Unrooted Neighbor-joining Tree Research Articles

Genetic Diversity and Population Structure of a Large USDA Sesame Collection.

Sesame, Sesamum indicum L., is one of the oldest domesticated crops used for its oil and protein in many parts of the world. To build genomic resources for sesame that could be used to improve sesame productivity and responses to stresses, a USDA sesame germplasm collection of 501 accessions originating from 36 countries was used in this study. The panel was genotyped using genotyping-by-sequencing (GBS) technology to explore its genetic diversity and population structure and the relatedness among its accessions. A total of 24,735 high-quality single-nucleotide polymorphism (SNP) markers were identified over the 13 chromosomes. The marker density was 1900 SNP per chromosome, with an average polymorphism information content (PIC) value of 0.267. The marker polymorphisms and heterozygosity estimators indicated the usefulness of the identified SNPs to be used in future genetic studies and breeding activities. The population structure, principal components analysis (PCA), and unrooted neighbor-joining phylogenetic tree analyses classified two distinct subpopulations, indicating a wide genetic diversity within the USDA sesame collection. Analysis of molecular variance (AMOVA) revealed that 29.5% of the variation in this population was due to subpopulations, while 57.5% of the variation was due to variation among the accessions within the subpopulations. These results showed the degree of differentiation between the two subpopulations as well as within each subpopulation. The high fixation index (FST) between the distinguished subpopulations indicates a wide genetic diversity and high genetic differentiation among and within the identified subpopulations. The linkage disequilibrium (LD) pattern averaged 161 Kbp for the whole sesame genome, while the LD decay ranged from 168 Kbp at chromosome LG09 to 123 Kbp in chromosome LG05. These findings could explain the complications of linkage drag among the traits during selections. The selected accessions and genotyped SNPs provide tools to enhance genetic gain in sesame breeding programs through molecular approaches.

Diversity of blaPOM in carbapenem-resistant opportunistic pathogenic Pseudomonas otitidis in municipal wastewater.

Metallo-β-lactamases (MBLs) encoding carbapenem resistance in wastewater are a well-known serious threat to human health. Twelve Pseudomonas otitidis isolates obtained from a municipal wastewater treatment plant (WWTP) in Hawaii were found to possess a subclass B3 MBL - POM (P. otitidis MBL), with a minimum inhibition concentration (MIC) range of 8-16 mg/L. The unrooted neighbor-joining phylogenetic tree showed that these blaPOM genes isolated in wastewater samples (n = 12) were distinctly different from other reference genes isolated from clinical, freshwater, animal, and soil samples except for isolates MR7, MR8, and MR11. MR7, MR8, and MR11 were found to have 4, 3, and 3 amino acid substitutions when compared to the type strain MC10330T and were closely clustered to the clinical reference genes. The meropenem hydrolysis experiment showed that isolates with multiple amino acid substitutions completely hydrolyzed 64 mg/L of meropenem in 7 h. The emergence of the opportunistic pathogen P. otitidis chromosomally encoding blaPOM in the treated municipal wastewater is an alarming call for the spread of this MBL in the environment. Further studies are required to understand the mechanism and regulation of this carbapenem-resistant β-lactamase in order to fill in the knowledge gap.

PHD-finger family genes in wheat (Triticum aestivum L.): Evolutionary conservatism, functional diversification, and active expression in abiotic stress.

