scholarly journals Characterization of Five New Earthworm Mitogenomes (Oligochaeta: Lumbricidae): Mitochondrial Phylogeny of Lumbricidae

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 580
Author(s):  
Hongyi Liu ◽  
Yufeng Zhang ◽  
Wei Xu ◽  
Yu Fang ◽  
Honghua Ruan
Keyword(s):  
Phylogenetic Trees ◽  
Mitochondrial Gene ◽  
Morphological Characteristics ◽  
Molecular Techniques ◽  
Phylogenetic Studies ◽  
Octolasion Tyrtaeum ◽  
Eisenia Nordenskioldi ◽  
Novel Strategy

Identification based on conventional morphological characteristics is typically difficult and time-consuming. The development of molecular techniques provides a novel strategy that relies on specific mitochondrial gene fragments to conduct authentication. For this study, five newly sequenced partial mitogenomes of earthworms (Bimastos parvus, Dendrobaena octaedra, Eisenia andrei, Eisenia nordenskioldi, and Octolasion tyrtaeum) with lengths ranging from 14,977 to 15,715 were presented. Each mitogenome possessed a putative control region that resided between tRNA-Arg and tRNA-His. All of the PCGs were under negative selection according to the value of Ka/Ks. The phylogenetic trees supported the classification of Eisenia and Lumbricus; however, the trees based on cox1 did not. Through various comparisons, it was determined that cox1 fragments might be more suitable for molecular identification. These results lay the foundation for further phylogenetic studies on Lumbricidae.

scholarly journals Genetic and Morphological Characterization of Mangifera indica L. Growing in Egypt

HortScience ◽  
2018 ◽  
Vol 53 (9) ◽  
pp. 1266-1270 ◽  
Author(s):  
Nader R. Abdelsalam ◽  
Hayssam M. Ali ◽  
Mohamed Z.M. Salem ◽  
Elsayed G. Ibrahem ◽  
Mohamed S. Elshikh
Keyword(s):  
Genetic Diversity ◽  
Mangifera Indica ◽  
Morphological Characteristics ◽  
Morphological Characterization ◽  
Molecular Techniques ◽  
Germplasm Management ◽  
Fruit Crops ◽  
The Family ◽  
High Diversity

Mango (Mangifera indica L.) is a fruit crops belong to the family Anacardiaceae and is the oldest cultivated tree worldwide. Cultivars maintained in Egypt have not been investigated previously. Mango was first brought to Egypt from South Asia. Morphological and molecular techniques were used to identify the genetic diversity within 28 mango cultivars. SSR and EST-SSR were used for optimizing germplasm management of mango cultivars. Significant variations were observed in morphological characteristics and genetic polymorphism, as they ranged from 0.71% to 100%. High diversity was confirmed as a pattern of morphological and genotypes data. Data from the present study may be used to calculate the mango relationship and diversity currently grown in Egypt.

scholarly journals Descriptions of diplostomid metacercariae (Digenea: Diplostomidae) from freshwater fishes in the Tshwane area

2013 ◽  
Vol 80 (1) ◽  
Author(s):  
Esmey B.E. Moema ◽  
Pieter H. King ◽  
Johnny N. Rakgole ◽  
Chantélle Baker
Keyword(s):  
Clarias Gariepinus ◽  
Morphological Characteristics ◽  
Molecular Techniques ◽  
Cranial Cavity ◽  
Base Pairs ◽  
Parasitic Species ◽  
Larval Stages ◽  
Digenetic Trematodes ◽  
Genomic Regions

The metacercarial (larval) stages of diplostomid digeneans are known to inhabit freshwater fish, causing tissue damage in the process. Due to their widespread diversity, little is known about their life cycle. The classification of these parasitic stages to the species level using only the morphology is very challenging due to the lack of genitalia; they are regarded to be the most important structures in the identification of these organisms. In this study, additional morphological information through light and scanning electron microscopy is given for two different diplostomids found in the cranial cavity of Clarias gariepinus and the vitreous chambers of Tilapia sparrmanii and Pseudocrenilabrus philander. The diplostomid metacercaria inhabiting the cranial cavity of Clarias gariepinus was morphologically identified as Diplostomulum (Tylodelphys) mashonenseand an unknown metacercaria of the genus Diplostomumwas found in the vitreous chambers of Pseudocrenilabrus philander and Tilapia sparrmanii. Both parasitic species’ 28S recombinant deoxyribonucleic acid genomic regions were successfully amplified using Dig 125/1500R primer pairs. The assay yielded a product of approximately 1300 base pairs as seen on the gel images. There were 14 nucleotide differences over the entire analysed sequences resulting in a 1.1% (14/1273) nucleotide difference. In line with the morphological characteristics of these parasites, there seemed to be a slight difference in their genetic makeup. The application of molecular techniques on digenetic trematodes seems very promising and may yield great potential in future descriptions of morphologically similar parasitic species.

