Mean Genetic Distance Research Articles

Comparison and Correlation of Genetic Variability of the HBV Pre-S Region in HIV/HBV Co-Infected Patients: Quasispecies Perspective.

BackgroundHuman immunodeficiency virus (HIV)/hepatitis B virus (HBV) co-infection can accelerate HBV-induced liver disease. A previous study showed that variation in the HBV pre-S region and quasispecies heterogeneity (Sn, mean genetic distance, dS, dN, and dS/dN) are both related to HBV-induced terminal liver disease in HBV mono-infection. Currently, data are lacking on quasispecies variation of the HBV pre-S region in HIV/HBV co-infection. Investigating the quasispecies variation of the HBV pre-S region and its related factors in HIV/HBV co-infection will help to better explore the pathogenic mechanism of HIV/HBV co-infection.MethodsAccording to the HIV antibody results obtained before treatment, chronic HBV-infected patients were divided into HIV/HBV co-infected and HBV mono-infected groups. The clinical characteristics of all patients were collected, and DNA was extracted from the serum. The HBV pre-S region was amplified by nested PCR and was further TA cloned. BioEdit software 7.0 was used for sequence alignment with reference to the standard sequence of the matched HBV genotype. We used 1:1 propensity score matching (PSM) to control for baseline confounding factors between the two groups.ResultsAfter 1:1 PSM, we identified 100 patients with similar propensities: 50 HIV/HBV co-infected patients and 50 HBV mono-infected patients. HBV quasispecies indices were lower in the HIV/HBV co-infected group than those in the HBV mono-infected group. A significant correlation was observed between all quasispecies indices and soluble cluster of differentiation 163 (sCD163) and interleukin-18 (IL-18) in the HIV/HBV co-infected group; however, this phenomenon was not found in the HBV mono-infected group.ConclusionCombined HIV infection reduces quasispecies heterogeneity in the HBV pre-S region, and the quasispecies heterogeneity is related to the sCD163 and IL-18 levels.

Identification of Edible Fish Species of Pakistan Through DNA Barcoding

Fish is a fundamentally healthy food, loaded with essential nutrients, high protein content, vitamin D, and omega-three fatty acid. Mislabeling is a common problem in the fish industry that causes an imbalance in prices and fluctuation in the market. DNA barcoding is a potential technique for authentication of mislabeled and misidentified fish species. In this study, 11 freshwater and 6 marine fish species were used for DNA barcoding and further authentication using the mitochondrial cytochrome b (Cyto b) gene. Cyto b was amplified using PCR, producing an average read length of 1,141 bp. The obtained sequences were compared to the National Center for Biotechnology Information database using the Basic Local Alignment Search Tool. The average AT content (55.20%) was higher than the average GC content (44.78%) in marine and freshwater fish species. The mean genetic Kimura 2-parameter distances for species, genus, families, and orders were 0.311, 0.308, 0.023, and 0.337, respectively. Phylogenetic tree analysis revealed that most of the freshwater fish species clustered together due to the fact that they were in the same order or family, while the marine fish species clustered distantly. Single nucleotide polymorphism (SNP) analysis of all species in the study revealed distinct features regarding unique sites. All fish species could be identified based on their unique SNP profiles. Based on SNP data, DNA sequence based QR codes were developed for accurate identification of fish species. This is the first study to develop DNA-based QR barcodes for proper authentication of species during the chain of custody using simple technology.

