scholarly journals Development of Single-Copy Nuclear Intron Markers for Species-Level Phylogenetics: Case Study with Paullinieae (Sapindaceae)

2017 ◽  
Vol 5 (9) ◽  
pp. 1700051 ◽  
Author(s):  
Joyce G. Chery ◽  
Chodon Sass ◽  
Chelsea D. Specht
Keyword(s):  
Single Copy ◽  
Species Level ◽  
Nuclear Intron

scholarly journals Identifying the North American Plum Species Phylogenetic Signal Using Nuclear, Mitochondrial, and Chloroplast DNA Markers

2016 ◽  
Vol 141 (6) ◽  
pp. 623-644 ◽  
Author(s):  
Dario J. Chavez ◽  
Thomas G. Beckman ◽  
José X. Chaparro
Keyword(s):  
Chloroplast Dna ◽  
Prunus Persica ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Its Region ◽  
Single Copy ◽  
Species Level ◽  
Species Relationships ◽  
The North

Prunus phylogeny has been extensively studied using chloroplast DNA (cpDNA) sequences. Chloroplast DNA has a slow rate of evolution, which is beneficial to determine species relationships at a deeper level. The chloroplast-based phylogenies have a limitation due to the transfer of this organelle by interspecific hybridization. This creates difficulties when studying species relationships. Interspecific hybrids in Prunus occur naturally and have been reported, which creates a problem when using cpDNA-based phylogenies to determine species relationships. The main goal of this project was to identify nuclear gene regions that could provide an improved phylogenetic signal at the species level in Prunus. A total of 11 species in Prunus and within section Prunocerasus were used. Two peach (Prunus persica) haploids were used to test the reliability of the molecular markers developed in this project to amplify single-copy genes. A total of 33 major genes associated with vernalization response, 16 with tree architecture, and 3 with isozymes, were tested. Similarly, 41 simple sequence repeat (SSR) markers, seven cpDNA regions, and the internal transcribed spacer (ITS) region, were used. Multiple gene regions were identified and provided the greatest number of characters, greatest variability, and improved phylogenetic signal at the species level in Prunus section Prunocerasus. Out of those, trnH-psbA, PGI, MAX4, AXR1, LFY, PHYE, and VRN1 are recommended for a phylogenetic analysis with a larger number of taxa. The use of potentially informative characters (PICS) as a measure of how informative a region will be for phylogenetic analyses has been previously reported beneficial in cpDNA regions and it clearly was important in this research. This will allow selecting the region(s), which can be used in phylogenetic studies with higher number of taxa.

scholarly journals THE INFLUENCE OF TIDAL AND RAINFALL CYCLES ON INTERTIDAL NEMATODES: A CASE STUDY IN A TROPICAL SANDY BEACH

2014 ◽  
Vol 62 (4) ◽  
pp. 247-256 ◽  
Author(s):  
Virag Venekey ◽  
Paulo Jorge Parreira dos Santos ◽  
Verônica Gomes da Fonsêca-Genevois
Keyword(s):  
Tidal Cycle ◽  
Sandy Beach ◽  
Assemblage Structure ◽  
Species Level ◽  
Future Studies ◽  
Nematode Assemblage ◽  
Tidal Cycles ◽  
Clear Identification ◽  
Rainfall Flood

The present study describes the nematode assemblage of the bay of Tamandaré (Brazil), a tropical sandy beach, during the low, flood, high and ebb tides of two consecutive tidal cycles in four different months of the year (May, July, September and November). The nematode assemblage was dominated by Metachromadora and Perepsilonema and varied significantly between months and tides. Densities were lower in July, and changes in assemblage structure occurred during the transitional periods between rainy and dry months, which showed the influence of rainfall. Flood and ebb tides appeared to exercise the greatest influences over the tidal cycle, although the patterns were not very clear. Identification at genera/species level is recommended for future studies, to better understand the patterns of nematode assemblages during tidal cycles.

Discovery of chloroplast capture in Juniperus excelsa complex by multi- locus phylogeny

Phytotaxa ◽  
2019 ◽  
Vol 413 (1) ◽  
pp. 11-26 ◽  
Author(s):  
FATEMEH HOJJATI ◽  
ROBERT P. ADAMS ◽  
RANDALL G. TERRY
Keyword(s):  
Concerted Evolution ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Its Region ◽  
Single Copy ◽  
Species Level ◽  
Lineage Sorting ◽  
Chloroplast Capture ◽  
Juniperus Excelsa ◽  
Cp Genome

Previous studies of nrDNA (nuclear DNA) of Juniperus seravschanica indicated its nuclear DNA (ITS) was from an ancestor of J. polycarpos. However, analysis of cpDNA (chloroplast DNA) suggested the taxon had derived its chloroplast from an ancestor of J. foetidissima. That study has been viewed as putative, because the ITS region is sometimes unreliable for the detection of ancestral hybrids due to concerted evolution and lineage sorting. The recent availability of several single copy nuclear genes (SCNGs) with primers specifically designed for Juniperus presented an opportunity to fully investigate this case of putative chloroplast capture. Three phylogenetic analyses using five SCNGs (LHCA4, maldehy, myb, CnAIP3 and 4CL), ITS region, and four cpDNAs (petN- psbM, trnD-trnT, trnL-trnF and trnS-trnG) were performed on J. seravschanica, as well as other members of the J. excelsa complex: J. excelsa, J. polycarpos, and J. p. var. turcomanica. Analyses revealed incongruence between SCNGs, ITS region and cpDNA showing that J. seravschanica contains an ancestral J. foetidissima/ J. thruifera cp genome. In addition, the phylogenies indicate that the J. excelsa complex is composed of three distinct clades at the species level: J. excelsa, J. polycarpos and J. seravschanica and two varieties of J. polycarpos: J. p. var. polycarpos and J. p. var. turcomanica.

