Characterization of an unusually conserved AluI highly reiterated DNA sequence family from the honeybee, Apis mellifera.

Abstract An AluI family of highly reiterated nontranscribed sequences has been found in the genome of the honeybee Apis mellifera. This repeated sequence is shown to be present at approximately 23,000 copies per haploid genome constituting about 2% of the total genomic DNA. The nucleotide sequence of 10 monomers was determined. The consensus sequences is 176 nucleotides long and has an A + T content of 58%. There are clusters of both direct and inverted repeats. Internal subrepeating units ranging from 11 to 17 nucleotides are observed, suggesting that it could have evolved from a shorter sequence. DNA sequence data reveal that this repeat class is unusually homogeneous compared to the other class of invertebrate highly reiterated DNA sequences. The average pairwise sequence divergence between the repeats is 2.5%. In spite of this unusual homogeneity, divergence has been found in the repeated sequence hybridization ladder between four different honeybee subspecies. Therefore, the AluI highly reiterated sequences provide a new probe for fingerprinting in A. m. mellifera.

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A new species of big-headed, fanged dicroglossine frog (Genus Limnonectes) from Thailand

Zootaxa ◽

10.11646/zootaxa.1807.1.2 ◽

2008 ◽

Vol 1807 (1) ◽

pp. 26 ◽

Cited By ~ 5

Author(s):

DAVID S. McLEOD

Keyword(s):

New Species ◽

Dna Sequence ◽

Sequence Data ◽

Sequence Divergence ◽

Type Material ◽

Base Pairs ◽

Dna Sequence Data ◽

16S Gene ◽

A New Species

A new species of the dicroglossine genus Limnonectes from eastern Thailand and its tadpole are described. Analysis of DNA sequence data from 2518 base-pairs of the mitochondrial 12S and 16S gene regions places the species within the complex of frogs currently referred to as Limnonectes kuhlii and demonstrates it to be a separate lineage (>18% sequence divergence from type-material of L. kuhlii from Java). The new species differs from L. kuhlii by having nuptial pads, a greater snout–vent length, and different relative finger lengths than specimens from Java. It has more extensive toe webbing, a different arrangement of nuptial pads, and a greater snout–vent length than Limnonectes laticeps. The new species, which lacks vocal slits, also can be distinguished from the morphologically similar Limnonectes namiyei from Japan, which possesses vocal slits.

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Revision of Batrachospermum sections Acarposporophytum and Aristata (Batrachospermales, Rhodophyta) with the establishment of the new genera Acarposporophycos and Visia

Phytotaxa ◽

10.11646/phytotaxa.395.2.1 ◽

2019 ◽

Vol 395 (2) ◽

pp. 51 ◽

Cited By ~ 6

Author(s):

ORLANDO NECCHI JR ◽

AURO GARCIA FILHO ◽

MONICA O. PAIANO

Keyword(s):

Dna Sequence ◽

Sequence Data ◽

Morphological Characteristics ◽

Sequence Divergence ◽

Morphological Evidence ◽

Similar Species ◽

Type Specimens ◽

Generic Level ◽

Dna Sequence Data ◽

Cell Layers

Sections of the paraphyletic genus Batrachospermum have been recently investigated using molecular (DNA sequence data) and morphological evidence. Some sections have been recognized as distinct genera in order to resolve paraphyly. Batrachospermum species of sections Acarposporophytum and Aristata are showed to form well-supported clades and, in this study, we propose to raise them to the generic level, Acarposporophycos gen. nov. and Visia gen. nov., respectively. In addition, we re-evaluated the characters used to circumscribe species by reexamining type specimens as well as new collections. Acarposporophycos, with the sole species A. brasiliensis, is characterized by the lack of carposporophytic stage, with the fertilized carpogonia germinating to form directly the filaments of the ‘Chantransia’ stage on the gametophyte. Of the five previously accepted species in the genus Visia, we recognize four species: V. cayennensis—type species (synonym Batrachospermum beraense), V. cylindrocellularis, V. longiarticulata and V. turgida. The species are circumscribed on the basis of morphological characteristics (shape and cell layers of primary fascicles, occurrence of secondary fascicles, post-fertilization development of carpogonia) and DNA sequence data (rbcL and COI-5P). Specimens described as Visia cayennensis from Australia and Brazil had a high sequence divergence in comparison to those from or near the type locality (French Guiana), and are here referred to as Visia spp. Further studies are recommended to better discriminate these morphologically similar species on a broad geographical scale and define their status at the species level. Descriptions, identification key and photomicrographs are presented for each recognized species.

