The puzzle of DNA sequences of Phytoseiidae (Acari:Mesostigmata) in the public GenBank database

2011 ◽  
Vol 25 (5) ◽  
pp. 389 ◽  
Author(s):  
Marie-Stéphane Tixier ◽  
Fabio Akashi Hernandes ◽  
Sabine Guichou ◽  
Serge Kreiter
Keyword(s):  
Dna Sequences ◽  
Insect Pests ◽  
Sequence Data ◽  
Pcr Primers ◽  
12S Rrna ◽  
Correct Identification ◽  
Neoseiulus Cucumeris ◽  
Voucher Specimen ◽  
The Public ◽  
Iphiseius Degenerans

The public database GenBank is an increasingly important source of sequence data for diagnostic and phylogenetic research; however, not all deposited sequences are necessarily correctly ascribed to a source species. We considered the example of the mite family Phytoseiidae to determine how the corresponding sequences could be accurately exploited. Phytoseiidae mites are well known worldwide for their ability to control certain mite and insect pests. The number of molecular approaches, especially for diagnostic purposes, has increased over the past decade, leading to an increase in the number of sequences registered in the GenBank database. The aim of the present paper was to evaluate the validity of the DNA sequences presently assigned to Phytoseiidae species in this database. Three hundred and fifty-one sequences, corresponding to the four most frequently registered DNA fragments (ITS, COI, Cytb and 12S rRNA), were considered. DNA extraction, amplification and sequencing were performed for the fragments 12S rRNA and ITS for Amblyseius andersoni, A. swirskii, Iphiseius degenerans, Euseius ovalis, E. stipulatus, Neoseiulus cucumeris and Typhlodromus pyri, as some identifications were questionable. Numerous problems were evident based on genetic distance analyses of these sequences. First, nomenclatural problems were encountered, preventing the correct identification of the taxa sequenced in one case. Suspected misidentifications were frequent, stressing the importance of voucher specimen availability. For the 12S rRNA fragment, sequences assigned to three Phytoseiidae species were those of their prey (Astigmata), underlining the care that must be taken when manipulating the DNA of such predators (sterile conditions and specific PCR primers). Finally, sequences of two regions of the COI mtDNA were encountered, leading to alignment problems between sequences of a same gene and same species. These results are discussed in relation to responsibilities of authors in terms of taxon identification and the great utility of open access DNA sequence databases, such as GenBank, for improving taxonomic identifications and advancing scientific research.

The phylogeography of Asian Schistosoma (Trematoda: Schistosomatidae)

Parasitology ◽  
2002 ◽  
Vol 125 (2) ◽  
pp. 99-112 ◽  
Author(s):  
S. W. ATTWOOD ◽  
E. S. UPATHAM ◽  
X. H. MENG ◽  
D.-C. QIU ◽  
V. R. SOUTHGATE
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Rrna Genes ◽  
12S Rrna ◽  
28S Rrna ◽  
Asian Origin ◽  
Dna Sequence Data ◽  
African Group ◽  
Mitochondrial 12S Rrna ◽  
Central Thailand

Partial (DNA) sequences are presented for 2 nuclear (18S and 28S rRNA genes) and 2 mitochondrial (12S rRNA and ND1 genes) loci for 5 species belonging to the Schistosoma japonicum, S. sinensium and S. indicum groups of Asian Schistosoma. Fresh field isolates were collected and cultured for the following taxa: S. incognitum (S. indicum group, central Thailand), S. mekongi (S. japonicum group, southern Laos), S. ovuncatum (S. sinensium group, northern Thailand), S. spindale (S. indicum group, northeast Thailand and central Thailand isolates) and S. sinensium (S. sinensium group, Sichuan Province, China). This represents the first published DNA sequence data for S. ovuncatum and for S. sinensiums.s. from the type locality in China. The paper also presents the first sequence data at the above loci for S. incognitum (except for the 28S sequences) and S. sinensium. Congruence was observed between the phylogenies estimated for each locus, although the relationships of S. incognitum were not so well resolved. Fitch–Margoliash, maximum likelihood (ML) and maximum parsimony methods were used to estimate the phylogenies and the agreement between them was similar to that observed between loci. The ML tree was considered to best represent the data and additional 28S sequences (taken from the GenBank), for S. haematobium, S. japonicum, S. mansoni and Orientobilharzia turkestanicum, were used to construct an overall phylogeny. The S. indicum group taxa showed considerable divergence from the other Asian species and closest affinity with the African group. S. ovuncatum and S. sinensium appeared as sister taxa but their status as sibling species remained supported. The findings are discussed in the context of phylogeographical hypotheses for the origin of Schistosoma. An Asian origin for Schistosoma is also considered.

scholarly journals Relationships of Tarentola (Reptilia: Gekkonidae) from the Cape Verde Islands estimated from DNA sequence data

2002 ◽  
Vol 23 (1) ◽  
pp. 47-54 ◽  
Author(s):  
António Brehm ◽  
José Jesus ◽  
D. James Harris
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Nuclear Gene ◽  
Mitochondrial Genes ◽  
Cape Verde ◽  
12S Rrna ◽  
Base Pairs ◽  
Cape Verde Islands ◽  
Dna Sequence Data