Identification of QTLs Controlling Resistance/Tolerance to Striga hermonthica in an Extra-Early Maturing Yellow Maize Population

Striga hermonthica parasitism is a major constraint to maize production in sub-Saharan Africa with yield losses reaching 100% under severe infestation. The application of marker-assisted selection is highly promising for accelerating breeding for Striga resistance/tolerance in maize but requires the identification of quantitative trait loci (QTLs) linked to Striga resistance/tolerance traits. In the present study, 194 F2:3 families of TZEEI 79 × TZdEEI 11 were screened at two Striga-endemic locations in Nigeria, to identify QTLs associated with S. hermonthica resistance/tolerance and underlying putative candidate genes. A genetic map was constructed using 1139 filtered DArTseq markers distributed across the 10 maize chromosomes, covering 2016 cM, with mean genetic distance of 1.70 cM. Twelve minor and major QTLs were identified for four Striga resistance/tolerance adaptive traits, explaining 19.4%, 34.9%, 14.2% and 3.2% of observed phenotypic variation for grain yield, ears per plant, Striga damage and emerged Striga plants, respectively. The QTLs were found to be linked to candidate genes which may be associated with plant defense mechanisms in S. hermonthica infested environments. The results of this study provide insights into the genetic architecture of S. hermonthica resistance/tolerance indicator traits which could be employed for marker-assisted selection to accelerate efficient transfer host plant resistance genes to susceptible genotypes.

Genetic characterization and phylogenetic analysis of feline astrovirus from Anhui province in eastern China

This study aimed to explore the phylogenetic and molecular characteristics of feline astrovirus. A total of 33 fecal samples of domestic cats with or without diarrhea were collected from the Anhui province, and two positive samples were detected. The complete genome and ORF2 of the two strains were sequenced and phylogenetically analyzed. AH-1-2020 and AH-2-2020 displayed 83.4% homology, and their homologies with other reference strains were 75.3%-83.4% and 83.4%-95.0%, respectively. Phylogenetic tree analysis revealed that all strains could be classified into three different clusters; therefore, the mean amino acid genetic distances (p-dist) among the three clusters were estimated. The results suggested that the two strains and other FeAstV strains were grouped into three genotypes, with AH-1-2020 belonging to a novel genotype. High similarity was observed (65.9%-66.5% nucleotide identity and 63.8%-64.8% amino acid identity) in ORF2 between porcine astrovirus type 1 and AH-1-2020. Furthermore, inter-specific recombination between porcine astrovirus type 1 and FeAstV was observed. We, therefore, inferred that inter-specific transmission may exist between pigs and cats; however, further studies are required to verify this. This is the first report on the genetic characterization and phylogenetic analysis of FeAstVs in the Anhui province and would further the current understanding of the genetic diversity and epidemiology of FeAstVs.

Development of EST-SSR markers and their application in the analysis of the genetic diversity of Sophora japonica Linn

We developed and identified a new set of polymorphic EST-SSR markers in Sophora japonica Linn. and analyzed their genetic diversity. Sophora japonica is a native species in China with ornamental and medicinal value. To explore the genetic diversity and the genetic differentiation of this species, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed based on de novo transcriptome sequencing. In total 35,844 unigenes were obtained with an average length of 923 bp. 7,520 potential EST-SSRs were identified from 6,084 unigenes, of which there was one SSR per 4.40 kb. The dinucleotide repeats were the most common SSRs. Based on the SSR-containing sequence, 30 superior EST-SSRs were developed from 100 primer pairs and further used to characterize the genetic diversity and genetic differentiation of S. japonica in five populations. The results showed that the genetic diversity of the five groups was high, but the frequency of gene exchange between the groups was not. The analysis of molecular variance (AMOVA) showed that the genetic variation within individuals was 86.10%, which means the individual variation was the more significant in selective breeding of S. japonica. Nei’s genetic identity and genetic distance analyses yielded a high genetic identity value of 0.896 and mean genetic distance of 0.1095 suggesting high similarities among the five tested S. japonica populations. Based on genetic distance, S. japonica populations were classified into two groups. The findings of this study provide insights into the genetic information of S. japonica and will guide the development of conservation and management strategies for existing S. japonica germplasm.