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Association of larvae and adults of Mexican species of Macrelmis (Coleoptera: Elmidae): a preliminary analysis using DNA sequences

Zootaxa ◽

10.11646/zootaxa.3361.1.5 ◽

2012 ◽

Vol 3361 (1) ◽

pp. 56-62 ◽

Cited By ~ 7

Author(s):

JOSEFINA CURIEL ◽

JUAN J. MORRONE

Keyword(s):

Dna Sequence ◽

Dna Sequences ◽

Preliminary Analysis ◽

Sequence Data ◽

Strong Association ◽

Life Stages ◽

Adult Morphology ◽

Dna Sequence Data ◽

Mexican Species ◽

Major Impediment

Insect life stages are known imperfectly in many cases, and classifications are usually based on adult morphology. This isunfortunate as information on other life stages may be useful for biomonitoring. The major impediment to using elmid(Coleoptera) larvae for freshwater biomonitoring is the lack of larval descriptions and illustrations. Reliable molecular proto-cols may be used to associate larvae and adults. After adults of seven species of Mexican Macrelmis were identified morpho-logically, seven larval specimens were associated to them based on two gene fragments: Cox1 and Cob. The phylogeneticanalysis allowed identifying the larval specimens as Macrelmis leonilae, M. scutellaris, M. species 7, M. species 10, and M.species 11. Two species based on adults associated uncertainly with one larva, and one larva did not match with any adult. Adult/larval association in elmids using DNA sequence data seems to be promising in terms of speed and reliability.

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Toward a Natural Classification of Botryosphaeriaceae: A Study of the Type Specimens of Botryosphaeria sensu lato

Frontiers in Microbiology ◽

10.3389/fmicb.2021.737541 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ying Zhang ◽

Yupei Zhou ◽

Wei Sun ◽

Lili Zhao ◽

D. Pavlic-Zupanc ◽

...

Keyword(s):

Dna Sequence ◽

Dna Sequences ◽

Sequence Data ◽

Morphological Characteristics ◽

Taxonomic Status ◽

Morphological Characters ◽

Phylogenetic Position ◽

Type Specimens ◽

Natural Classification ◽

Dna Sequence Data

The genus Botryosphaeria includes more than 200 epithets, but only the type species, Botryosphaeria dothidea and a dozen or more other species have been identified based on DNA sequence data. The taxonomic status of the other species remains unconfirmed because they lack either morphological information or DNA sequence data. In this study, types or authentic specimens of 16 “Botryosphaeria” species are reassessed to clarify their identity and phylogenetic position. nuDNA sequences of four regions, ITS, LSU, tef1-α and tub2, are analyzed and considered in combination with morphological characteristics. Based on the multigene phylogeny and morphological characters, Botryosphaeria cruenta and Botryosphaeria hamamelidis are transferred to Neofusicoccum. The generic status of Botryosphaeria aterrima and Botryosphaeria mirabile is confirmed in Botryosphaeria. Botryosphaeria berengeriana var. weigeliae and B. berengeriana var. acerina are treated synonyms of B. dothidea. Botryosphaeria mucosa is transferred to Neodeightonia as Neodeightonia mucosa, and Botryosphaeria ferruginea to Nothophoma as Nothophoma ferruginea. Botryosphaeria foliicola is reduced to synonymy with Phyllachorella micheliae. Botryosphaeria abuensis, Botryosphaeria aesculi, Botryosphaeria dasylirii, and Botryosphaeria wisteriae are tentatively kept in Botryosphaeria sensu stricto until further phylogenetic analysis is carried out on verified specimens. The ordinal status of Botryosphaeria apocyni, Botryosphaeria gaubae, and Botryosphaeria smilacinina cannot be determined, and tentatively accommodate these species in Dothideomycetes incertae sedis. The study demonstrates the significance of a polyphasic approach in characterizing type specimens, including the importance of using of DNA sequence data.

