Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences

Five taxa in the genus Neidium, N. iridis, N. beatyi sp. nov., N. vandusenense sp. nov., N. collare sp. nov. and N. lavoieanum sp. nov. are documented from a pond and stream system in the VanDusen Botanical Garden, Vancouver, Canada. Neidium beatyi is a large linear species with multiple longitudinal canals and sagittate apices. The areolae are occluded by finger-like silica extensions on the external surface. This taxon is distinguished from Neidium iridis by the number of longitudinal canals (>5), shape of the valve apices, and smaller size. Neidium vandusenense is broadly linear with distinct rostrate apices. Two-three longitudinal canals are present along each margin. Plastid rbcL sequence data associates this taxon with N. amphigomphus. Neidium collare is an elliptic lanceolate taxon with one longitudinal canal. This taxon is genetically related to N. bisculatum sensu lato, but with a different shape form. Neidium lavoieanum has a valve shape form similar to Neidium potapovae, but is larger and genetically similar to N. productum sensu lato. The five Neidium taxa were observed in a small stream next to Lake Victoria (pond) in the VanDusen Botanical Garden Vancouver, Canada. The water was mildly alkaline with a pH of 7.86, a conductance of 163 µS/cm, higher nutrient loads and low metal content.

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Hybridization in the Temperate Bamboos (Poaceae: Bambusoideae: Arundinarieae): A Phylogenetic Study Using AFLPs and cpDNA Sequence Data

Systematic Botany ◽

10.1600/036364421x16128061189503 ◽

2021 ◽

Vol 46 (1) ◽

pp. 48-69

Author(s):

Jimmy K. Triplett ◽

Lynn G. Clark

Keyword(s):

Dna Sequences ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Intergeneric Hybrid ◽

Plastid Dna ◽

Sensu Stricto ◽

Phylogenetic Study ◽

Aflp Data ◽

The North ◽

Cpdna Sequence

Abstract—The temperate bamboos are a taxonomically difficult group with nearly 600 species in approximately 30 genera and at least 12 constituent lineages. In this study, phylogenetic relationships were explored using amplified fragment length polymorphism (AFLP) data in comparison with a phylogeny based on plastid DNA sequences, with an emphasis onArundinariaof North America and its allies in East Asia (theArundinariaclade). Molecular analyses involved 248 individuals in 10 genera and 60 species. Hybridization was detected both within and among genera. Comparative analyses indicated hybrid origins for species in several widespread and well-known genera, includingHibanobambusa,Sasaella, andSemiarundinaria. Evidence also indicated thatPseudosasa japonica(the type species ofPseudosasa) is an intergeneric hybrid involvingPleioblastusandSasamorpha. In addition, cryptic hybrids were detected within and amongPleioblastus,Sasa, andSasamorpha. After accounting for hybrids, phylogenetic analyses of AFLP data provided resolution for core lineages in theArundinariaclade, includingPleioblastussensu stricto,Sasas. s., andSasamorpha.AFLP data also provided evidence for the monophyly of the North American cane bamboos (Arundinaria, three species) but failed to identify their closest relative among the East Asian taxa. The broader evolutionary implications of hybridization in the temperate bamboos are discussed along with recommendations for future studies.

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A Novel Rickettsia Species Detected in Vole Ticks (Ixodes angustus) from Western Canada

Applied and Environmental Microbiology ◽

10.1128/aem.02286-13 ◽

2013 ◽

Vol 79 (24) ◽

pp. 7583-7589 ◽

Cited By ~ 29

Author(s):

Clare A. Anstead ◽

Neil B. Chilton

Keyword(s):

Dna Sequences ◽

Genomic Dna ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Spotted Fever ◽

Ixodid Ticks ◽

Western Canada ◽

Rickettsia Species ◽

Content Type ◽

Putative Species

ABSTRACTThe genomic DNA of ixodid ticks from western Canada was tested by PCR for the presence ofRickettsia. No rickettsiae were detected inIxodes sculptus, whereas 18% of theI. angustusand 42% of theDermacentor andersoniorganisms examined were PCR positive forRickettsia. The rickettsiae from each tick species were characterized genetically using multiple genes. Rickettsiae within theD. andersoniorganisms had sequences at four genes that matched those ofR. peacockii. In contrast, theRickettsiapresent within the larvae, nymphs, and adults ofI. angustushad novel DNA sequences at four of the genes characterized compared to the sequences available from GenBank for all recognized species ofRickettsiaand all other putative species within the genus. Phylogenetic analyses of the sequence data revealed that the rickettsiae inI. angustusdo not belong to the spotted fever, transitional, or typhus groups of rickettsiae but are most closely related to “CandidatusRickettsia kingi” and belong to a clade that also includesR. canadensis, “CandidatusRickettsia tarasevichiae,” and “CandidatusRickettsia monteiroi.”