Identification of Duplicates in Ginger Germplasm Collection from Odisha Using Morphological and Molecular Characterization

In this investigation, sixty morphologically different ginger rhizomes, collected from an active germplasm conservatory of High Altitude Research Station, Odisha, India, were characterized using morphological traits and molecular markers. Larger variations in morphological characters were observed among the 45 ginger accessions out of 60 accessions. Out of 22 markers, 9 ISSR and 13 SSR markers used for analysis generated 42 and 160 polymorphic bands accounting to 55% and 63.29% of the total polymorphic bands, respectively; this depicts that SSR markers have better efficiency over ISSR markers. A high degree of variation is detected in multivariate analysis (PCA and UPGMA) of both morphological traits and combined molecular markers, in which the ginger accessions clustered into five and four distinct groups. This explains the existence of large variation in morphological traits despite markers used. Genetic distance between the accessions determined from Nei’s dissimilarity matrix was used to find out the potential duplicates within the accessions collected. Twenty-nine accessions having mean genetic distance (MGD) less than threshold MGD (average MGD) value 0.174 were considered as ‘potential duplicate’ accessions and were reduced to one group, and the rest 31 were considered distinct genotype out of 60 accessions. From this analysis, 48.3% of the collection were considered as potential duplicates and deemed to be redundant. However, careful elimination of redundant through molecular analysis supported with passport data will help to eradicate existing synonyms used by farmers and improve management practices of the ginger germplasm conservatory.

Phylogenetic investigation of HCV-4d epidemic in Paris MSM HIV population reveals a still active outbreak and a strong link to the Netherlands

ObjectivesThe hepatitis C virus (HCV) epidemic is evolving quickly despite new treatments, and due to behaviour changes increasing at-risk situations. We investigated potential origins and evolution of the HCV-4d French emergence among human immunodeficiency virus (HIV)-infected men who have sex with men (MSM), in Paris in 2003. MethodsWe analysed all HCV sequences from the initial Paris outbreak with all newly available sequences publicly available, including sampling date and geographical location, resulting in 184, 68, 156, 107, 13 and 2 sequences from France, The Netherlands, other European countries, Africa, the Middle East or Turkey, Americas and Asia, respectively. Phylogenetic reconstruction was performed using maximum likelihood and Bayesian approaches. ResultsHCV-4d sequences from Europe were strongly separated from non-European sequences. Sequences from the initial Paris outbreak were all included into two well-separated and supported clusters with branch support at 100%, mean genetic distance <2.8 substitutions/100 nucleotides and >3.4 substitutions/100 nucleotides between their common ancestor and the previous node. The largest cluster interleaved French (n = 98) and Dutch (n = 28) sequences, suggesting several translocations between these countries. This cluster included 41 French sequences from Lyon sampled after 2014, highlighting its continuous spread within France since the initial outbreak. The smallest cluster included one Paris sequence with UK sequences (n = 9). DiscussionA few previous works have shown HCV-4d transmissions occurring between a few countries. In our work, we suggest a new and large connection between France and The Netherlands MSM communities and highlight a well-separated pan-European transmission network. Large collaborative networks are needed to investigate ongoing transmissions across countries and help specific prevention measures.

New occurrence of the invasive alien leaf‐footed bug Leptoglossus gonagra (Hemiptera: Coreidae) in South Korea

AbstractThe invasive alien leaf‐footed bug Leptoglossus gonagra (Fabricius 1775), native to the Americas, is herein recorded from South Korea for the first time. Forty nymphs and adults were collected on 22 September 2016 from arable lands of two separate sites. These individuals were identified based on the analysis of morphological characters and cytochrome oxidase c subunit 1 sequences. A neighbor‐joining tree indicated the existence of two clades: Group A from Brazil, and Group B from Asia and Oceania. Mean genetic distance between clades was 8.11%, range 7.60–8.57%. Within clades, mean genetic distance was 0.42% (0.17–0.83%) in Group A and, 0.45% (0.00–0.83%) in Group B. Colonies of 2nd‐final instar nymphs and adults were found, on top of leaves, flowers, fruits, and between the stems of pumpkins (Cucurbita moschata). Nymphs and adults damaged host plants by sucking their leaves, stems, fruits, and buds. After the first discovery in 2016, we were unable to find the bugs again (in 2017–2019). Therefore, the invasion of this species seems to have occurred only temporarily, during the warm season. We suggest that the species may have failed to overwinter as it is normally distributed in regions warmer than Korea. Nevertheless, possible appearances of this species must be continuously monitored as it is a potential pest of various plants cultivated in South Korea.