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Hierarchical Models for Mitochondrial DNA Sequence Data

Austrian Journal of Statistics ◽

10.17713/ajs.v36i1.320 ◽

2016 ◽

Vol 36 (1) ◽

Author(s):

Paola Berchialla

Keyword(s):

Mitochondrial Dna ◽

Dna Sequence ◽

Dna Sequences ◽

Sequence Data ◽

Population History ◽

Parametric Models ◽

Italian Population ◽

Bayesian Hierarchical ◽

Dna Sequence Data ◽

Mitochondrial Dna Sequence

We introduce a Bayesian hierarchical model for mitochondrial DNA sequence data, which is fitted via acceptance-rejection algorithms. The model incorporates parametric models of population history explicitly as well as a mutational process allowing for a simultaneous parameter estimation whose importance has become increasingly clear in many recent studies. The model is applied to a sample of DNA sequences from the Italian population.

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Ecology and seasonality of Pseudo-nitzschia species (Bacillariophyceae) in the northwestern Adriatic Sea over a 30-years period (1988–2020)

Mediterranean Marine Science ◽

10.12681/mms.26021 ◽

2021 ◽

Vol 22 (3) ◽

pp. 505

Author(s):

SONIA GIULIETTI ◽

TIZIANA ROMAGNOLI ◽

ALESSANDRA CAMPANELLI ◽

CECILIA TOTTI ◽

STEFANO ACCORONI

Keyword(s):

Dna Sequence ◽

Dna Sequences ◽

Species Complex ◽

Adriatic Sea ◽

Sequence Data ◽

Coastal Station ◽

Dna Sequence Data ◽

The Mean ◽

First Time ◽

North Western

The ecology and seasonality of Pseudo-nitzschia species and their contribution to phytoplankton community were analysed for the first time at the coastal station of the LTER-Senigallia-Susak transect (north-western Adriatic Sea) from 1988 to 2020. Species composition was addressed using DNA sequence data obtained from 106 monoclonal strains isolated from January 2018 to January 2020. The mean annual cycle of total phytoplankton in the study period (Feb 1988–Jan 2020) showed maximum abundances in winter followed by other peaks in spring and autumn. Diatoms were the main contributors in terms of abundance during the winter and the spring blooms. The autumn peak was due to phytoflagellates and diatoms. In summer phytoflagellates dominated the community, followed by diatoms and dinoflagellates, which in this season reached their annual maximum. Pseudo-nitzschia spp. represented on average 0.4–17.6% of diatom community, but during their blooms they could reach up to up to 90% of the total diatom abundances with 106 cells l-1. By LM, six different taxa were recognized: Pseudo-nitzschia cf. delicatissima and P. cf. pseudodelicatissima were the most abundant, followed by P. cf. fraudulenta, P. pungens, P. multistriata and P. cf. galaxiae. P. cf. fraudulenta and P. pungens were indicator taxa of winter. P. cf. delicatissima and P. cf. pseudodelicatissima were spring and summer taxa, respectively. P. galaxiae showed maximum abundances in autumn. DNA sequences revealed the presence of two species belonging to the ’P. seriata group’ (i.e. P. fraudulenta and P. pungens) and four species belonging to the ‘P. delicatissima group’ (P. calliantha and P. mannii within the P. pseudodelicatissima species complex, and P. delicatissima and P. cf. arenysensis within the P. delicatissima species complex). The presence of several cryptic and pseudo-cryptic species highlights the need to combine LM observations with DNA sequence data when the ecology of Pseudo-nitzschia is investigated.