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Morphology corroborates DNA sequence data in the species-level recognition of Gaultheria trichophylla var. tetracme (Ericaceae)

Journal of the Botanical Research Institute of Texas ◽

10.17348/jbrit.v11.i2.1074 ◽

2017 ◽

Vol 11 (2) ◽

pp. 343-349

Author(s):

Peter W. Fritsch ◽

Lu Lu ◽

Ming-Ying Zhang ◽

Hong Wang ◽

De-Zhu Li

Keyword(s):

Plant Height ◽

Dna Sequence ◽

Morphological Variation ◽

Dna Sequences ◽

Sequence Data ◽

Plastid Dna ◽

Geographic Range ◽

Species Level ◽

Dna Sequence Data ◽

Statistical Support

Gaultheria trichophylla var. tetracme of G. series Trichophyllae (Ericaceae) has been distinguished from the nominate variety of G. trichophylla by the presence of two awns on each anther theca (versus one). Phylogenetic data based on plastid DNA sequences placed G. t. var. tetracme in a different clade than the nominate variety with strong statistical support, suggesting that G. trichophylla is not monophyletic. To investigate this further, we studied the morphology of these two taxa in the field and with herbarium material. We found that G. t. var. tetracme differs substantially from the nominate variety in morphology, not only by the number of anther awns, but also the larger size of many features, e.g., plant height, leaves, and pedicels, a greater number of leaf marginal setae, and a distinct geographic range. On this basis, we elevate G. t. var. tetracme to the species level as Gaultheria tetracme, endemic to the Hengduan Shan in Sichuan Province, China. We note the wide morphological variation in the remainder of G. trichophylla and indicate specific problems that should be investigated in more detail for better understanding the taxonomy of this species.

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Characterization of squalene synthase gene from Gymnema sylvestre R. Br.

Beni-Suef University Journal of Basic and Applied Sciences ◽

10.1186/s43088-020-00094-4 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Kuldeepsingh A. Kalariya ◽

Ram Prasnna Meena ◽

Lipi Poojara ◽

Deepa Shahi ◽

Sandip Patel

Keyword(s):

Dna Sequences ◽

Genomic Dna ◽

Competitive Inhibition ◽

Sequence Data ◽

Homology Model ◽

Squalene Synthase ◽

Gymnema Sylvestre ◽

Gardenia Jasminoides ◽

Ramachandran Plots ◽

Flanking Regions

Abstract Background Squalene synthase (SQS) is a rate-limiting enzyme necessary to produce pentacyclic triterpenes in plants. It is an important enzyme producing squalene molecules required to run steroidal and triterpenoid biosynthesis pathways working in competitive inhibition mode. Reports are available on information pertaining to SQS gene in several plants, but detailed information on SQS gene in Gymnema sylvestre R. Br. is not available. G. sylvestre is a priceless rare vine of central eco-region known for its medicinally important triterpenoids. Our work aims to characterize the GS-SQS gene in this high-value medicinal plant. Results Coding DNA sequences (CDS) with 1245 bp length representing GS-SQS gene predicted from transcriptome data in G. sylvestre was used for further characterization. The SWISS protein structure modeled for the GS-SQS amino acid sequence data had MolProbity Score of 1.44 and the Clash Score 3.86. The quality estimates and statistical score of Ramachandran plots analysis indicated that the homology model was reliable. For full-length amplification of the gene, primers designed from flanking regions of CDS encoding GS-SQS were used to get amplification against genomic DNA as template which resulted in approximately 6.2-kb sized single-band product. The sequencing of this product through NGS was carried out generating 2.32 Gb data and 3347 number of scaffolds with N50 value of 457 bp. These scaffolds were compared to identify similarity with other SQS genes as well as the GS-SQSs of the transcriptome. Scaffold_3347 representing the GS-SQS gene harbored two introns of 101 and 164 bp size. Both these intronic regions were validated by primers designed from adjoining outside regions of the introns on the scaffold representing GS-SQS gene. The amplification took place when the template was genomic DNA and failed when the template was cDNA confirmed the presence of two introns in GS-SQS gene in Gymnema sylvestre R. Br. Conclusion This study shows GS-SQS gene was very closely related to Coffea arabica and Gardenia jasminoides and this gene harbored two introns of 101 and 164 bp size.