An alternative to ITS, a hypervariable, single-copy nuclear intron in corals, and its use in detecting cryptic species within the octocoral genus Carijoa

Coral Reefs ◽  
2007 ◽  
Vol 27 (2) ◽  
pp. 323-336 ◽  
Author(s):  
G. T. Concepcion ◽  
M. W. Crepeau ◽  
D. Wagner ◽  
S. E. Kahng ◽  
R. J. Toonen
Keyword(s):  
Cryptic Species ◽  
Single Copy ◽  
Nuclear Intron

scholarly journals A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Thomas H. A. Ederveen ◽  
Jos P. H. Smits ◽  
Karima Hajo ◽  
Saskia van Schalkwijk ◽  
Tessa A. Kouwenhoven ◽  
...  
Keyword(s):  
Phylogenetic Inference ◽  
Species Level ◽  
Single Locus ◽  
Bioinformatics Pipeline ◽  
Discriminative Ability ◽  
Staphylococcus Capitis ◽  
Complex Microbial Community ◽  
Reference Genomes

AbstractWe present TaxPhlAn, a new method and bioinformatics pipeline for design and analysis of single-locus sequence typing (SLST) markers to type and profile bacteria beyond the species-level in a complex microbial community background. TaxPhlAn can be applied to any group of phylogenetically-related bacteria, provided reference genomes are available. As TaxPhlAn requires the SLST targets identified to fit the phylogenetic pattern as determined through comprehensive evolutionary reconstruction of input genomes, TaxPhlAn allows for the identification and phylogenetic inference of new biodiversity. Here, we present a clinically relevant case study of high-resolution Staphylococcus profiling on skin of atopic dermatitis (AD) patients. We demonstrate that SLST enables profiling of cutaneous Staphylococcus members at (sub)species level and provides higher resolution than current 16S-based techniques. With the higher discriminative ability provided by our approach, we further show that the presence of Staphylococcus capitis on the skin together with Staphylococcus aureus associates with AD disease.

Multiple lineages of FRUITFULL exhibit dynamic patterns of gene evolution after genome triplication in the Brassiceae tribe (Brassicaceae)

Botany ◽  
2019 ◽  
Vol 97 (5) ◽  
pp. 293-310 ◽  
Author(s):  
Kelsey C. Brock ◽  
Jocelyn C. Hall
Keyword(s):  
Gene Evolution ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Single Copy ◽  
Stabilizing Selection ◽  
Relaxed Selection ◽  
Major Species ◽  
Genome Triplication

Phylogenetic analyses of important development genes are necessary to identify trends in sequence divergence and gene retention/loss that underlie diversification after polyploidization. We investigated the evolution of FRUITFULL (FUL) in the tribe Brassiceae (Brassicaceae), where a recent genome triplication allows investigation into the fate of paralogs. Many Brassiceae members possess a unique fruit type exhibiting segmentation and variable dehiscence called heteroarthrocarpy, providing a case study to compare with FUL’s evolution, as a single copy is known to control fruit dehiscence in Arabidopsis. We constructed a phylogeny containing all major species lineages to investigate the number of retained FUL paralogs, trends in selective pressure and intron evolution, and their relationship to heteroarthrocarpy. We recovered four well-supported lineages that likely correspond to three FUL copies from hexaploidization. Rates of selection varied across lineages and comparatively relaxed selection was associated with fruit indehiscence. However, stabilizing selection predominated all lineages, indicating that paralogs retain functionality. Longer introns were correlated with relaxed selection on exons and, on average, heteroarthrocarpic taxa had longer introns and retained different FUL paralogs than nonheteroarthrocarpic taxa, although correlations were complex. The dynamic pattern of FUL evolution invites investigation into the role of upstream regulators in the dehiscence of heteroarthrocarpic fruits.

scholarly journals groEL Gene-Based Phylogenetic Analysis of Lactobacillus Species by High-Throughput Sequencing

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 530 ◽  
Author(s):  
Xie ◽  
Pan ◽  
Jiang ◽  
Liu ◽  
Lu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Hypervariable Region ◽  
Single Copy ◽  
Species Level ◽  
Gene Profiling ◽  
Lactobacillus Species ◽  
Groel Gene ◽  
Lactobacillus Mucosae

Lactobacillus is a fairly diverse genus of bacteria with more than 260 species and subspecies. Many profiling methods have been developed to carry out phylogenetic analysis of this complex and diverse genus, but limitations remain since there is still a lack of comprehensive and accurate analytical method to profile this genus at species level. To overcome these limitations, a Lactobacillus-specific primer set was developed targeting a hypervariable region in the groEL gene—a single-copy gene that has undergone rapid mutation and evolution. The results showed that this methodology could accurately perform taxonomic identification of Lactobacillus down to the species level. Its detection limit was as low as 104 colony-forming units (cfu)/mL for Lactobacillus species. The assessment of detection specificity using the Lactobacillus groEL profiling method found that Lactobacillus, Pediococcus, Weissella, and Leuconostoc genus could be distinguished, but non-Lactobacillus Genus Complex could not be detected. The groEL gene sequencing and Miseq high-throughput approach were adopted to estimate the richness and diversity of Lactobacillus species in different ecosystems. The method was tested using kurut (fermented yak milk) samples and fecal samples of human, rat, and mouse. The results indicated that Lactobacillus mucosae was the predominant gut Lactobacillus species among Chinese, and L. johnsonii accounted for the majority of lactobacilli in rat and mouse gut. Meanwhile, L. delbrueckii subsp. bulgaricus had the highest relative abundance of Lactobacillus in kurut. Thus, this groEL gene profiling method is expected to promote the application of Lactobacillus for industrial production and therapeutic purpose.

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