scholarly journals Phylogeny of Meloidogyne spp. based on 18S rDNA and the intergenic region of mitochondrial DNA sequences

Nematology ◽  
2005 ◽  
Vol 7 (6) ◽  
pp. 851-862 ◽  
Author(s):  
Regina Carneiro ◽  
Don Dickson ◽  
Ayyamperumal Jeyaprakash ◽  
Byron Adams ◽  
Myrian Tigano
Keyword(s):  
Mitochondrial Dna ◽  
16S Rrna ◽  
Dna Sequences ◽  
18S Rdna ◽  
Phylogenetic Trees ◽  
Optimality Criteria ◽  
Cytochrome Oxidase Subunit ◽  
Meloidogyne Spp ◽  
Rdna Analysis ◽  
Cytochrome Oxidase Subunit Ii

AbstractThe 18S rDNA of 19 populations of Meloidogyne spp. was amplified and directly sequenced. The region of mitochondrial DNA, located in the 3′ portion of the gene that codes for cytochrome oxidase subunit II (COII) through a portion of the 16S rRNA (lRNA) gene, from 16 of these populations was cloned and sequenced. Heteroplasmic sequences were identified from both rDNA and mtDNA regions for several taxa. Several sequences sampled from nominal taxa differed from previously published accounts. Phylogenetic trees based on alignments of these sequences were constructed using distance, parsimony and likelihood optimality criteria. For 18S rDNA data, three main clades were identified. One well supported clade (86–91% bootstrap) included the most common and widely disseminated species, e.g.,M. arenaria, M. javanica and M. incognita, some recently described or redescribed species (M. floridensis, M. paranaensis, and M. ethiopica) plus numerous unidentified isolates. All mitotic parthenogenetic species, except for M. oryzae, were included in this clade. Other, less well supported clades included the amphimictic and facultative meiotic species M. hapla, M. microtyla, M. maritima and M. duytsi. One such clade comprised three meiotic parthenogens (M. exigua, M. graminicola and M. chitwoodi) and M. oryzae. This clade was moderately supported (77% bootstrap) but the relationships within this clade were poor. For mitochondrial DNA data, only the species in clade I from rDNA analysis, and M. hapla were analysed. These species formed a well supported clade (100% bootstrap) to the exclusion of M. mayaguensis and M. hapla. The addition of taxa and mtDNA data to publicly available records improved the discrimination sensitivity of species and atypical, non-identified, isolates.

New species of Diamesa (Diptera: Chironomidae) from Tibet: conspecific males and females associated with mitochondrial DNA

Zootaxa ◽  
2005 ◽  
Vol 1049 (1) ◽  
pp. 19 ◽  
Author(s):  
ENDRE WILLASSEN
Keyword(s):  
Mitochondrial Dna ◽  
New Species ◽  
Cytochrome Oxidase ◽  
Dna Sequences ◽  
Type Material ◽  
Cytochrome Oxidase Subunit ◽  
Oxidase Subunit ◽  
Complete Type ◽  
Males And Females ◽  
Insect Collection

Undescribed females representing four morphological types were found in a collection of adult Diamesa from about 5000 m altitude in Rongbuk, Tibet. Short DNA sequences of cytochrome oxidase subunit 2 were used to associate two single males in the material with conspecific females. Diamesa solhoyi n.sp. and Diamesa aculeata n.sp. are described. The complete type material and additional specimens have been deposited in the Insect Collection at the Institute of Zoology, Academia Sinica, Beijing (IZAS). The sequences are deposited in Genbank with accession numbers AM051227–AM051233.

scholarly journals Phylogenetic Analysis of Mitochondrial Genes of Malaysian Tupaia Reveals Composite Species in Tupaia Glis

2021 ◽  
Vol 3 (1) ◽  
pp. 197-203
Author(s):  
Jayaraj Vijaya Kumaran ◽  
Ahmad Sofiman Othman ◽  
Shahrul-Anuar Mohd Sah ◽  
Seri Intan Mokhtar
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Mitochondrial Genes ◽  
Peninsular Malaysia ◽  
Universal Primers ◽  
Cyt B ◽  
Southern Thailand ◽  
Tupaia Glis

Recent morphometric analysis on T. glis in Peninsular Malaysia indicates that there were more than one morphotypes in this species. Thus this study attempts to examine this phenomenon using mitochondrial DNA sequences of Cyt b and CO1 genes. A total of 74 DNA sequences for both genes were generated using available universal primers. Samples from Southern Thailand were found to be misidentified as T. glis when in fact these samples clustered with T. belangeri while one T. tana from Borneo was miss-identified as T. minor. The phylogenetic trees showed that there are at least one confirmed morphotype of Tupaia (new Tupaia sp.) that have yet to be described. The results also showed that the separation of T. glis morphotype 1 and 11 were visible in the combined genes tree, congruent with the morphometric phylogeny but had poor phylogenetic support.