First record of Pampus minor (Actinopterygii: Perciformes: Stromateidae) from the coastal waters of Wenzhou, China

Pampus fishes (Perciformes: Stromateidae) are important commercial species and include six valid species in China. The southern lesser pomfret (Pampus minor Liu and Li, 1998) is a species of Pampus for which knowledge is incomplete. This report confirms the occurrence of P. minor in the coastal waters of Wenzhou, China, by analyzing five specimens of P. minor obtained in Wenzhou in March 2019. Morphometric measurements and meristic counts were performed. The diagnostic morphological features of these species were consistent with those of the neotype specimen of P. minor and sufficient for separating the examined specimens from other Pampus species. This study was based on the Cytochrome Oxidase Subunit 1 (CO1) gene, which was sequenced for the purpose of identification. The genetic distances between P. minor and other Pampus species ranged from 13.4% to 15.5%, and the mean genetic distance within the P. minor group was 0.2%. Given that P. minor has not been reported in this region, our findings represent the first record from the coastal waters of Wenzhou and extend the distribution range of this species to the central and northern East China Sea. The reason for the observed northward migration of some P. minor individuals from their northernmost recorded habitat (Taiwan Strait) might be global warming. The collection of additional specimens is needed to further study the geographic limits of P. minor and its presumed northern expansion.

Introduction of human gammaherpesvirus 8 genotypes A, B, and C into Brazil from multiple geographic regions

Variations in the open reading frame (ORF) K1 gene sequence of human gammaherpesvirus 8 (HHV-8) has led to the identification of 6 major genotypic clades (A, B, C, D, E, and F) in specimens isolated from around the world. These clades exhibit clear clustering among individuals in different ethnic groups and from different geographic regions. The human population of Brazil varies greatly in ethnicity because of multiple immigration events from Africa, Europe, Asia, and indigenous communities. However, there is scant information about the HHV-8 genotypes currently circulating in Brazil. Here, we describe HHV-8 genotypic diversity in isolates from Brazilian HIV-infected patients living with Kaposi’s sarcoma (KS) by analysis of the complete ORF-K1 region. We also identified the most likely geographic origins of these different Brazilian genotypes. We extracted HHV-8 DNA (24 positive samples) from individuals with HIV/KS from the states of São Paulo and Rio de Janeiro, amplified the ORF-K1 gene using nested PCR (about 870 base pairs), performed sequencing and phylogenetic analysis, and then calculated the mean genetic distances of Brazilian sequences from sequences in other regions of the world (523 sequences analyzed). Phylogenetic analysis showed that genotypes C, A, and B were present in 45.8 %, 29.2 % and 25 % of the isolates from Brazil, respectively. These isolates grouped into separate clades, rather than a single monophyletic cluster. Mean genetic distance analyses suggested that these genotypes were introduced into the Brazil multiple times from different geographical regions. HHV-8/A isolates appear to be from Ukraine, Russia, and the Tartar ethnic group; HHV-8/B isolates appear to be from Congo and Democratic Republic of the Congo; and HHV-8/C isolates appear to be from Australia, Algeria, England, and French Guiana. These results contribute to a better understanding of the genetic diversity and origins of HHV-8 strains circulating in Brazil, and will provide a foundation for further epidemiological and evolutionary studies of HHV-8.