Plant homeodomain (PHD) transcription factors (TFs) are a class of proteins with conserved Cys4-His-Cys3 domains that play important roles in plant growth and development and in response to abiotic stresses. Although characterization of PHDs has been performed in plants, little is known about their function in wheat (Triticum aestivum L.), especially under stress conditions. In the present study, 244 TaPHDs were identified in wheat using comparative genomics. We renamed them TaPHD1-244 based on their chromosomal distribution, and almost all PHD proteins were predicted to be located in the nucleus. According to the unrooted neighbor-joining phylogenetic tree, gene structure, and motif analyses, PHD genes were divided into four clades. A total of 149 TaPHD genes were assigned to arise from duplication events. Furthermore, 230 gene pairs came from wheat itself, and 119, 186, 168, 7, 2, and 6 gene pairs came from six other species (Hordeum vulgareto, Zea mays, Oryza sativa, Arabidopsis thaliana, Brassica rapa, and Gossypium raimondii, respectively). A total of 548 interacting protein branches were identified to be involved in the protein interaction network. Tissue-specific expression pattern analysis showed that TaPHDs were highly expressed in the stigma and ovary during flowering, suggesting that the TaPHD gene plays an active role in the reproductive growth of wheat. In addition, the qRT-PCR results further confirmed that these TaPHD genes are involved in the abiotic stress response of wheat. In conclusion, our study provides a theoretical basis for deciphering the molecular functions of TaPHDs, particularly in response to abiotic stress.

The Differences and Genetic Relationships of 4 Dendrobium Species Based on High Throughput GBS-SNP Markers

The differences and genetic relationships of 4 Dendrobium species ( Dendrobium huoshanense, Dendrobium officinale, Dendrobium moniliforme, Dendrobium Fanjingshanense ) were analyzed based on high throughput SNP markers obtained by GBS, using  Dendrobium catenatum  as the reference genome, for providing reference for the study of these 4 Dendrobium species. The results showed that the number of clean reads per each sample in  D.  huoshanense ,  D .  officinale ,  D .  moniliforme ,  D .  Fanjingshanense  were 1 300 724, 1 286 162, 1 380 009 and 1 170 337, respectively, and the number of SNPs per each sample were 1 507 746, 893 333, 1 364 605 and 1 227 006, respectively. The genetic structure based on Admixture software revealed that the samples of  D .  officinale were clustered into one branch, and the remaining Dendrobium samples were clustered into the other branch, when the best K value was 2; when k = 3, the samples of  D .  officinale  were grouped into one cluster, some samples of  D .  huoshanense , all samples of  D .  moniliforme  and  D. fanjingshanense  were grouped into the second cluster, and some samples of  D .  huoshanense  were grouped into the third cluster; When k = 4, it was divided into four branches: the samples of  D .  officinale  were grouped one branch, the samples of  D .  moniliforme  and  D .  fanjingshanense  were grouped one branch, the samples of  D .  huoshanense were divided into two branches, which was similar to the result of an unrooted neighbor-joining phylogenetic tree (NJ tree); Furthermore, principal coordinates analyses (PCoA) revealed that 91 Dendrobium samples were classed into three cluster. All samples of  D. of ficinale  and  D. hu oshanense  were grouped together, respectively, and the samples of  D. monil iforme  and  D . fanjingshan ense  were grouped together. According to the results of this study, the genetic relation of  D. off icinale  and the other 3 species of Dendrobium are relatively distant, and the genetic relationship of  D. mo niliforme  and  D.  fanjingshanense  were relatively close, 72 samples of  D .  huoshanense  in the study were divided into two branches, the genetic relationship in one of which was relatively close to  D .  moniliforme  and  D .  fanjingshanense . The study verified that the genetic relationship between different Dendrobium species or different species of plants was investigated using SNPs detected by GBS.

Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers.

In India, rice (Oryza sativa L.) is cultivated under a variety of climatic conditions. Due to the fragility of the coastal ecosystem, rice farming in these areas has lagged behind. Salinity coupled with floods has added to this trend. Hence, to prevent genetic erosion, conserving and characterizing the coastal rice, is the need of the hour. This work accessed the genetic variation and population structure among 2,242 rice accessions originating from India’s east coast comprising Andhra Pradesh, Orissa, and Tamil Nadu, using 36 SNP markers, and have generated a core set (247 accessions) as well as a mini-core set (30 accessions) of rice germplasm. All the 36 SNP loci were biallelic and 72 alleles found with average two alleles per locus. The genetic relatedness of the total collection was inferred using the un-rooted neighbor-joining tree, which grouped all the genotypes (2,242) into three major clusters. Two groups were obtained with a core set and three groups obtained with a mini core set. The mean PIC value of total collection was 0.24, and those of the core collection and mini core collection were 0.27 and 0.32, respectively. The mean heterozygosity and gene diversity of the overall collection were 0.07 and 0.29, respectively, and the core set and mini core set revealed 0.12 and 0.34, 0.20 and 0.40 values, respectively, representing 99% of distinctiveness in the core and mini core sets. Population structure analysis showed maximum population at K = 4 for total collection and core collection. Accessions were distributed according to their population structure confirmed by PCoA and AMOVA analysis. The identified small and diverse core set panel will be useful in allele mining for biotic and abiotic traits and managing the genetic diversity of the coastal rice collection. Validation of the 36-plex SNP assay was done by comparing the genetic diversity parameters across two different rice core collections, i.e., east coast and northeast rice collection. The same set of SNP markers was found very effective in deciphering diversity at different genetic parameters in both the collections; hence, these marker sets can be utilized for core development and diversity analysis studies.