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EMBL2checklists: A Python package to facilitate the user-friendly submission of plant DNA barcoding sequences to ENA

10.1101/435644 ◽

2018 ◽

Author(s):

Michael Gruenstaeudl ◽

Yannick Hartmaring

Keyword(s):

Dna Barcoding ◽

Dna Sequence ◽

Dna Sequences ◽

Sequence Data ◽

Software Tool ◽

Plant Dna ◽

Dna Sequence Data ◽

User Friendly ◽

Common Plant ◽

Python Package

AbstractBackgroundThe submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data. Despite the centrality of database submissions to biological research, the range of available software tools that facilitate the preparation of sequence data for database submissions is low, especially for sequences generated via plant DNA barcoding. Current submission procedures can be complex and prohibitively time expensive for any but a small number of input sequences. A user-friendly software tool is needed that streamlines the file preparation for database submissions of DNA sequences that are commonly generated in plant DNA barcoding.MethodsA Python package was developed that converts DNA sequences from the common EMBL and GenBank flat file formats to submission-ready, tab-delimited spreadsheets (so-called “checklists”) for a subsequent upload to the public sequence database of the European Nucleotide Archive (ENA). The software tool, titled “EMBL2checklists”, automatically converts DNA sequences, their annotation features, and associated metadata into the idiosyncratic format of marker-specific ENA checklists and, thus, generates output that can be uploaded via the interactive Webin submission system of ENA.ResultsEMBL2checklists provides a simple, platform-independent tool that automates the conversion of common plant DNA barcoding sequences into easily editable spreadsheets that require no further processing but their upload to ENA via the interactive Webin submission system. The software is equipped with an intuitive graphical as well as an efficient command-line interface for its operation. The utility of the software is illustrated by its application in the submission of DNA sequences of two recent plant phylogenetic investigations and one fungal metagenomic study.DiscussionEMBL2checklists bridges the gap between common software suites for DNA sequence assembly and annotation and the interactive data submission process of ENA. It represents an easy-to-use solution for plant biologists without bioinformatics expertise to generate submission-ready checklists from common plant DNA sequence data. It allows the post-processing of checklists as well as work-sharing during the submission process and solves a critical bottleneck in the effort to increase participation in public data sharing.

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Bipinnate acacias (Acacia subg. Phyllodineae sect. Botrycephalae) of eastern Australia are polyphyletic based on DNA sequence data

Australian Systematic Botany ◽

10.1071/sb05039 ◽

2006 ◽

Vol 19 (4) ◽

pp. 315 ◽

Cited By ~ 11

Author(s):

Gillian K. Brown ◽

Siti R. Ariati ◽

Daniel J. Murphy ◽

Joseph T. H. Miller ◽

Pauline Y. Ladiges

Keyword(s):

Phylogenetic Analysis ◽

Dna Sequence ◽

Sequence Data ◽

Sequence Divergence ◽

Morphological Characters ◽

Dna Sequence Data ◽

Main Clade ◽

Eastern Australia ◽

Limited Sequence

A phylogenetic analysis of Acacia subg. Phyllodineae sect. Botrycephalae, endemic to eastern Australia, is presented based on a combined dataset of ITS and ETS sequences of nrDNA. A smaller set of species was sequenced also for the cpDNA trnK region. A limited number of morphological characters was also combined with the ITS+ETS dataset for most taxa. Thirty-eight of 41 Botrycephalae species were sequenced, together with a sample of ten uninerved phyllodinous species (sect. Phyllodineae). Although these DNA regions showed limited sequence divergence, bootstrap supported nodes of the consensus ITS+ETS tree indicate that Botrycephalae as currently defined is polyphyletic. Eight bipinnate species fell outside the main clade of Botrycephalae species while seven phyllodinous species were nested within it, near the base. The few derived but homoplasious morphological characters that were discovered included: presence of appressed unicellular hairs, presence of jugary and interjugary glands, number of pinnae > 7 and the funicle half–fully encircling the seed. Section Botrycephalae requires redefinition.