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Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection

Microorganisms ◽

10.3390/microorganisms9030666 ◽

2021 ◽

Vol 9 (3) ◽

pp. 666

Author(s):

Niccolò Forin ◽

Alfredo Vizzini ◽

Federico Fainelli ◽

Enrico Ercole ◽

Barbara Baldan

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Illumina Miseq ◽

Botanical Garden ◽

Molecular Study ◽

Its2 Sequence ◽

Type Specimens ◽

Its1 Sequence ◽

Dna Sequence Data ◽

Nomen Novum

In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo’s fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically re-examine via a morphological and molecular approach nine different Roselliniasensu Saccardo types. ITS1 and/or ITS2 sequences were successfully obtained applying Illumina MiSeq technology and phylogenetic analyses were carried out in order to elucidate their current taxonomic position. Only the ITS1 sequence was recovered for Rosellinia areolata, while for R. geophila, only the ITS2 sequence was recovered. We proposed here new combinations for Rosellinia chordicola, R. geophila and R. horridula, while for R. ambigua, R. areolata, R. australis, R. romana and R. somala, we did not suggest taxonomic changes compared to the current ones. The name Rosellinia subsimilis Sacc. is invalid, as it is a later homonym of R. subsimilis P. Karst. & Starbäck. Therefore, we introduced Coniochaeta dakotensis as a nomen novum for R. subsimilis Sacc. This is the first time that these types have been subjected to a molecular study. Our results demonstrate that old types are an important source of DNA sequence data for taxonomic re-examinations.

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Molecular systematics of Gagea and Lloydia (Liliaceae; Liliales): implications of analyses of nuclear ribosomal and plastid DNA sequences for infrageneric classification

Annals of Botany ◽

10.1093/aob/mcp103 ◽

2009 ◽

Vol 104 (1) ◽

pp. 125-142 ◽

Cited By ~ 24

Author(s):

M. Zarrei ◽

P. Wilkin ◽

M. F. Fay ◽

M. J. Ingrouille ◽

S. Zarre ◽

...

Keyword(s):

Molecular Systematics ◽

Dna Sequences ◽

Plastid Dna ◽

Infrageneric Classification

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Molecular evolution of homologous gene sequences in germline-limited and somatic chromosomes of Acricotopus

Genome ◽

10.1139/g04-026 ◽

2004 ◽

Vol 47 (4) ◽

pp. 732-741 ◽

Cited By ~ 2

Author(s):

Wolfgang Staiber

Keyword(s):

Molecular Evolution ◽

Dna Sequences ◽

Sequence Data ◽

Structural Evolution ◽

5S Rdna ◽

Oligonucleotide Primer ◽

Homologous Gene ◽

Gene Sequences ◽

Nucleotide Substitutions ◽

Degenerate Oligonucleotide

The origin of germline-limited chromosomes (Ks) as descendants of somatic chromosomes (Ss) and their structural evolution was recently elucidated in the chironomid Acricotopus. The Ks consist of large S-homologous sections and of heterochromatic segments containing germline-specific, highly repetitive DNA sequences. Less is known about the molecular evolution and features of the sequences in the S-homologous K sections. More information about this was received by comparing homologous gene sequences of Ks and Ss. Genes for 5.8S, 18S, 28S, and 5S ribosomal RNA were choosen for the comparison and therefore isolated first by PCR from somatic DNA of Acricotopus and sequenced. Specific K DNA was collected by microdissection of monopolar moving K complements from differential gonial mitoses and was then amplified by degenerate oligonucleotide primer (DOP)-PCR. With the sequence data of the somatic rDNAs, the homologous 5.8S and 5S rDNA sequences were isolated by PCR from the DOP-PCR sequence pool of the Ks. In addition, a number of K DOP-PCR sequences were directly cloned and analysed. One K clone contained a section of a putative N-acetyltransferase gene. Compared with its homolog from the Ss, the sequence exhibited few nucleotide substitutions (99.2% sequence identity). The same was true for the 5.8S and 5S sequences from Ss and Ks (97.5%100% identity). This supports the idea that the S-homologous K sequences may be conserved and do not evolve independently from their somatic homologs. Possible mechanisms effecting such conservation of S-derived sequences in the Ks are discussed.Key words: microdissection, DOP-PCR, germline-limited chromosomes, molecular evolution.