Evolutionary Dynamics of the Lineage 2 West Nile Virus That Caused the Largest European Epidemic: Italy 2011-2018.

Lineage 2 West Nile virus (WNV) caused a vast epidemic in Europe in 2018, with the highest incidence being recorded in Italy. To reconstruct the evolutionary dynamics and epidemiological history of the virus in Italy, 53 envelope gene and 26 complete genome sequences obtained from human and animal samples were characterised by means of next-generation sequencing. Phylogenetic analysis revealed two Italian strains originating between 2010 and 2012: clade A, which apparently became extinct in 2013–2014, and clade B, which was responsible for the 2018 epidemic. The mean genetic distances in clade B increased over time and with the distance between sampling locations. Bayesian birth-death and coalescent skyline plots of the clade B showed that the effective number of infections and the effective reproduction number (Re) increased between 2015 and 2018. Our data suggest that WNV-2 entered Italy in 2011 as a result of one or a few penetration events. Clade B differentiated mainly as a result of genetic drift and purifying selection, leading to the appearance of multiple locally circulating sub-clades for different times. Phylodynamic analysis showed a current expansion of the infection among reservoir birds and/or vectors.

Phylogenetic analysis highlights the role of older people in the transmission of HIV-1 in Fuyang, Anhui Province, China

BackgroundThe proportion of older HIV-1 infected people in China has increased rapidly in recent years. Elucidation of the transmission characteristics of this high-risk population subgroup is helpful for the development of tailored interventions.MethodsA phylogenetic analysis was performed that uses available HIV-1 pol sequences amplified with nested RT-PCR from plasma samples of all newly diagnosed participants spanning from October 2017 to September 2018 in Fuyang, Anhui Province. Transmission clusters were identified as two or more sequences that shared a corresponding node with an aLRT-SH value ≥90 in the maximum-likelihood phylogenetic tree and had an overall mean genetic distance of ≤1.5%. A local transmission cluster was defined as a cluster that had more than 80% of its sequences from Fuyang. The role of older people in local HIV-1 transmission was determined using an integration of molecular and demographic data.ResultsOf 362 available sequences, 14 subtypes, and 28 local transmission clusters were identified. It was found that the proportion of older people in the local transmission cluster (69/77, 89.61%) was much higher than that of younger people (46/114, 40.35%) (χ2 test, P < 0.001). In the pretreatment drug resistance analysis, the proportion of sequences with PDRMs in the local transmission cluster was not significantly different between the older people group (57.14%, 4/7) and non-old-aged group (11.11%, 1/9) (Fisher’s exact test, P > 0.05).ConclusionBy combining phylogenetic analyses with demographic data, more detailed information was provided about the local transmission structure in Fuyang. These findings suggested that older people play an important role in local transmission, and more tailored interventions for this population subgroup are urgently needed.

Genetic resources of relict populations of Pinus sylvestris (L.) in Western Carpathians assessed by chloroplast microsatellites

The relict character of the Scots pine populations from the Tatra Mts. (Western Carpathians) was formed on scarcely accessible, ecologically extreme habitats, in areas which were not under human activity. An exhaustive genetic analysis of the Scots pine populations from the refugial locations in the Tatra Mts. (Poland) had not yet been. In this study, we characterize the genetic variation and differentiation of the relict Scots pine populations from the Tatra Mts., to provide information on their genetic resources and the conservation implications. Eight paternally inherited chloroplast microsatellite loci were used to investigate the genetic structure of 4 relict populations, which were compared with the natural populations from the Baltic region (5 populations from Lithuania, Latvia and Estonia) and to a northern range from Russia (5 populations from the Kola Peninsula and Arkhangelsk Oblast). The four relict pine populations were characterized by a lower level of genetic variation when compared to the Baltic and northern populations, which was expressed in lower values of particular genetic parameters: numbers of alleles and haplotypes, haplotype genetic diversity, haplotype differentiation, and mean genetic distance between individuals in the population. Our results revealed a very high and significant genetic differentiation between all the analyzed populations, as well as between the three analyzed regions (PhiPT = 8%). Furthermore, the relict populations within a close geographic location showed higher differentiation (PhiPT = 5%) compared to the northern Russian and Baltic populations that were separated by tens and hundreds of kilometers. The relict populations of P. sylvestris from the Tatra Mts. deserve conservation efforts due to the fact that they are an important component if the species-poor Tatra forests.