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Inferring evolutionary processes from DNA sequence data

Evolutionary Genetics ◽

10.1093/oso/9780198830917.003.0007 ◽

2019 ◽

pp. 145-172

Author(s):

Glenn-Peter Sætre ◽

Mark Ravinet

Keyword(s):

Molecular Evolution ◽

Dna Sequence ◽

Genetic Markers ◽

Dna Sequences ◽

Sequence Data ◽

Neutral Theory ◽

Evolutionary Genetics ◽

Haplotype Structure ◽

Dna Sequence Data ◽

Neutrality Tests

The allelic evolutionary genetic models explored so far are applicable to genetic markers. However, DNA sequences harbor a lot of information about the evolutionary past that would be missed if different sequences were simply treated as different alleles. This chapter introduces some important methods and concepts applicable to the analysis of DNA-sequence data. The null models for analyzing sequence data are derived from the neutral theory of molecular evolution. Historically, however, the neutral theory has made a large impact on evolutionary genetics. Therefore, this chapter starts by reviewing its important contribution. Then, important parameters and statistics for analyzing sequence variation are introduced, including a plethora of neutrality tests. The chapter ends with a cautious focus on the powerful tool of genome scan analysis and its utility for identifying regions of the genomes potentially under selection. This includes a section on more recently derived statistics which incorporate information on haplotype structure.

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Phylogeny and PCR Identification of Clinically Important Zygomycetes Based on Nuclear Ribosomal-DNA Sequence Data

Journal of Clinical Microbiology ◽

10.1128/jcm.37.12.3957-3964.1999 ◽

1999 ◽

Vol 37 (12) ◽

pp. 3957-3964 ◽

Cited By ~ 124

Author(s):

Kerstin Voigt ◽

Elizabeth Cigelnik ◽

Kerry O'donnell

Keyword(s):

Dna Sequence ◽

Ribosomal Dna ◽

Dna Sequences ◽

Sequence Data ◽

Large Subunit ◽

Gene Tree ◽

Strong Support ◽

Nuclear Ribosomal Dna ◽

Syncephalastrum Racemosum ◽

Dna Sequence Data

A molecular database for all clinically important Zygomycetes was constructed from nucleotide sequences from the nuclear small-subunit (18S) ribosomal DNA and domains D1 and D2 of the nuclear large-subunit (28S) ribosomal DNA. Parsimony analysis of the aligned 18S and 28S DNA sequences was used to investigate phylogenetic relationships among 42 isolates representing species of Zygomycetes reported to cause infections in humans and other animals, together with commonly cultured contaminants, with emphasis on members of the Mucorales. The molecular phylogeny provided strong support for the monophyly of the Mucorales, exclusive of Echinosporangium transversale andMortierella spp., which are currently misclassified within the Mucorales. Micromucor ramannianus, traditionally classified within Mortierella, and Syncephalastrum racemosum represent the basal divergences within the Mucorales. Based on the 18S gene tree topology, Absidia corymbiferaand Rhizomucor variabilis appear to be misplaced taxonomically. A. corymbifera is strongly supported as a sister group of the Rhizomucor miehei-Rhizomucor pusillusclade, while R. variabilis is nested withinMucor. The aligned 28S sequences were used to design 13 taxon-specific PCR primer pairs for those taxa most commonly implicated in infections. All of the primers specifically amplified DNA of the size predicted based on the DNA sequence data from the target taxa; however, they did not cross-react with phylogenetically related species. These primers have the potential to be used in a PCR assay for the rapid and accurate identification of the etiological agents of mucormycoses and entomophthoromycoses.

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