samples collected in our lab respectively on the Illumina platform. Validation were performed by PCR and Sanger sequencing. Results: 22 novel exonic L-indels (17 deletions and 5 insertions) were identified with a median size of 1,616 bp (range: 25-6,684 bp) from NA12878 sequencing data and 100% successfully confirmed by Sanger sequencing. In addition, 6 out of 9 reported L-indels were also found with the rest awaiting for further exploration. Strikingly, a 2,446 bp deletion on MSH6, encodes an important component in mismatch repair (MMR) system, was detected on a FFPE sample of a lung cancer adenocarcinoma, which prompted to consideration of MMR deficiency otherwise. Conclusions: We have developed and validated a novel and accurate method for NGS large indels detection dedicated for targeted sequencing data in clinical cancer setting. Equipment of this method will greatly increase the capability of comprehensively understanding genomic alterations from a single NGS-based assay, and provide more information for potential clinical use.

scholarly journals Cryptic diversity in Mediterranean gastropods of the genus Aplus (Neogastropoda: Buccinidae)

2016 ◽  
Vol 80 (4) ◽  
pp. 521 ◽  
Author(s):  
Chrifa Aissaoui ◽  
Nicolas Puillandre ◽  
Philippe Bouchet ◽  
Giulia Fassio ◽  
Maria Vittoria Modica ◽  
...  
Keyword(s):  
Eastern Mediterranean ◽  
Single Species ◽  
Integrative Taxonomy ◽  
Morphological Data ◽  
Molecular Evidence ◽  
African Species ◽  
Mediterranean Populations ◽  
Extant Species ◽  
Molecular Phylogenetic ◽  
The Mediterranean

Northeastern Atlantic and Mediterranean gastropods previously ascribed to the buccinid genus Pollia Gray, 1837 are more correctly classified in the genus Aplus de Gregorio, 1885. Using an integrative taxonomy approach combining molecular, morphological and geographic data, we revisit the limits of the extant species in the area, and propose a molecular phylogenetic hypothesis based on 66 specimens from various localities in the Mediterranean Sea, including type localities of some nominal taxa. We used a preliminary morphological inspection, followed by a DNA-barcoding approach to propose species hypotheses, subsequently consolidated using additional data (phylogenetic, geographic and refined morphological data). Seven species hypotheses were eventually retained within our molecularly assayed samples, versus three classical morphologically recognized species. Among these, three correspond to Aplus dorbignyi (Payreaudeau, 1826) with its hitherto unrecognized geographical cognates A. gaillardoti (Puton, 1856) (eastern Mediterranean) and Aplus nodulosus (Bivona Ant., 1832) (Sicily); two closely related, yet considerably divergent, lineages are treated as a single species under Aplus scaber (Locard, 1892); the classically admitted Aplus scacchianus (Philippi, 1844) is confirmed by molecular evidence; Mediterranean populations attributable to Aplus assimilis (Reeve, 1846) may represent either cryptic native populations or an ongoing invasion of the Mediterranean by what was hitherto considered to be a West African species; finally, specimens from the Strait of Gibraltar may represent an undescribed species, but we conservatively refrain from formally introducing it pending the analysis of more material, and it is compared with the similar Aplus campisii (Ardovini, 2014), recently described from Sicily and not assayed molecularly, and Aplus scaber.

scholarly journals Disentangling relationships among eastern Mediterranean Cymbalaria including description of a novel species from the southern Peloponnese (Greece)

2021 ◽  
Vol 307 (2) ◽  
Author(s):  
Pau Carnicero ◽  
Núria Garcia-Jacas ◽  
Llorenç Sáez ◽  
Theophanis Constantinidis ◽  
Mercè Galbany-Casals
Keyword(s):  
Eastern Mediterranean ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Distribution Patterns ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Long Distance ◽  
Aegean Islands ◽  
Molecular Phylogenetic