Understanding population structure in an evolutionary context: population-specific FST and pairwise FST.

Populations are shaped by their history. It is crucial to interpret population structure in an evolutionary context. Pairwise FST measures population structure, whereas population-specific FST measures deviation from the ancestral population. To understand the current population structure and a population’s history of range expansion, we propose a representation method that overlays population-specific FST estimates on a sampling location map, and on an unrooted neighbor-joining tree and a multi-dimensional scaling plot inferred from a pairwise FST distance matrix. We examined the usefulness of our procedure using simulations that mimicked population colonization from an ancestral population and by analyzing published human, Atlantic cod, and wild poplar data. Our results demonstrated that population-specific FST values identify the source population and trace the evolutionary history of its derived populations. Conversely, pairwise FST values represent the current population structure. By integrating the results of both estimators, we obtained a new picture of the population structure that incorporates evolutionary history. The generalized least squares estimate of genome-wide population-specific FST indicated that the wild poplar population expanded its distribution to the north, where daylight hours are long in summer, to coastal areas with abundant rainfall, and to the south where summers are dry. Genomic data highlight the power of the bias-corrected moment estimators of FST, whether global, pairwise, or population-specific, that provide unbiased estimates of FST. All FST moment estimators described in this paper have reasonable processing times and are useful in population genomics studies.

Screening of Salt Tolerant Potato Genotypes using Salt Stress and Molecular Markers

Aims: To screen potato genotypes for salt tolerance using in vitro salt stress and moleulcar markers.
 Experimental Design: The experiment was arranged in Completely Randomized Design (CRD) with three replications.
 Place of the Study: The experiment was conducted at the Molecular Biology and Tissue Culture Laboratories, Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh.
 Methodology: In vitro screening of five potato genotypes (CIP 112, CIP 117, CIP 120, CIP 127, and CIP 128) was done in an agar medium using tissue culture technique at different concentrations of salt viz. 0.0, 10, 20, 40, 60, 80, 100, 120 mM of NaCl. All genotypes were further analysed through SSR markers using three primers. The DNA bands were visualized on gel electrophoresis and scored for polymorphic loci, gene diversity, and genetic distance. NTSYSpc program was used for constructing unrooted neighbor-joining tree and scatter diagram.
 Results: Potato genotypes CIP 112 and CIP 117 emerged as the most salt tolerant genotypes with the highest plant height, shoot dry weight, root length, and root dry weight at different concentrations of NaCl. CIP 127 and CIP 128 were poorly tolerant to salt stress. The most sensitive genotype CIP 120 produced minimum plant height, shoot dry weight, root length, and root dry weight at different NaCl concentrations. Results indicated that significant differences were found among cultivars. The banding pattern of microsatellite confirmed a distinct polymorphism among salt tolerant, moderately salt tolerant and salt sensitive lines. The clustering pattern of the potato genotypes suggests that variations occur due to genotypic variation and possibly not epigenetic adaptation under salt stress conditions.
 Conclusion: The salt tolerant pototo genotypes CIP 112 and CIP 117 can be used for developing salt tolerant genotypes.

Phylogenetic characteristics, virulence properties and antibiogram profile of motile Aeromonas spp. isolated from ornamental guppy (Poecilia reticulata).