Pollen morphological variation of Primula merrilliana and its systematic significance

Primula merrilliana is a distylous, rare, vulnerable herb and of high value in horticulture. Previous studies indicated that the genetic differentiation among populations of this species was remarkably greater than that of its closely related species, suggesting that it may not be a single homogeneous species. In order to further explore the natural variation and identity of the species, pollen morphology and ITS DNA sequences of 18 populations covering its whole distribution were investigated. According to the pollen shape and aperture type, P. merilliana has two different pollen types; six populations from the northwest corner of the distribution area have stephanocolpate and suboblate pollen grains, while the remaining 12 populations possess pantoporate and spherical pollen grains. The mean genetic distance among populations with the same pollen type (mean 0.009) was significantly lower than that of populations with different pollen types (mean 0.023). Pollen morphological characteristics of P. merrilliana have taxonomic value for species identification, suggesting that P. merrilliana is a species complex that comprises two different species. Pollen size variations support the hypothesis that Fenghuangshan (FHS) and Dongshan (DSC) populations, having both sexual organs at the mouth of corolla tube, are long-homostyled populations (not a phenotype with stamen modification of a long-styled morph), while the Qidu (QD) population, having both sexual organs at the middle of the corolla tube, is a short-homostyled population (i.e. not a stamen modification of a short-styled morph).

Genetic variability of Brazilian wheat germplasm obtained by high-density SNP genotyping

Abstract The aim of this study was to evaluate the genetic diversity of the wheat germplasm using high-density genotyping with SNP markers. A set of 211 wheat varieties genotyped with 35,142 SNP markers were used in the experiment. Genetic distances ranged from 0.013 to 0.471, with the highest frequency of distances varying between 0.31 and 0.40. In the cluster analysis by the UPGMA method, 81% of the varieties were clustered in three groups. Genetic variability in the Brazilian wheat germplasm has remained constant for over 70 years. Mean genetic distances among the varieties developed in each decade ranged from 0.33 to 0.34. A trend of genetic distance between genotypes from different eras has been observed over time as a result of breeding. Results described in this study can help Brazilian wheat breeders to manage more adequately genetic variability in the Brazilian wheat germplasm.

Genetic Diversity of Maize Genotypes with Variable Resistance to Striga asiatica Based on SSR Markers

Genetic diversity among breeding populations is key in plant breeding programs. This study aimed to determine the extent of genetic diversity among 37 diverse maize genotypes using simple sequence repeat (SSR) markers. The maize genotypes were selected based on their variable resistance to Striga asiatica. Maize genotypes were fingerprinted using 18 polymorphic SSR markers. Marker and population diversity parameters were computed. A total of 191 alleles were detected and the number of effective alleles varied from 2 to 21 per locus with a mean of 11. The polymorphic information content (PIC) of the SSR markers varied from 0.59 to 0.96, with a mean of 0.80. Significant differences were observed among populations, individuals and within individuals. Within and among individual variances accounted for 85% and 13% of the total gene diversity. The genotypes were grouped into three main genetic clusters, which were not influenced by genotype origin. Mean genetic distance (0.43) and low geneflow (0.18) were observed among the populations. High mean genetic identity (0.65) was recorded, indicating potential genetic ‘bottleneck’ among the selected germplasm. The following open pollinated varieties; Border King, Colorado, CIMMYT’s ZM OPVs, Mac Pearl, Shesha, Nel Choice, Natal 8Lines, Nel Choice QPM, Hickory King, Kep Select, Obatanpa and the Striga resistant synthetic variety DSTRYSYN15 were selected from different clusters for breeding.