AbstractThirteen specimens of Tarentola from the Cape Verde islands were sequenced for 695 base pairs of 12S rRNA and cytochrome b mitochondrial genes, and analysed with published sequences. Our results support many of the relationships previously proposed. We report the presence of Tarentola gigas Bocage, 1875 on São Nicolau and Tarentola caboverdiana nicolauensis Schleich, 1984 on São Vicente. This increases the number of genetically distinct forms on these islands; hence community structure appears to be more complex than previously understood. We also sequenced seven individuals for 375 base pairs of the nuclear gene, C-mos. Two sites were variable, much less than expected given the high levels of differentiation based on mitochondrial DNA sequences.

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

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.

Morphometric, genetic diversity and phylogenetic analysis of Taenia hydatigena (Pallas, 1766) larval stage in Iranian livestock

Parasitology ◽  
2019 ◽  
Vol 147 (2) ◽  
pp. 231-239
Author(s):  
Shahabeddin Sarvi ◽  
Laya Ebrahimi Behrestaghi ◽  
Abbas Alizadeh ◽  
Seyed Abdollah Hosseini ◽  
Shaban Gohardieh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Larval Stage ◽  
Sequence Data ◽  
Genetic Difference ◽  
12S Rrna ◽  
Northern Iran ◽  
Taenia Hydatigena ◽  
Cysticercus Tenuicollis ◽  
Significant Difference ◽  
Cox 1

AbstractCysticercus tenuicollis as metacestode of Taenia hydatigena is the most prevalent taeniid species in livestock. Eighty-eight C. tenuicollis samples were collected from sheep (n = 44) and goats (n = 44) of the northern Iran from 2015 to 2016. The isolated parasites were characterized by morphometric keys. The DNA of the larval stage was extracted, amplified and sequenced targeting mitochondrial 12S rRNA and Cox 1 markers. A significant difference in larval rostellar hook length was observed in 12S rRNA haplotypes. Analysis of molecular variance of 12S rRNA indicated a moderate genetic diversity in the C. tenuicollis isolates. The pairwise sequence distance of C. tenuicollis showed an intra-species diversity of 0.3–0.5% and identity of 99.5–100%. Using the 12S rRNA sequence data we found a moderate genetic difference (Fst; 0.05421) in C. tenucollis isolates collected from livestock of the northern and southeastern regions of Iran. We concluded that the genetic variants of C. tenuicollis are being undoubtedly distributing mostly in different parts of Iran. Further studies with a larger number of T. hydatigena isolates collected from various intermediate and definitive hosts are needed to study this evolutionary assumption and also to determine the apparent genetic differences observed in the studied regions.

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

Genome ◽  
2004 ◽  
Vol 47 (4) ◽  
pp. 732-741 ◽  
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.

scholarly journals AN ALTERNATIVE APPROACH TO IDENTIFY KEY INDUSTRIES: ISSUES TO SELECTION CRITERIA

2014 ◽  
Vol 15 (3) ◽  
pp. 577-598
Author(s):  
Abul Quasem Al-Amin ◽  
Abdul Hamid Jaafar
Keyword(s):  
Selection Criteria ◽  
Public Investment ◽  
Correct Identification ◽  
The Public ◽  
Study Approach ◽  
Sectoral Planning ◽  
Alternative Approach ◽  
The Subject ◽  
Key Industries ◽  
High Degree

Within a process of modeling exercise, this study aimed to understand appropriate selection criteria to identify key industries. There are many key sector identification linkage measures in the subject matter and sensitivity issue among them can be tricky because many of these measures differ only slightly but can result in outcomes that are quite dissimilar. With this background, we proposed an alternate approach that helps to resolve this issue. The proposed approach utilizes in this study by five sub-methods and high degree of the frequency of their occurrences in sub-methods to determine the key sectors. The study approach is applied to Malaysia as the public sector investment remains a large share in the national economy, like other developing countries, and the correct identification is still a challenge for sectoral planning. The experiences from this study can be used to guide appropriate public investment in Malaysia and elsewhere with similar economic forms.

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

mSystems ◽  
2018 ◽  
Vol 3 (3) ◽  
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.

Molecular phylogeny of Australasian anopsobiine centipedes (Chilopoda : Lithobiomorpha)

2004 ◽  
Vol 18 (3) ◽  
pp. 235 ◽  
Author(s):  
Gregory D. Edgecombe ◽  
Gonzalo Giribet
Keyword(s):  
South Africa ◽  
New Species ◽  
New Zealand ◽  
New Caledonia ◽  
Sequence Data ◽  
Mitochondrial Protein ◽  
Molecular Data ◽  
12S Rrna ◽  
28S Rrna ◽  
16S Rna