Aeromonas spp. are opportunistic pathogenic bacteria related to an assembly of infectious diseases in ornamental fish. In the present study, virulence properties and antibiotic susceptibility of 52 guppy-borne Aeromonas spp. were investigated. The isolates were identified as A. veronii (n = 34), A. dhakensis (n = 10), A. hydrophila (n = 3), A. caviae (n = 3) and A. enteropelogenes (n = 2) by gyrB gene sequencing. The gyrB sequence deviation within and among the species ranged from 0 to 2.6% and 2.7-9.2%. Each species formed a distinct group in the unrooted neighbor-joining phylogenetic tree. The phenotypic virulence factors such as β-hemolysis, slime, caseinase, DNase, gelatinase and lipase production were observed in 28 (53.9%), 33 (63.5%), 28 (53.9%), 42 (80.8%), 37 (71.2%) and 42 (80.8%) isolates, respectively. The virulence genes were detected by PCR assay in the following proportions- act (84.6%), hly (80.8%), aer (73.1%), lip (73.1%), gcaT (73.1%), ascV (53.8%), ahyB (53.8%) fla (51.9%), alt (48.1%), ast (36.5%) and ser (34.6%), respectively. The amoxicillin, ampicillin, imipenem, nalidixic acid, oxytetracycline and rifampicin were resistant to more than 70.0% of the isolates in antibiotic susceptibility test. Our study suggests that the ornamental guppy can be a potential reservoir of virulent and multi-drug resistant Aeromonas spp.

<p class="HeadingRunIn"><strong>Phylogenetics of a small caddisfly genus (Thremmatidae: <em>Oligophlebodes</em>): comparison among multiple hypotheses from DNA barcode data</strong></p>

Barcoding datasets can serve as a resource for species associations and delineations, but single-gene trees estimated by distance methods do not provide strong estimates of phylogeny. Using DNA data from the Barcode of Life Database (BOLD), we calculate a phylogenetic tree for Oligophlebodes (Trichoptera: Thremmatidae), a small genus of caddisfly endemic to the Western United States. Here we estimate a preliminary phylogeny for Oligophlebodes using Bayesian likelihood, and compare it to trees produced by distance and standard likelihood methods. Using the barcode region of the cytochrome oxidase 1 (COI) gene, we analyzed 44 individuals representing five species (and 2 unknowns) and a sister-genus outgroup (Neophylax) from locations ranging from Southern New Mexico northwest into British Columbia. Partitioned Bayesian likelihood analysis under the F81 (1st codon positions) and HKY80 + I + Γ (for both the 2nd and 3rd codon positions) model gave the consensus topology (Neophylax toshi, (O. sierra, (O. ruthae inc. spc. 1 & 2, O. sigma, (spc. 3 & 4, (O. ardis, O. minutus)))). Species identifications were supported by monophyly of most species-level taxa. However, confirmation of species identifications of unknowns was complicated by incomplete taxon sampling for spc. 1 & 2. Placement of spc. 3 & 4 may serve as support for taxonomic review of O. minutus. Compared with an existing published phylogeny of Oligophlebodes BOLD sequences constructed under RAxML, the Bayesian hypothesis had higher resolution at the basal node of Oligophlebodes. Because of their support values, both likelihood trees are recommended over the BOLD TaxonID tree (an unrooted neighbor joining tree using the Kimura 2-parameter model). The novel topology produced in the Bayesian tree supports further explorations by likelihood-based methods, including partitioned analyses, of our preliminary Oligophlebodes dataset that can be used as additional lines of evidence to support morphological work.