scholarly journals (284) Characterization of the Genus Corylopsis

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1051D-1051
Author(s):  
Mark S. Roh ◽  
Eunju Cheong ◽  
Ik-Young Choi ◽  
Eun-Ha Yoo ◽  
Jae-Young Kim ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Rapd Markers ◽  
Morphological Characteristics ◽  
Single Nucleotide ◽  
Ribosomal Rna Gene ◽  
Snp Data ◽  
Intraspecific Variations ◽  
Subspecies Level

We investigated the interspecific relationships and intraspecific variations in the genus Corylopsis using RAPD and single nucleotide polymorphism (SNP) in the internal transcribed spacer1(ITS1), 5.8S ribosomal RNA gene specific in C. glabrescens Franch. & Sav. Differences in species identification between morphological characteristics and RAPD result were noticed in some accessions. All C. glabrescens, C. coreana Uyeki, and C. glabrescens f. gotoana (Makino) T. Yamanaka accessions clustered in one major group. However, they could be divided into five subgroups that are not related to the geographical origins. For example, C. coreana accessions from Korea were clustered with C. glabrescens from Japan. Although grouping based on SNP data does not agree with that by RAPD markers, it revealed the limitation in identification and classification of the genus due to high intraspecific variations in SNP. At SNP positions 464, 465, 466, 467, and 496, most accessions of C. glabrescens and C. coreana have C, G, A, A, and T, respectively. In both analyses, C. glabrescens, C. coreana, and C. glabrescens f. gotoana Japan are closely related and this suggests that nomenclature for these three species should be discussed. Although ITS1 5.8S ribosomal RNA gene can not be used for identification at a subspecies level of C. glabrescens, it proved to be useful to differentiate C. sinensisfrom C. sinensis var. calvescens. It is suggested to use C. glabrescens f. gotoana or C. glabrescens f. coreana rather than using C. coreana.

scholarly journals A GLANCE AT MOLECULAR IDENTIFICATION OF BAMBOO (Poaceae: Bambusoideae)

2020 ◽  
pp. 19
Author(s):  
Nabilah Mohamad Khairi ◽  
Wilson Thau Lym Yong ◽  
Julius Kulip ◽  
Kenneth Francis Rodrigues
Keyword(s):  
Plant Species ◽  
Rural Areas ◽  
Morphological Characteristics ◽  
Vital Role ◽  
Molecular Techniques ◽  
Morphological Identification ◽  
Correct Identification ◽  
Bamboo Species ◽  
Plant Resources

Conservation of plant species plays a vital role in preventing the loss of valuable plant resources. The success of conservation depends on the correct identification and characterization of plant species. Bamboo is one of the most important plants with multiple uses that have contributed to the economy and socio-economy of many people in rural areas. It is under the subfamily of Bambusoideae that includes both woody and herbaceous bamboo. Conventionally, like other plants, bamboo has been classified dependently based on morphological characteristics. However, morphological identification leads to difficulties and misclassification of bamboo species due to their infrequent flowering behaviour and peculiar reproductive biology. Since then, molecular markers have been introduced to overcome the problems associated with bamboo taxonomy and phylogeny. This paper provides an overview of the diverse, predominantly molecular techniques used to assess and determine the genetic diversity of bamboo species.

scholarly journals Visual Characterization of Misclassified Class C GPCRs through Manifold-based Machine Learning Methods

2015 ◽  
Vol 1 (1) ◽  
pp. 19 ◽  
Author(s):  
Martha Ivon Cardenas ◽  
Alfredo Vellido ◽  
Caroline König ◽  
René Alquezar ◽  
Jesús Giraldo
Keyword(s):  
Phylogenetic Trees ◽  
Nonlinear Dimensionality Reduction ◽  
Learning Methods ◽  
Dimensionality Reduction Technique ◽  
Cell Membrane Proteins ◽  
Class C ◽  
G Protein Coupled ◽  
Sequence Transformations

G-protein-coupled receptors are cell membrane proteins of great interest in biology and pharmacology. Previous analysis of Class C of these receptors has revealed the existence of an upper boundary on the accuracy that can be achieved in the classification of their standard subtypes from the unaligned transformation of their primary sequences. To further investigate this apparent boundary, the focus of the analysis in this paper is placed on receptor sequences that were previously misclassified using supervised learning methods. In our experiments, these sequences are visualized using a nonlinear dimensionality reduction technique and phylogenetic trees. They are subsequently characterized against the rest of the data and, particularly, against the rest of cases of their own subtype. This exploratory visualization should help us to discriminate between different types of misclassification and to build hypotheses about database quality problems and the extent to which GPCR sequence transformations limit subtype discriminability. The reported experiments provide a proof of concept for the proposed method.