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Molecular Systematics of Tribe Physarieae (Brassicaceae) Based on Nuclear ITS, LUMINIDEPENDENS, and Chloroplast ndhF

Systematic Botany ◽

10.1600/036364421x16312067913318 ◽

2021 ◽

Author(s):

Sara Fuentes-Soriano ◽

Elizabeth A. Kellogg

Keyword(s):

Sequence Data ◽

Plastid Dna ◽

Sister Relationship ◽

Data Set ◽

Woody Perennial ◽

History Of ◽

Nuclear Its ◽

Phylogenetic Framework ◽

Phylogenetic Hypotheses ◽

Relationship Of

Physarieae is a small tribe of herbaceous annual and woody perennial mustards that are mostly endemic to North America, with its members including a large amount of variation in floral, fruit, and chromosomal variation. Building on a previous study of Physarieae based on morphology and ndhF plastid DNA, we reconstructed the evolutionary history of the tribe using new sequence data from two nuclear markers, and compared the new topologies against previously published cpDNA-based phylogenetic hypotheses. The novel analyses included ca. 420 new sequences of ITS and LUMINIDEPENDENS (LD) markers for 39 and 47 species, respectively, with sampling accounting for all seven genera of Physarieae, including nomenclatural type species, and 11 outgroup taxa. Maximum parsimony, maximum likelihood, and Bayesian analyses showed that these additional markers were largely consistent with the previous ndhF data that supported the monophyly of Physarieae and resolved two major clades within the tribe, i.e., DDNLS (Dithyrea, Dimorphocarpa, Nerisyrenia, Lyrocarpa, and Synthlipsis)and PP (Paysonia and Physaria). New analyses also increased internal resolution for some closely related species and lineages within both clades. The monophyly of Dithyrea and the sister relationship of Paysonia to Physaria was consistent in all trees, with the sister relationship of Nerisyrenia to Lyrocarpa supported by ndhF and ITS, and the positions of Dimorphocarpa and Synthlipsis shifted within the DDNLS Clade depending on the employed data set. Finally, using the strong, new phylogenetic framework of combined cpDNA + nDNA data, we discussed standing hypotheses of trichome evolution in the tribe suggested by ndhF.

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SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control

mSystems ◽

10.1128/msystems.00202-17 ◽

2018 ◽

Vol 3 (3) ◽

Cited By ~ 15

Author(s):

Gabriel A. Al-Ghalith ◽

Benjamin Hillmann ◽

Kaiwei Ang ◽

Robin Shields-Cutler ◽

Dan Knights

Keyword(s):

Quality Control ◽

Dna Sequences ◽

Sequence Data ◽

Background Knowledge ◽

Sequencing Technology ◽

Data Set ◽

Short Read ◽

Dna Quality ◽

Public Data ◽

User Friendly

ABSTRACT Next-generation sequencing technology is of great importance for many biological disciplines; however, due to technical and biological limitations, the short DNA sequences produced by modern sequencers require numerous quality control (QC) measures to reduce errors, remove technical contaminants, or merge paired-end reads together into longer or higher-quality contigs. Many tools for each step exist, but choosing the appropriate methods and usage parameters can be challenging because the parameterization of each step depends on the particularities of the sequencing technology used, the type of samples being analyzed, and the stochasticity of the instrumentation and sample preparation. Furthermore, end users may not know all of the relevant information about how their data were generated, such as the expected overlap for paired-end sequences or type of adaptors used to make informed choices. This increasing complexity and nuance demand a pipeline that combines existing steps together in a user-friendly way and, when possible, learns reasonable quality parameters from the data automatically. We propose a user-friendly quality control pipeline called SHI7 (canonically pronounced “shizen”), which aims to simplify quality control of short-read data for the end user by predicting presence and/or type of common sequencing adaptors, what quality scores to trim, whether the data set is shotgun or amplicon sequencing, whether reads are paired end or single end, and whether pairs are stitchable, including the expected amount of pair overlap. We hope that SHI7 will make it easier for all researchers, expert and novice alike, to follow reasonable practices for short-read data quality control. IMPORTANCE Quality control of high-throughput DNA sequencing data is an important but sometimes laborious task requiring background knowledge of the sequencing protocol used (such as adaptor type, sequencing technology, insert size/stitchability, paired-endedness, etc.). Quality control protocols typically require applying this background knowledge to selecting and executing numerous quality control steps with the appropriate parameters, which is especially difficult when working with public data or data from collaborators who use different protocols. We have created a streamlined quality control pipeline intended to substantially simplify the process of DNA quality control from raw machine output files to actionable sequence data. In contrast to other methods, our proposed pipeline is easy to install and use and attempts to learn the necessary parameters from the data automatically with a single command.

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