Exploring the genomic resources of carrot for cross-genera transferability and phylogenetic assessment among orphan spices and vegetables of Apiaceae family

Carrot (Daucus carota L.) is a member of the Apiaceae family that includes economically important medicinal, ornamentals, seed spices and vegetables. However, the genomic resources in these crops are limited compared to carrot, which is enriched with a number of molecular markers that are publicly available. Hence, we studied the usefulness of the 30 carrot molecular markers for eight different genera composed of five seed spices/condiments and three vegetables. The study revealed the transferability of these carrot markers and the genetic diversity across the genera for respective loci were compared by phylogenetic assessment using an un-rooted neighbour joining tree (NJ) and principle coordinate analysis (PCoA). An average of 66.66% amplification with a total of 73 alleles from 30 loci was observed across eight crops with an average of 3.39 alleles/loci. The average polymorphic information content was 0.50, the effective number of alleles was 2.92, gene diversity was 0.56 with a highest fixation index of 0.82 observed among 18 polymorphic markers. These results indicate the practical use of these markers in the respective crops. Interestingly, phylogenetic analysis grouped the eight crops into three clusters, but the PCoA identified four groups in which carrot was out grouped and kept the other cluster composition intact. Comprehensive study of these eight crops with many more molecular markers would help to understand the evolutionary relatedness for distant hybridization among Apiaceae family members to either transfer genes of interest or to create novel crops.

Exploration and Exploitation of Novel SSR Markers for Candidate Transcription Factor Genes in Lilium Species.

Lilies (Lilium sp.) are commercially important horticultural crops widely cultivated for their flowers and bulbs. Here, we conducted large-scale data mining of the lily transcriptome to develop transcription factor (TF)-associated microsatellite markers (TFSSRs). Among 216,768 unigenes extracted from our sequence data, 6966 unigenes harbored simple sequence repeats (SSRs). Seventy-one SSRs were associated with TF genes, and these were used to design primers and validate their potential as markers. These 71 SSRs were accomplished with 31 transcription factor families; including bHLH, MYB, C2H2, ERF, C3H, NAC, bZIP, and so on. Fourteen highly polymorphic SSRs were selected based on Polymorphic Information Content (PIC) values and used to study genetic diversity and population structure in lily accessions. Higher genetic diversity was observed in Longiflorum compared to Oriental and Asiatic populations. Lily accessions were divided into three sub-populations based in our structure analysis, and an un-rooted neighbor-joining tree effectively separated the accessions according to Asiatic, Oriental, and Longiflorum subgroups. Finally, we showed that 46 of the SSR-associated genes were differentially expressed in response to Botrytis elliptica infection. Thus, our newly developed TFSSR markers represent a powerful tool for large-scale genotyping, high-density and comparative mapping, marker-aided backcrossing, and molecular diversity analysis of Lilium sp.

DNA fingerprinting and genetic diversities in some Bangladeshi aus rice (Oryza sativa L.) genotypes

The allelic diversity and relationship among 120 Aus rice landraces were determined through DNA fingerprinting using microsatellite (SSR) markers. A total of 85 SSR markers were used to characterize and discriminate all tested Aus rice genotypes, 45 of which were polymorphic for different chromosome numbers. The number of alleles per locus varied from 6 alleles (RM484 and RM541) to 30 alleles (RM519) with an average of 13 alleles per locus. The polymorphic information content (PIC) values varied ranged from 0.5211 (RM536) to 0.9369 (RM519) with an average 0.8217. The highest PIC value (0.9369) was obtained for RM519 followed by RM286 (0.9357). The genetic distance-based results seen in the unrooted neighbor-joining tree clustering revealed nine genetic groups. Being grouped into distant clusters and with highest genetic distance, eleven genotypes viz., Atithi dhan, Kadar chap, Pankiraj, Japanese-7, Jamri saity, Logi jota, Joba, Lada moni, Manik Mondal-2, Boilum and Brmulka-2 could be selected as potential parents for crop improvement for their distinctive characters. Panchash and Parija had closest distance in the SSR based CS-Chord distance (0.000) might have same genetic background. The highest genetic dissimilarity (1.000) was found among the nineteen Aus genotypes combinations followed by the second highest (0.9778) among 94 Aus rice combinations. Whereas lowest genetic dissimilarity was found between Kala and Kalo Hizli (0.1778) followed by Holat and Holae (0.2667). This information will be useful in the selection of diverse parents, background selection during backcross breeding programs and assist in broadening germplasm-based rice breeding programs in the near future.SAARC J. Agri., 15(1): 123-137 (2017)