scholarly journals Development of Plastid Genomic Resources for Discrimination and Classification of Epimedium wushanense (Berberidaceae)

2019 ◽  
Vol 20 (16) ◽  
pp. 4003 ◽  
Author(s):  
Guo ◽  
Ren ◽  
Xu ◽  
Liao ◽  
Song ◽  
...  
Keyword(s):  
Related Species ◽  
Phylogenetic Trees ◽  
Morphological Characteristics ◽  
Rrna Genes ◽  
Closely Related Species ◽  
Protein Coding ◽  
Important Species ◽  
Plastid Genomes ◽  
First Time

Epimedium wushanense (Berberidaceae) is recorded as the source plant of Epimedii Wushanensis Folium in the Chinese Pharmacopoeia. However, controversies exist on the classification of E. wushanense and its closely related species, namely, E. pseudowushanense, E. chlorandrum, E. mikinorii, E. ilicifolium, and E. borealiguizhouense. These species are often confused with one another because of their highly similar morphological characteristics. This confusion leads to misuse in the medicinal market threatening efficiency and safety. Here, we studied the plastid genomes of these Epimedium species. Results show that the plastid genomes of E. wushanense and its relative species are typical circular tetramerous structure, with lengths of 156,855–158,251 bp. A total of 112 genes were identified from the Epimedium plastid genomes, including 78 protein-coding, 30 tRNA, and 4 rRNA genes. A loss of rpl32 gene in E. chlorandrum was found for the first time in this study. The phylogenetic trees constructed indicated that E. wushanense can be distinguished from its closely related species. E. wushanense shows a closer relationship to species in ser. Dolichocerae. In conclusion, the use of plastid genomes contributes useful genetic information for identifying medicinally important species E. wushanense and provides new evidence for understanding phylogenetic relationships within the Epimedium genus.

scholarly journals Haslea nusantara (Bacillariophyceae), a new blue diatom from the Java Sea, Indonesia: morphology, biometry and molecular characterization

2019 ◽  
Vol 152 (2) ◽  
pp. 188-202 ◽  
Author(s):  
Fiddy Semba Prasetiya ◽  
Romain Gastineau ◽  
Michel Poulin ◽  
Claude Lemieux ◽  
Monique Turmel ◽  
...  
Keyword(s):  
New Species ◽  
Molecular Characterization ◽  
Mitochondrial Gene ◽  
Morphological Characteristics ◽  
Molecular Techniques ◽  
Mitochondrial Genomes ◽  
Chloroplast Gene ◽  
Its Gene ◽  
Java Sea ◽  
A New Species

Background and aims – The present study aims to describe a new species of pennate blue diatom from the genus Haslea, H. nusantara sp. nov., collected from Semak Daun Island, the Seribu Archipelago, in Indonesian marine waters. Methods – Assessment for species identification was conducted using light microscopy, Scanning Electron Microscopy and molecular techniques. The morphological characteristics of H. nusantara have been described, illustrated and compared to other morphologically similar blue Haslea taxa, distributed worldwide. Additionally, molecular characterization was achieved by sequencing plastidial and mitochondrial genomes. Key results – This new species, named Haslea nusantara, cannot be discriminated by its morphology (stria density) but it is characterized by its gene sequences (rbcL chloroplast gene and cox1 mitochondrial gene). Moreover, it differentiates from other blue Haslea species by the presence of a thin central bar, which has been previously reported in non-blue species like H. pseudostrearia. The complete mitochondrion (36,288 basepairs, bp) and plastid (120,448 bp) genomes of H. nusantara were sequenced and the gene arrangements were compared with other diatom genomes. Phylogeny analyses established using rbcL indicated that H. nusantara is included in the blue Haslea cluster and close to a blue Haslea sp. found in Canary Islands (H. silbo sp. ined.). Conclusions – All investigations carried out in this study show that H. nusantara is a new blue-pigmented species, which belongs to the blue Haslea clade, with an exceptional geographic distribution in the Southern Hemisphere.

scholarly journals Complete Mitochondrial Genomes of Babylonia Formosae and Babylonia Zeylanica (Neogastropoda: Babyloniidae) and Increased Sampling Give New Insights Into Neogastropoda Phylogeny

