scholarly journals Identification of High Molecular Variation Loci in Complete Chloroplast Genomes of Mammillaria (Cactaceae, Caryophyllales)

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 830
Author(s):  
Delil A. Chincoya ◽  
Alejandro Sanchez-Flores ◽  
Karel Estrada ◽  
Clara E. Díaz-Velásquez ◽  
Antonio González-Rodríguez ◽  
...  
Keyword(s):  
Population Genetics ◽  
Molecular Markers ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Molecular Variation ◽  
Short Sequence ◽  
Dna Variation ◽  
Chloroplast Genomes ◽  
Evolutionary Studies ◽  
Phylogenetic Resolution

In plants, partial DNA sequences of chloroplasts have been widely used in evolutionary studies. However, the Cactaceae family (1500–1800 species) lacks molecular markers that allow a phylogenetic resolution between species and genera. In order to identify sequences with high variation levels, we compared previously reported complete chloroplast genomes of seven species of Mammillaria. We identified repeated sequences (RSs) and two types of DNA variation: short sequence repeats (SSRs) and divergent homologous loci. The species with the highest number of RSs was M. solisioides (256), whereas M. pectinifera contained the highest amount of SSRs (84). In contrast, M. zephyranthoides contained the lowest number (35) of both RSs and SSRs. In addition, five of the SSRs were found in the seven species, but only three of them showed variation. A total of 180 homologous loci were identified among the seven species. Out of these, 20 loci showed a molecular variation of 5% to 31%, and 12 had a length within the range of 150 to 1000 bp. We conclude that the high levels of variation at the reported loci represent valuable knowledge that may help to resolve phylogenetic relationships and that may potentially be convenient as molecular markers for population genetics and phylogeographic studies.

Monophyly of Verbascum (Scrophularieae : Scrophulariaceae): evidence from nuclear and plastid phylogenetic analyses

2014 ◽  
Vol 62 (8) ◽  
pp. 638 ◽  
Author(s):  
Farrokh Ghahremaninejad ◽  
Mehrshid Riahi ◽  
Melina Babaei ◽  
Faride Attar ◽  
Lütfi Behçet ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Nrdna Its ◽  
Starting Point ◽  
High Species Diversity ◽  
Phylogenetic Estimation

Verbascum is one of the main genera of Scrophulariaceae, but delimitation and phylogenetic relationships of this genus are unclear and have not yet been studied using DNA sequences. Here, using four selected molecular markers (nrDNA ITS and the plastid spacers trnS/G, psbA-trnH and trnY/T), we present a phylogeny of Verbascum and test previous infrageneric taxonomic hypotheses as well as its monophyly with respect to Scrophularia. We additionally discuss morphological variation and the utility of morphological characters as predictors of phylogenetic relationships. Our results show that while molecular data unambiguously support the circumscription of Verbascum inferred from morphology, they prove to be of limited utility in resolving infrageneric relationships, suggesting that Verbascum ‘s high species diversity is due to rapid and recent radiation. Our work provides phylogenetic estimation of the genus Verbascum using molecular data and can serve as a starting point for future investigations of Verbascum and relatives.

scholarly journals Phylogenetic Resolution in Juglans Based on Complete Chloroplast Genomes and Nuclear DNA Sequences

2017 ◽  
Vol 8 ◽  
Author(s):  
Wenpan Dong ◽  
Chao Xu ◽  
Wenqing Li ◽  
Xiaoman Xie ◽  
Yizeng Lu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Chloroplast Genomes ◽  
Phylogenetic Resolution

Phylogeny of Trematomus (Notothenioidei: Nototheniidae) inferred from mitochondrial and nuclear gene sequences

2009 ◽  
Vol 21 (6) ◽  
pp. 565-570 ◽  
Author(s):  
Kristen L. Kuhn ◽  
Thomas J. Near
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Single Copy ◽  
Morphological Characters ◽  
Mitochondrial Genes ◽  
Phylogenetic Resolution

AbstractThe biota of Antarctica is amazingly rich and highly endemic. The phylogenetics of notothenioid fishes has been extensively investigated through analyses of morphological characters, DNA sequences from mitochondrial genes, and single copy nuclear genes. These phylogenetic analyses have produced reasonably similar phylogenetic trees of notothenioids, however a number of phylogenetic questions remain. The nototheniid clade Trematomus is an example of a group where phylogenetic relationships remain unresolved. In this paper we revisit the phylogenetic relationships of Trematomus using both increased taxon sampling and an expanded dataset which includes DNA sequences from two mitochondrial genes (ND2 and 16S rRNA) and one single-copy nuclear gene (RPS7). The Bayesian phylogeny resulting from the analysis of the combined mitochondrial and nuclear gene datasets was well resolved and contained more interspecific nodes supported with significant Bayesian posteriors than either the mitochondrial or nuclear gene phylogenies alone. This demonstrates that the addition of nuclear gene sequence data to mitochondrial data can enhance phylogenetic resolution and increase node support. Additionally, the results of the combined mitochondrial and nuclear Bayesian analyses provide further support for the inclusion of species previously classified as Pagothenia and Cryothenia in Trematomus.

scholarly journals Comparative Chloroplast Genomes of Sorghum Species: Sequence Divergence and Phylogenetic Relationships