Clinical and virological properties of hepatitis C virus genotype 4 infection in patients treated with different direct-acting antiviral agents.

BackgroundThe efficacy of direct-acting antivirals (DAAs) depends on the hepatitis C virus (HCV) genotype 4 (GT4) subtype which are used in the treatment of HCV. We aimed to retrospectively investigate the baseline prevalence of HCV NS5A and NS5B polymorphisms and their impact on virological outcome in GT4-infected patients treated with various DAA regimens.Patients and methodsAvailable plasma samples from HCV GT4-infected patients treated with different DAA regimens were analyzed at baseline and after treatment failure, where applicable. Sanger sequencing of patient-derived NS5A and NS5B regions was performed on all available samples, while ultradeep pyrosequencing (UDPS) of NS5A and NS5B regions was performed only on samples from treatment failures at different time points.ResultsSustained virological response (SVR) was achieved by 96% (48/50) of patients. Of 16 patients with baseline NS5A sequence, polymorphisms at amino acid positions associated with drug resistance were detected only at position 58: P58 (69.2%) and T58 (30.8%). Of 21 patients with baseline NS5B sequence, N142S was detected only in the two treatment failures, both with GT4d were treated with sofosbuvir (SOF)-based regimens, suggesting a potential involvement in SOF efficacy. Two patients (patient 1 [Pt1] and patient 2 [Pt2]) relapsed. In Pt1, NS5A-T56I and NS5A-Y93H/S emerged. In Pt2, NS5A-L28F emerged and a novel NS5B resistance-associated substitution (RAS), L204F, representing 1.5% of the viral population at baseline, enriched to 71% and 91.6% during and after treatment failure, respectively. UDPS of NS5B from Pt2 indicated a mixed infection of approximately 1:5, GT1a:GT4d, at baseline and GT4d during failure. Phylogenetic analysis of NS5A sequences indicated no clustering of HCV strains from patients achieving SVR vs patients who relapsed. The mean genetic distance in NS5A sequences was 5.8%, while a lower genetic distance (3.1%) was observed in NS5B sequences.ConclusionResults from these analyses confirm the importance of UDPS in the analysis of viral quasispecies variability and the identification of novel RASs potentially associated with DAA treatment failure in HCV GT4-infected patients.

Genetic diversity and population structure of endemic mushroom Leucocalocybe mongolica in Mongolian Plateau uncovered by EST-SSR markers

Leucocalocybe mongolica (S. Imai) X.D. Yu &Y.J. Yao is an endemic mushroom with a distribution in Mongolian Plateau. It is an important edible and medicinal mushroom which is often collected unscrupulously. Wild L. mongolica is facing an unprecedented threat and is in a critically endangered state. Exploration of the genetic diversity and population structure of L. mongolica is important for conservation biology. The main distribution areas were investigated. In total, 402 alleles of 223 individuals from 17 wild geographical populations were obtained based on the eight simple sequence repeat loci. The total number of alleles from each population ranged from 11 to 31 with an average of 24 per population. The average observed heterozygosity (HO) and expected heterozygosity (HE) ranged from 0.300 to 0.875 and from 0.188 to 0.621, respectively. Analysis of molecular variance (AMOVA) indicated that 14.19% of the total molecular variance could be attributed to differences between populations (p <.001), whereas 85.81% to differences within populations. The mean genetic distance (FST) value of 0.171 suggested low genetic differentiation among populations. The UPGMA dendrogram generated from the SSR data suggested that the 17 populations separated into three main sister clusters on the Nei's genetic identity coefficient 0.8. The 223 L. mongolica individuals were divided into three groups by STRUCTURE analysis. Keeping and enriching the population diversity is crucial for the conservation of L. mongolica. The data about the population structure and genetic diversity obtained in this study will facilitate the establishment of conservation measures.AbbreviationsAMOVA: analysis of molecular variance; Dest: estimator of actual differentiation; EST-SSR: Expressed sequence tag- simple sequence repeats; Fis: Inbreeding coefficient; Fit: total inbreeding coefficient; Fst: fixation index; GST coefficient of gene differentiation; G’ST: standardized measure of genetic differentiation; HE: expected Heterozygosity; H0: observed heterozygosity; HS: mean genetic diversity within populations; HT: total genetic diversity for species; I: Shannon’s diversity index; km: kilometer; L. mongolica: Leucocalocybe mongolica; N: sample size; NA: number of average alleles; NE: number of effective alleles; Nm: gene flow; NP: number of private alleles; NR: allelic richness; NT: number of total alleles; PCoA: principal coordinate analysis; PIC: polymorphism information content; PPB: Percentage of polymorphic loci; TP-M13-SSR: tailed primer M13; UHE: unbiased expected Heterozygosity