2021 ◽  
Author(s):  
Hongwei Huang ◽  
huai Yang ◽  
Jiji Li ◽  
baoying Guo ◽  
Yingying Ye
Keyword(s):  
Phylogenetic Trees ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Trna Genes ◽  
Phylogenetic Studies ◽  
Marine Snails ◽  
Fundamental Information ◽  
Complete Mitogenome ◽  
Genome Arrangement ◽  
Complete Mitochondrial Genomes

Abstract The phylogenetic relationships of Neogastropoda, a group of highly complex predatory marine snails, have been controversial. The two newly sequenced mitogenomes of Babylonia formosae and Babylonia zeylanica (Neogastropoda: Babyloniidae) are described. The mitogenomes of B. zeylanica and B. formosae were 16, 214 bp and 16, 181 bp in length, respectively. The mitogenomes of both species contain 13 PCGs, 22 tRNA genes, and 2 ribosomal RNA genes. The sequence of genes differed from the ancestral mitochondrial gene arrangement of Caenogastropoda mitogenomes. Also, 63 Neogastropoda species were analyzed for the genome organization of seventeen major lineage of Neogastropoda, five types of mitochondrial genome arrangement were identified. Bayesian Inference phylogenetic trees and Maximum likehood of Neogastropoda were established according to complete mitogenome. The monophyly of Neogastropoda families is strongly supported by this study, in contrast to previous molecular studies. Our results shed light on gene sequence distribution/arrangement characteristics of Neogastropoda mitogenomes, provide fundamental information for further phylogenetic studies on Neogastropoda.

scholarly journals Genital warts in Burmeister's porpoises: characterization of Phocoena spinipinnis papillomavirus type 1 (PsPV-1) and evidence for a second, distantly related PsPV

2007 ◽  
Vol 88 (7) ◽  
pp. 1928-1933 ◽  
Author(s):  
Marie-Françoise Van Bressem ◽  
Patricia Cassonnet ◽  
Annabel Rector ◽  
Christian Desaintes ◽  
Koen Van Waerebeek ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Genital Warts ◽  
Bovine Papillomavirus ◽  
Reading Frame ◽  
Bona Fide ◽  
Type 3

We identified sequences from two distantly related papillomaviruses in genital warts from two Burmeister's porpoises, including a PV antigen-positive specimen, and characterized Phocoena spinipinnis papillomavirus type 1 (PsPV-1). The PsPV-1 genome comprises 7879 nt and presents unusual features. It lacks an E7, an E8 and a bona fide E5 open reading frame (ORF) and has a large E6 ORF. PsPV-1 L1 ORF showed the highest percentage of nucleotide identity (54–55 %) with human papillomavirus type 5, bovine papillomavirus type 3 (BPV-3) and Tursiops truncatus papillomavirus type 2 (TtPV-2). This warrants the classification of PsPV-1 as the prototype of the genus Omikronpapillomavirus. PsPV-1 clustered with TtPV-2 in the E6 and E1E2 phylogenetic trees and with TtPV-2 and BPV-3 in the L2L1 tree. This supports the hypothesis that PV evolution may not be monophyletic across all genes.

Taxonomy of the rhizobia

1992 ◽  
Vol 38 (6) ◽  
pp. 446-450 ◽  
Author(s):  
G. H. Elkan
Keyword(s):  
Genetic Relationships ◽  
Molecular Techniques ◽  
New Genera ◽  
Genetic Studies ◽  
Minimum Standards ◽  
Slow Growing ◽  
Taxonomic Characterization ◽  
Comprehensive Study

Extensive cross testing on a relatively few legume hosts led initially to a taxonomic characterization of rhizobia based on bacteria–plant cross–inoculation groups. This has gradually become less acceptable, and has been replaced by taxonomic groupings derived from numerical taxonomy, carbohydrate metabolism, antibiotic susceptiblities, serology, and various molecular techniques. It has long been recognized that there are two distinct groups of rhizobia based on growth rate. The fast-growing genus Rhizobium includes R. leguminosarum, R. meliloti, R. loti, R. galegae, R. tropici, and R. huakuii. The slow-growing genus Bradyrhizobium contains only one recognized species, B. japonicum. Two new genera have been recognized: Azorhizobium, with one recognized species (A. caulinadans), and Sinorhizobium, with two species (S. fredii and S. xinjiangensis). Genetic studies of both the fast- and slow-growing groups show unacceptably wide intrageneric and intergeneric diversity. Although there have been some elegant studies of some of the genetic relationships among rhizobia, overall there has (have) not been the comprehensive study(ies) needed to allow a conclusive taxonomic scheme. Because proposals for revision are accelerating, minimum standards have been proposed by the International Subcommittee for the Taxonomy of Rhizobium and Agrobacterium. Key words: Rhizobium taxonomy, classification of rhizobia, interrelationships of rhizobia.

Sign in / Sign up

Export Citation Format

Share Document