Estimating population structure and genetic diversity of five Moroccan sheep breeds by microsatellite markers

Investigating the genetic variability and structure of Moroccan sheep breeds will reveal crucial information for the conservation and management of this population. This study used 22 microsatellite markers to assess the genetic diversity among and within five Moroccan sheep breeds: Sardi (N=35), Boujaad (N=31), Timadhite (N=35), Beni Guil (N=35), and D⿿man_Morroco (N=35). In the whole sample, a total of 299 alleles were detected. The five breeds showed a relatively high level of gene diversity ranging between 0.725 (D⿿man_Morocco) and 0.764 (Timahdite). The Analysis of Molecular Variance (AMOVA) indicated that variability among populations contributed only 3.64% of the observed genetic diversity. Wilcoxon tests of excess heterozygosity under the two-phase model (TPM) did not provide strong evidence for recent bottlenecks in the five studied breeds. Unrooted neighbour joining (NJ) tree for the modified Cavalli-Sforza chord distance (DA), pairwise multilocus estimates of an effective number of migrants (Nm) and the Bayesian clustering method cohesively revealed poor structure of genetic variation among breeds. Our results also show that in spite of the high level of phenotypic diversity in the Moroccan sheep breeds, the past breeding strategies could lead to genetic admixture occurring as a result of relatively high gene-flow among the breeds.

Characterization of Five Microsatellite Markers For Genetic Diversity Structure Analysis of Walnut (Juglans Regia L) in Five Village in Duhok Province

Five microsatellites markers (WGA202, WGA009, WGA332, WGA225 and WGA069) were used to characterize Persian walnuts (Juglans regia L.) populations in five villages (Sharanesh, Bedohe, Kanizarke (Akre), Kashane and Kuzo) of Duhok province. The microsatellites amplified (PCR products) a total of 186 alleles across all populations. The number of alleles per locus ranged from 4 alleles in Sharanesh and Kashane populations to 10 alleles also in Sharanesh and Kashane populations, with an average of 7.4. The molecular sizes of the amplified bands ranged from 158 bp to 289 bp in all populations. The observed heterozygosity (Ho) within populations ranged from 0.59 at WGA225 to 0.65 in the locus WGA202 with an average of 0.61. The PIC value (0.88) indicated that all markers were highly informative and useful for genetic diversity studies in these populations. The proportion of genetic variation presented among populations accounted for 8.4% of the total genetic diversity so it indicated a moderate level of genetic diversity between populations. The Fis average 0.24 indicated that, there was a regular tendency toward heterozygote deficiency and indicated the presence of inbreeding within the populations. The phylogenetic analysis or unrooted neighbor-joining tree highlighted the genetic distance among those five populations and separated them into two main groups placing each population according to its genetic background. The first group consists of populations Bedohe and Sharanesh in one subgroup and Kashane in second subgroup. The second group consists of populations Akre and Kuzo.

Genetic diversity and population genetic structure of Wels (Silurus glanis Linnaeus, 1758) in the northwest of Iran

The genetic diversity and genetic structure of four Silurus glanis (Linnaeus, 1758) populations were evaluated using ISSR markers in the northwestern Iran to understand the potential benefit of these populations for breeding purposes and/or any necessary conservation programs. Four populations were evaluated from three geographic regions; two populations from the Urmia Lake basin (one from the Mahabad Dam Lake and the other from the Zarineh River), one population from the Anzali Lagoon basin and one population from the Aras River basin. ISSR primers produced 99 discernible bands in the four populations. The Anzali Lagoon population showed lower level of diversity than other populations. The percentage of polymorphic bands and unbiased expected heterozygosity were 98.99 and 0.342, representing a considerable genetic variation through the studied populations. The analysis of molecular variance results showed significant variations among geographic regions (P < 0.001). Comparison of pairwise ΦPT values revealed significant differences between geographic regions; however, the Zarineh and the Mahabad populations within the Urmia Lake basin did not show any significant difference (P < 0.05). The northwest Iranian S. glanis populations were gathered into two discrete groups after constructed unrooted neighbour-joining tree based on Nei’s unbiased genetic distance. One group formed by the Anzali population and other by the Mahabad, the Zarineh and the Aras populations. The Mantel test revealed significant correlation between genetic distance and geographical distance matrices. The present study can suggest reasonable potential benefits of these populations for breeding purposes, while the Anzali Lagoon population needs to be considered for any future conservation programs.