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Yun Song ◽  
Yan Chen ◽  
Jizhou Lv ◽  
Jin Xu ◽  
Shuifang Zhu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Markers ◽  
Species Identification ◽  
Dna Markers ◽  
Phylogenetic Relationships ◽  
Sequence Divergence ◽  
Monophyletic Group ◽  
Ecological Diversity ◽  
Chloroplast Genomes ◽  
Gc Contents

Sorghum comprises 31 species that exhibit considerable morphological and ecological diversity. The phylogenetic relationships among Sorghum species still remain unresolved due to lower information on the traditional DNA markers, which provides a limited resolution for identifying Sorghum species. In this study, we sequenced the complete chloroplast genomes of Sorghum sudanense and S. propinquum and analyzed the published chloroplast genomes of S. bicolor and S. timorense to retrieve valuable chloroplast molecular resources for Sorghum. The chloroplast genomes ranged in length from 140,629 to 140,755 bp, and their gene contents, gene orders, and GC contents were similar to those for other Poaceae species but were slightly different in the number of SSRs. Comparative analyses among the four chloroplast genomes revealed 651 variable sites, 137 indels, and nine small inversions. Four highly divergent DNA regions (rps16-trnQ, trnG-trnM, rbcL-psaI, and rps15-ndhF), which were suitable for phylogenetic and species identification, were detected in the Sorghum chloroplast genomes. A phylogenetic analysis strongly supported that Sorghum is a monophyletic group in the tribe Andropogoneae. Overall, the genomic resources in this study could provide potential molecular markers for phylogeny and species identification in Sorghum.

scholarly journals The Evaluation of Genetic Relationships within Acridid Grasshoppers (Orthoptera, Caelifera, Acrididae) on the Subfamily Level Using Molecular Markers

2019 ◽  
Vol 67 (3) ◽  
pp. 119-126
Author(s):  
Igor Sukhikh ◽  
Kirill Ustyantsev ◽  
Alexander Bugrov ◽  
Michael Sergeev ◽  
Victor Fet ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Phylogenetic Relationships ◽  
Genome Mapping ◽  
Genetic Relationships ◽  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
Its2 Region ◽  
Phylogenetic Groups ◽  
Phylogenetic Resolution ◽  
Complete Protein

Over the last few decades, molecular markers have been extensively used to study phylogeny, population dynamics, and genome mapping in insects and other taxa. Phylogenetic methods using DNA markers are inexpensive, fast and simple to use, and may help greatly to resolve phylogenetic relationships in groups with problematic taxonomy. However, different markers have various levels of phylogenetic resolution, and it's important to choose the right set of molecular markers for a studied taxonomy level. Acrididae is the most diverse family of grasshoppers. Many attempts to resolve the phylogenetic relationships within it did not result in a clear picture, partially because of the limited number of molecular markers used. We have tested a phylogenetic resolution of three sets of the most commonly utilized mitochondrial molecular markers available for Acrididae sequences in the database: (i) complete protein-coding mitochondrial sequences, (ii) concatenated mitochondrial genes COI, COII, and Cytb, and (iii) concatenated mitochondrial genes COI and COII. We then complemented the analysis by testing the nuclear ITS2 region. Adequate phylogenetic resolution of Acrididae subfamilies can be achieved using three (COI, COII, and Cytb) or more mitochondrial markers. Moreover, we found the ITS2 and concatenated COI/COII markers to be the least informative, providing a poor resolution. All the studied acridids fall into three well-supported phylogenetic groups that include 13 subfamilies. Acridinae, Gomphocerinae, Oedipodinae, and Catantopinae are shown to be polyphyletic, while the remaining subfamilies are in accordance with current Acrididae systematics. Our study provides a basis for more comprehensive phylogenetic analyses of Acrididae on the subfamily and lower levels.

scholarly journals Isoenzimas

2017 ◽  
pp. 77
Author(s):  
Nidia Pérez-Nasser ◽  
Daniel Piñero
Keyword(s):  
Population Genetics ◽  
Life History ◽  
Molecular Markers ◽  
Natural Selection ◽  
Evolutionary Biology ◽  
Mating Systems ◽  
Wild Relatives ◽  
Cultivated Plants ◽  
Origin And Evolution ◽  
Evolutionary Studies

This work presents a review of the use of enzymes as molecular markers for evolutionary studies, in particular population genetics. First, the methodology of starch electrophoresis is shown as a useful tool To detect variation within and among populations. Second, applications to evolutionary biology are presented. In plants these markers have been used for 1] to study mating systems, 2] do phylogenetics and taxonomy, 3] study natural selection components, 4] to correlate genetics and life history characters and 5] understand the origin and evolution of cultivated plants and their wild relatives

Complete chloroplast genomes of Leptodermis scabrida complex: comparative genomic analyses and phylogenetic relationships

Gene ◽  
2021 ◽  
pp. 145715
Author(s):  
Ying Zhang ◽  
Zhengfeng Wang ◽  
Yanan Guo ◽  
Sheng Chen ◽  
Xianyi Xu ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Comparative Genomic ◽  
Chloroplast Genomes ◽  
Genomic Analyses
Sign in / Sign up

Export Citation Format

Share Document