AbstractThe eastern Mediterranean basin hosts a remarkably high plant diversity. Historical connections between currently isolated areas across the Aegean region and long-distance dispersal events have been invoked to explain current distribution patterns of species. According to most recent treatments, at least two Cymbalaria species occur in this area, Cymbalaria microcalyx and C. longipes. The former comprises several intraspecific taxa, treated at different ranks by different authors based on morphological data, evidencing the need of a taxonomic revision. Additionally, some populations of C. microcalyx show exclusive morphological characters that do not match any described taxon. Here, we aim to shed light on the systematics of eastern Mediterranean Cymbalaria and to propose a classification informed by various sources of evidence. We performed molecular phylogenetic analyses using ITS, 3’ETS, ndhF and rpl32-trnL sequences and estimated the ploidy level of some taxa performing relative genome size measures. Molecular data combined with morphology support the division of traditionally delimited C. microcalyx into C. acutiloba, C. microcalyx and C. minor, corresponding to well-delimited nrDNA lineages. Furthermore, we propose to combine C. microcalyx subsp. paradoxa at the species level. A group of specimens previously thought to belong to Cymbalaria microcalyx constitute a well-defined phylogenetic and morphological entity and are described here as a new species, Cymbalaria spetae. Cymbalaria longipes is non-monophyletic, but characterized by being glabrous and diploid, unlike other eastern species. The nrDNA data suggest at least two dispersals from the mainland to the Aegean Islands, potentially facilitated by marine regressions.

Taxonomic revision of species of Haematoloechus Looss, 1899 (Digenea: Plagiorchioidea), with molecular phylogenetic analysis and the description of three new species from Mexico

Zootaxa ◽  
2018 ◽  
Vol 4526 (3) ◽  
pp. 251 ◽  
Author(s):  
VIRGINIA LEÓN-RÈGAGNON ◽  
JANET TOPAN
Keyword(s):  
New Species ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Nomen Nudum ◽  
Phylogenetic Hypothesis ◽  
Molecular Phylogenetic ◽  
Phylogenetic Hypotheses ◽  
Three New Species ◽  
Host Parasite ◽  
Species Inquirendae

Lung flukes of the genus Haematoloechus Looss, 1899 are common parasites of anurans worldwide, but the taxonomy of the group has been confusing. In this taxonomic revision, 89 species of Haematoloechus (= Pneumonoeces Looss, 1902, Ostioloides Odening, 1960, Ostiolum Pratt, 1903, Skrjabinoeces Sudarikov, 1950, Neohaematoloechus Odening, 1960, Metahaematoloechus Yamaguti, 1971) are listed. Of these, 70 are considered valid, three are species inquirendae (H. legrandi Mañé–Garzón & Gil, 1959, H. latoricensis Kozák, 1968 & H. vitelloconfluentum (Rai, 1962) Saeed, Al–Barwari & Al-Harmni, 2007), one is a nomen nudum H. sudarikovi Belouss, 1962, 14 are junior synonyms and one belongs to Ostioloides. This publication also describes three new species, H. occidentalis n. sp., H. veracruzanus n. sp. and H. mexicanus n. sp., parasitizing species of Rana Linnaeus in Mexico and redescribes Haematoloechus caballeroi (Skrjabin & Antipin, 1962) Yamaguti, 1971. The phylogenetic hypotheses based on sequences of mitochondrial and ribosomal DNA of Haematoloechus spp. show that genera proposed on the basis of morphological characters are not supported. The host records for species of Haematoloechus, together with the phylogenetic hypothesis of the genus, suggest that this host-parasite association predates the ranid diversification in the Cretaceous. 

A molecular phylogenetic and DNA barcode assessment of the tribe Pterosiphonieae (Ceramiales, Rhodophyta) emphasizing the Northeast Pacific

Botany ◽  
2016 ◽  
Vol 94 (10) ◽  
pp. 917-939 ◽  
Author(s):  
Amanda M. Savoie ◽  
Gary W. Saunders
Keyword(s):  
South African ◽  
North American ◽  
New Genus ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Dna Barcode ◽  
Sensu Stricto ◽  
North American Species ◽  
African Species ◽  
Molecular Phylogenetic

Sequence data (COI-5P and rbcL) for North American members of the tribe Pterosiphonieae were compared with collections from around the world. Phylogenetic analyses resolved Pterosiphonia as polyphyletic and many species required transfer to other genera. In our analyses Pterosiphonia sensu stricto included only the type species P. cloiophylla (C. Agardh) Falkenberg and P. complanata (Clemente) Falkenberg, as well as the South African species P. stegengae sp. nov. A new genus, Xiphosiphonia gen. nov., was described for X. ardreana (Maggs & Hommersand) comb. nov., X. pennata (C. Agardh) comb. nov., and X. pinnulata (Kützing) comb. nov. Some Asian, European and North American species previously attributed to Pterosiphonia were transferred to Symphyocladia including S. baileyi (Harvey) comb. nov., S. dendroidea (Montagne) comb. nov., S. plumosa nom. nov. (for P. gracilis Kylin), and S. tanakae (S. Uwai & M. Masuda) comb. nov. We also described two new North American species, Symphyocladia brevicaulis sp. nov. and S. rosea sp. nov. Other species formed a well-supported clade for which the genus name Polyostea Ruprecht was resurrected. Included in Polyostea were P. arctica (J. Agardh) comb. nov., P. bipinnata (Postels & Ruprecht) Ruprecht, P. hamata (E.S. Sinova) comb. nov., and P. robusta (N.L. Gardner) comb. nov.