Transmission clustering among newly diagnosed HIV patients in Chicago, 2008 to 2011: using phylogenetics to expand knowledge of regional HIV transmission patterns.

HIV transmission cluster analyses can inform HIV prevention efforts. We describe the first such assessment for transmission clustering among HIV patients in Chicago. We performed transmission cluster analyses using HIV pol sequences from newly diagnosed patients presenting to Chicago's largest HIV clinic between 2008 and 2011. We compared sequences through progressive pairwise alignment, using neighbor joining to construct an unrooted phylogenetic tree. We defined clusters as >2 sequences among which each sequence had at least 1 partner within a genetic distance of ≤1.5%. We used multivariable regression to examine factors associated with clustering and used geospatial analysis to assess geographic proximity of phylogenetically clustered patients. We compared sequences from 920 patients, median age of 35 years, 75% male, 67% black, 23% Hispanic, and 8% had a rapid plasma reagin titer ≥1:16 concurrent with their HIV diagnosis. We had HIV transmission risk data for 54%; 43% identified as men who have sex with men (MSM). Phylogenetic analysis demonstrated 123 patients (13%) grouped into 26 clusters, the largest having 20 members. In multivariable regression, age <25, black race, MSM status, male gender, higher HIV viral load, and rapid plasma reagin ≥1:16 associated with clustering. We did not observe geographic grouping of genetically clustered patients. Our results demonstrate high rates of HIV transmission clustering, without local geographic foci, among young black MSM in Chicago. Applied prospectively, phylogenetic analyses could guide prevention efforts and help break the cycle of transmission.

The equine arteritis virus isolate from the 2010 Argentinian outbreak.

A semen sample from a stallion infected during the 2010 equine arteritis virus (EAV) outbreak was received for viral isolation prior to castration of the animal. The virus was identified using a polyclonal antibody immunofluorescence test. Reverse-transcription polymerase chain reaction (RT-PCR) was used to amplify a region of the GP5 gene with primers GL105F and GL673R. The PCR products were purified and sequences of both strands were determined in a MegaBACE™1000 with inner primers CR2 and EAV32. A phylogenetic dataset was built with the previously reported sequences of five strains isolated in Argentina, together with a group of selected sequences obtained from GenBank. The unrooted neighbour-joining tree was constructed using molecular evolutionary genetic analysis (MEGA) and bootstrap analyses were conducted using 1,000 replicate datasets. Evolutionary distances were computed using the maximum composite likelihood method. A NetNGlyc server analysis at the Technical University of Denmark (www.cbs.dtu.dk/services/NetNGlyc/) was used to predict N-glycosylation in GP5 sequences. The phylogenetic analysis revealed that the new strain GLD-LP-ARG), together with other strains previously isolated, belongs to the European group EU-1 but in a different branch. The new strain shows 99% nucleotide identity with strain Al1and 98.1% with the Belgian strain 08P178. Persistently infected stallions and their cryopreserved semen constitute a reservoir of EAV, which ensures its persistence in the horse population around the world. These findings reinforce the importance of careful monitoring of persistently infected stallions, as well as semen straws, by RT-PCR or test mating, in accordance with national regulations.