scholarly journals A novel PCR-clamping assay reducing plant host DNA amplification significantly improves prokaryotic endo-microbiome community characterization

2020 ◽  
Vol 96 (7) ◽  
Author(s):  
Emilie Lefèvre ◽  
Courtney M Gardner ◽  
Claudia K Gunsch
Keyword(s):  
Mitochondrial Dna ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Dna Amplification ◽  
Rrna Gene ◽  
Plant Host ◽  
Plant Chloroplast

ABSTRACT Due to the sequence homology between the bacterial 16S rRNA gene and plant chloroplast and mitochondrial DNA, the taxonomic characterization of plant microbiome using amplicon-based high throughput sequencing often results in the overwhelming presence of plant-affiliated reads, preventing the thorough description of plant-associated microbial communities. In this work we developed a PCR blocking primer assay targeting the taxonomically informative V5-V6 region of the 16S rRNA gene in order to reduce plant DNA co-amplification, and increase diversity coverage of associated prokaryotic communities. Evaluation of our assay on the characterization of the prokaryotic endophytic communities of Zea mays, Pinus taeda and Spartina alternifora leaves led to significantly reducing the proportion of plant reads, yielded 20 times more prokaryotic reads and tripled the number of detected OTUs compared to a commonly used V5-V6 PCR protocol. To expand the application of our PCR-clamping assay across a wider taxonomic spectrum of plant hosts, we additionally provide an alignment of chloroplast and mitochondrial DNA sequences encompassing more than 200 terrestrial plant families as a supporting tool for customizing our blocking primers.

scholarly journals Mitochondrial DNA Sequence Phylogeny of Daucus

2020 ◽  
Vol 45 (2) ◽  
pp. 403-408 ◽  
Author(s):  
David M. Spooner ◽  
Holly Ruess ◽  
Philipp Simon ◽  
Douglas Senalik
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Plastid Dna ◽  
Nuclear Data ◽  
Bootstrap Support ◽  
Illumina Hiseq ◽  
Data Set ◽  
Closely Related Species ◽  
Mitochondrial Sequences

Abstract—We explored the phylogenetic utility of mitochondrial DNA sequences in Daucus and compared the results with prior phylogenetic results using the same 36 accessions of Daucus (and two additional outgroups) with plastid DNA sequences and with other nuclear results. As in the plastid study we used Illumina HiSeq sequencer to obtain resequencing data of the same accessions of Daucus and outgroups, and analyzed the data with maximum parsimony and maximum likelihood. We obtained data from 47 of 71 total mitochondrial genes but only 17 of these 47 genes recovered major clades that were common in prior plastid and nuclear studies. Our phylogenetic trees of the concatenated data set of 47 genes were moderately resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. There are areas of hard incongruence with phylogenies using plastid and nuclear data. In agreement with other studies, we conclude that mitochondrial sequences are generally poor phylogenetic markers, at least at the genus level, despite their utility in some other studies.

scholarly journals Undocumented translocations spawn taxonomic inflation in Sri Lankan fire rasboras (Actinopterygii, Cyprinidae)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6084 ◽  
Author(s):  
Hiranya Sudasinghe ◽  
Jayampathi Herath ◽  
Rohan Pethiyagoda ◽  
Madhava Meegaskumbura
Keyword(s):  
Mitochondrial Dna ◽  
River Basin ◽  
Dna Sequences ◽  
Valid Species ◽  
Sri Lankan ◽  
Cytochrome Oxidase Subunit ◽  
Shared Haplotype ◽  
Selective Sampling ◽  
Taxonomic Analysis ◽  
Cytochrome Oxidase Subunit 1

A recent (2013) taxonomic review of the freshwater-fish genus Rasboroides, which is endemic to Sri Lanka, showed it to comprise four species: R. vaterifloris, R. nigromarginatus, R. pallidus and R. rohani. Here, using an integrative-taxonomic analysis of morphometry, meristics and mitochondrial DNA sequences of cytochrome b (cytb) and cytochrome oxidase subunit 1 (coi), we show that R. nigromarginatus is a synonym of R. vaterifloris, and that R. rohani is a synonym of R. pallidus. The creation and recognition of unnecessary taxa (‘taxonomic inflation’) was in this case a result of selective sampling confounded by a disregard of allometry. The population referred to R. rohani in the Walawe river basin represents an undocumented trans-basin translocation of R. pallidus, and a translocation into the Mahaweli river of R. vaterifloris, documented to have occurred ca 1980, in fact involves R. pallidus. A shared haplotype suggests the latter introduction was likely made from the Bentara river basin and not from the Kelani, as claimed. To stabilize the taxonomy of these fishes, the two valid species, R. vaterifloris and R. pallidus, are diagnosed and redescribed, and their distributions delineated. We draw attention to the wasteful diversion of conservation resources to populations resulting from undocumented translocations and to taxa resulting from taxonomic inflation. We argue against translocations except where mandated by a conservation emergency, and even then, only when supported by accurate documentation.

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