Diversity of The Ornate Lorikeet (Trichoglossus ornatus) Birds Based on Mitochondrial DNA Protein Coding Gene

Ornate lorikeet (Trichoglossus ornatus) is an endemic bird in Sulawesi. Endemism is one of the factors in declining bird’s population. In the case of the birds conservation programme, information about gene diversity is important for basic strategy. Mitochondrial DNA of animals consists of protein coding genes including ND2 gene. This study informs diversity of the Ornate Lorikeet (Trichoglossus ornatus) birds based on DNA sequences of ND2 gene. DNA total was extracted from blood samples of 21 birds. PCR (Polymerase Chain Reaction) was performed and successfully amplified a single DNA fragment of ND2 gene for all birds. DNA fragments were sequenced and totally 997 base pairs were analyzed. NJ tree was constructed using MEGA5. All DNA sequence data showed that between the birds there were 20 polymorphic (segregating) sites with mean genetic distance was 0.004 ± 0.002 (ranged from 0,000 – 0,008), and had 17 sequence haplotypes (HTor1- HTo17). Haplotype diversity (Hd) was 0.967 ± 0.30387 and nucleotide diversity (Pi) was 0.00439 ± 0.0012. Genetic diversity information could be potential relevance to the breeding management for conservation of the birds.

Microsatellite Analysis of Genetic Variation in Intraspecific Hybrids and Self-Breds of Steelhead Trout and Golden Rainbow Trout

Genetic diversity of the hybrids and inbreds of Steelhead trout and golden rainbow trout, altogether four populations, was studied based on 15 polymorphic microsatellite locus. Two hundred and forty individuals (sixty individuals per one population) were collected from the Yudu hill aquaculture experimental station of Beijing Fisheries Research Institute, Beijing, China. The genetic variation of the hybrids and inbreds of Steelhead trout and golden rainbow trout were all relatively high. The mean observed heterozygosity value of YJ, YY, JJ and JY were respectively 0.6600, 0.7733, 0.7822, and 0.6533. The mean Fis and Fit value were respectively (-0.5065, -0.6037, -0.5728, -0.4620) and (-0.3857, -0.5272, -0.4987, -0.4069), showing an average excess of heterozygote proportion. The mean Fst value was respectively 0.0802, 0.0477, 0.0471, and 0.0376. The mean genetic distance between JJ and YY was the closest (0.0097), next to YJ and YY (0.0655), and that between JY and YY was the most distant (0.1096). The dendrogram showed JY and YJ firstly clustered together, and then they clustered together with the inbred offspring (JJ and YY). Duo to Fst (little genetic differentiation) and Nm (the Nm values of 15 locus > 1), JY was a finer variety the two hybrids of Steelhead trout and golden rainbow trout. Our data offer supporting evidence that inbreeding depression of Steelhead trout and golden rainbow trout involves multiple related genes, favoring partial dominance over dominance.