Genetic diversity and population structure of common bean (Phaseolus vulgaris) landraces from China revealed by a new set of EST-SSR markers

A new set of EST-SSR markers were developed and employed to analyze the genetic diversity and population structure of Phaseolus vulgaris in China. A total of 2452 microsatellites were identified in 2144 unigenes assembled from P. vulgaris ESTs, indicating that merely 6.9% of the 30,952 unigene sequences contained SSRs. Seventeen of 153 randomly designed EST-SSR primer pairs successfully amplified polymorphic products in 31 landraces from six major production provinces of China, with the mean number of alleles per locus of 2.700 and polymorphism information content of 0.378. The observed and expected heterozygosity ranged from 0.100 to 0.954 and 0.081 to 0.558, respectively. Using these markers, both an unrooted neighbor-joining tree and principal coordinates analysis showed that almost all of the landraces were separated according with their regional distribution. Moreover, population structure analysis revealed that all genotypes formed into three distinct clusters (k = 3), suggesting that geographic and climatic factors could provide diverse degrees of selection pressure. Accordingly, germplasm collection and cross breeding among different regions are suggested to accelerate the process of diverse germplasm creation and broaden germplasm resources of Chinese common bean.

Genetic species identification and population structure of Halophila(Hydrocharitaceae) from the Western Pacific to the Eastern Indian Ocean

BackgroundThe Indo-Pacific region has the largest number of seagrass species worldwide and this region is considered as the origin of the Hydrocharitaceae. Halophila ovalis and its closely-related species belonging to the Hydrocharitaceae are well-known as a complex taxonomic challenge mainly due to their high morphological plasticity. The relationship of genetic differentiation and geographic barriers of H. ovalis radiation was not much studied in this region. Are there misidentifications between H. ovalis and its closely related species? Does any taxonomic uncertainty among different populations of H. ovalis persist? Is there any genetic differentiation among populations in the Western Pacific and the Eastern Indian Ocean, which are separated by the Thai-Malay peninsula? Genetic markers can be used to characterize and identify individuals or species and will be used to answer these questions.ResultsPhylogenetic analyses of the nuclear ribosomal internal transcribed spacer region based on materials collected from 17 populations in the Western Pacific and the Eastern Indian Ocean showed that some specimens identified as H. ovalis belonged to the H. major clade, also supported by morphological data. Evolutionary divergence between the two clades is between 0.033 and 0.038, much higher than the evolutionary divergence among H. ovalis populations. Eight haplotypes were found; none of the haplotypes from the Western Pacific is found in India and vice versa. Analysis of genetic diversity based on microsatellite analysis revealed that the genetic diversity in the Western Pacific is higher than in the Eastern Indian Ocean. The unrooted neighbor-joining tree among 14 populations from the Western Pacific and the Eastern Indian Ocean showed six groups. The Mantel test results revealed a significant correlation between genetic and geographic distances among populations. Results from band-based and allele frequency-based approaches from Amplified Fragment Length Polymorphism showed that all samples collected from both sides of the Thai-Malay peninsula were clustered into two clades: Gulf of Thailand and Andaman Sea.ConclusionsOur study documented the new records of H. major for Malaysia and Myanmar. The study also revealed that the Thai-Malay peninsula is a geographic barrier between H. ovalis populations in the Western Pacific and the Eastern Indian Ocean.

A Study of Genomic Diversity of Three Tribal Populations of Chhattisgarh, India

The diverse linguistic and ethnic tribal populations harboring state Chhattisgarh is a hotspot for human genomic diversity research. Genetic analysis of individual variation at the DNA level is widely used to investigate the extent of genetic diversity and to understand the population structure among different populations. The present study was conducted to find out the extent of affinities and diversities among three tribal populations of Chhattisgaarh, India namely Halba, Gadba and Oraon. They belong to different language families. Halba belongs to Indo-European, Gadba belongs to Austro-Asiatic while Oraon belongs to Dravidian language family. Analysis on seven widely distributed polymorphic insertion/deletion loci (Alu APO, Alu ACE, Alu D1, Alu PV92, Alu FXIIIB, Alu CD4 del and Alu PLAT) in 160 unrelated individuals of both sexes were done. All loci were highly polymorphic except Alu CD4 del locus. All the three tribes showed lowest heterozygosity for CD4 locus. GST value was recorded lowest for Alu PLAT locus (0.0004) while the highest was recorded for Alu PV92 locus (0.1029). The unrooted Neighbor-Joining (NJ) tree showed Gadba and Oraon form one cluster while Halba tribe differentiates from them.