scholarly journals Young relicts and old relicts: a novel palaeoendemic vertebrate from the Australian Central Uplands

2016 ◽  
Vol 3 (10) ◽  
pp. 160018 ◽  
Author(s):  
Paul M. Oliver ◽  
Peter J. McDonald
Keyword(s):  
Late Miocene ◽  
Arid Zone ◽  
Dominant Role ◽  
Morphological Data ◽  
New Taxon ◽  
Isolated Populations ◽  
Show Evidence ◽  
Molecular Phylogenetic ◽  
Surrounding Areas ◽  
Close Relatives

Climatic change, and in particular aridification, has played a dominant role in shaping Southern Hemisphere biotas since the mid-Neogene. In Australia, ancient and geologically stable ranges within the vast arid zone have functioned as refugia for populations of mesic taxa extirpated from surrounding areas, yet the extent to which relicts may be linked to major aridification events before or after the Pliocene has not been examined in detail. Here we use molecular phylogenetic and morphological data to show that isolated populations of saxicoline geckos in the genus Oedura from the Australian Central Uplands, formerly confounded as a single taxon, actually comprise two divergent species with contrasting histories of isolation. The recently resurrected Oedura cincta has close relatives occurring elsewhere in the Australian arid biomes with estimated divergence dates concentrated in the early Pliocene. A new taxon (described herein) diverged from all extant Oedura much earlier, well before the end of the Miocene. A review of data for Central Uplands endemic vertebrates shows that for most (including Oedura cincta ), gene flow with other parts of Australia probably occurred until at least the very late Miocene or Pliocene. There are, however, a small number of palaeoendemic taxa—often ecologically specialized forms—that show evidence of having persisted since earlier intensification of aridity in the late Miocene.

scholarly journals Primula sunhangii (Primulaceae): a new species from Hubei, Central China

PhytoKeys ◽  
2020 ◽  
Vol 156 ◽  
pp. 103-112
Author(s):  
Jiao Sun ◽  
Dai-Gui Zhang ◽  
Xian-Han Huang ◽  
Komiljon Tojibaev ◽  
Jing-Yuan Yang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Hubei Province ◽  
Central China ◽  
Morphological Data ◽  
Molecular Phylogenetic Analysis ◽  
Molecular Phylogenetic ◽  
A New Species

This report provides a description of Primula sunhangii from the Shennongjia Forestry District, Hubei Province in Central China, which is categorized as a new species of the primrose family. Primula sunhangii is morphologically similar to P. involucrata Wall. ex Duby in terms of its simple umbel, efarinose, and prolonged bracts. However, P. sunhangii is distinguished by its glabrous sepal, short petiole (compare with blade) and cylindrical calyx and capsule. Molecular phylogenetic analysis based on nuclear and cpDNA genes demonstrates that P. sunhangii and P. involucrata are closely related. Combining genetic and morphological data, the recognition of P. sunhangii as a unique new species is supported.

scholarly journals Bembidiina of Afrotropical Region. 2- Odontium subg. Microserrullula Netolitzky, 1921 (Coleoptera, Carabidae, Bembidiina)

2021 ◽  
pp. 127-144
Author(s):  
Paolo Bonavita ◽  
Augusto Vigna Taglianti
Keyword(s):  
South Africa ◽  
New Species ◽  
Democratic Republic ◽  
Democratic Republic Of Congo ◽  
African Species ◽  
Republic Of Congo ◽  
Afrotropical Region

The afrotropical species of the subgenus Microserrullula netolitzky, 1921, of the genus Odontium LeConte, 1848 are here revised. We redescribe the three-known species, Odontium aegyptiacum (Dejean, 1831), O. icterodes (Alluaud, 1933) and O. pogonopsis (Alluaud, 1933), and describe four new species: Odontium australe n. sp. (Kenya, Mozambique, Madagascar, South africa); Odontium basilewskyi n. sp. (Democratic Republic of Congo); Odontium okavangum n. sp. (angola, namibia, Zambia); Odontium clarkei n. sp. (Ethiopia). A key for the identification of the african species of the subgenus Microserrullula is presented.

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