Species assigned to the anopsobiine centipede genera Anopsobius Silvestri, 1899, and Dichelobius Attems, 1911, are widely distributed on fragments of the Gondwanan supercontinent, including temperate and tropical Australia, New Zealand, New Caledonia, the Cape region of South Africa, and southern South America. Phylogenetic relationships between Australasian and other Gondwanan Anopsobiinae are inferred based on parsimony and maximum likelihood analyses (via direct optimisation) of sequence data for five markers: nuclear ribosomal 18S rRNA and 28S rRNA, mitochondrial ribosomal 12S rRNA and 16S RNA, and the mitochondrial protein-coding cytochrome c oxidase subunit I. New molecular data are added for Anopsobius from South Africa and New Zealand, Dichelobius from New Caledonia, and a new species from Queensland, Australia, Dichelobius etnaensis, sp. nov. The new species is based on distinctive morphological and molecular data. The molecular phylogenies indicate that antennal segmentation in the Anopsobiinae is a more reliable taxonomic character than is spiracle distribution. The former character divides the Gondwanan clade into a 17-segmented group (Dichelobius) and a 15-segmented group (Anopsobius). Confinement of the spiracles to segments 3, 10 and 12 has at least two origins in the Gondwanan clade. The area cladogram for Dichelobius (Queensland (Western Australia + New Caledonia)) suggests a relictual distribution pruned by extinction.

Experimental studies on Lecanora rupicola (L.) Zahlbr.: chemical and microscopical investigations of the mycobiont and re-synthesis stages

2006 ◽  
Vol 38 (6) ◽  
pp. 577-585 ◽  
Author(s):  
Georg BRUNAUER ◽  
Armin HAGER ◽  
Wolf Dietrich KRAUTGARTNER ◽  
Roman TÜRK ◽  
Elfie STOCKER-WÖRGÖTTER
Keyword(s):  
Electron Microscope ◽  
Scanning Electron Microscope ◽  
Sequence Data ◽  
Experimental Studies ◽  
Culture Conditions ◽  
Voucher Specimen ◽  
Dna Sequence Data ◽  
Standard Culture ◽  
Voucher Specimens ◽  
Scanning Electron

Culture experiments that trigger the axenically grown mycobionts of Lecanora rupicola to produce the polyketide chemosyndrome typical of the naturally grown lichen are reported. This chemosyndrome comprises lecanoric, haematommic and orsellinic acids, sordidone, eugenitol and atranorin, all of which were hardly produced under standard culture conditions. The only exception was arthothelin that was only present in the voucher specimen. It has been shown that almost the complete acetyl-polymalonyl-pathway leading to depsides and chromones can be induced in culture, but apparently not the xanthones. The mycobiont was also successfully re-synthesized with its original photobiont, as confirmed by Scanning Electron Microscope studies (SEM). Cultures of the resynthesised lichen biosynthesized additional satellite substances, which were not detected either in the voucher specimens or in the aposymbiontically (without the photobiont) grown mycobiont cultures. The identity of cultured mycobionts of L. rupicola was confirmed by comparing ITS-DNA-sequence data from the original lichen with publicly available (GeneBank) sequences of that species.

scholarly journals Diversity of echinostomes (Digenea: Echinostomatidae) in their snail hosts at high latitudes

Parasite ◽  
2021 ◽  
Vol 28 ◽  
pp. 59
Author(s):  
Camila Pantoja ◽  
Anna Faltýnková ◽  
Katie O’Dwyer ◽  
Damien Jouet ◽  
Karl Skírnisson ◽  
...  
Keyword(s):  
North America ◽  
Dna Sequences ◽  
Sequence Data ◽  
Molecular Data ◽  
Migratory Bird ◽  
Parasite Fauna ◽  
Life Cycles ◽  
Freshwater Ecosystems ◽  
Trematode Species ◽  
Host Life

The biodiversity of freshwater ecosystems globally still leaves much to be discovered, not least in the trematode parasite fauna they support. Echinostome trematode parasites have complex, multiple-host life-cycles, often involving migratory bird definitive hosts, thus leading to widespread distributions. Here, we examined the echinostome diversity in freshwater ecosystems at high latitude locations in Iceland, Finland, Ireland and Alaska (USA). We report 14 echinostome species identified morphologically and molecularly from analyses of nad1 and 28S rDNA sequence data. We found echinostomes parasitising snails of 11 species from the families Lymnaeidae, Planorbidae, Physidae and Valvatidae. The number of echinostome species in different hosts did not vary greatly and ranged from one to three species. Of these 14 trematode species, we discovered four species (Echinoparyphium sp. 1, Echinoparyphium sp. 2, Neopetasiger sp. 5, and Echinostomatidae gen. sp.) as novel in Europe; we provide descriptions for the newly recorded species and those not previously associated with DNA sequences. Two species from Iceland (Neopetasiger islandicus and Echinoparyphium sp. 2) were recorded in both Iceland and North America. All species found in Ireland are new records for this country. Via an integrative taxonomic approach taken, both morphological and molecular data are provided for comparison with future studies to elucidate many of the unknown parasite life cycles and transmission routes. Our reports of species distributions spanning Europe and North America highlight the need for parasite biodiversity assessments across large geographical areas.

Sign in / Sign up

Export Citation Format

Share Document