High Nucleotide Diversity Research Articles

Variability in ITS1 and ITS2 sequences of historic herbaria and extant (fresh) Phalaris species (Poaceae)

BackgroundPhalaris species (Poaceae) occupy diverse environments throughout all continents except Antarctica. Phalaris arundinacea is an important forage, ornamental, wetland restoration and biofuel crop grown globally as well as being a wetland invasive. The nuclear ribosomal internal transcribed spacer (ITS) region has been used for Phalaris barcoding as a DNA region with high nucleotide diversity for Phalaris species identification. Recent findings that P. arundinacea populations in Minnesota USA are most likely native and not European prompted this analysis to determine whether Eurasian vs. native North American P. arundinacea differed in ITS regions. Our objectives were to amplify and compare ITS regions (ITS1 and ITS2) of historic herbaria (1882–2001) and extant (fresh) Phalaris specimens; analyze ITS regions for species-specific polymorphisms (diagnostic SNPs) and compare ITS regions of historic Phalaris specimens with known, extant Phalaris species.ResultsWe obtained complete ITS1 and ITS2 sequences from 31 Phalaris historic (herbaria samples, 1908 to 2001) and five extant (fresh) specimens. Herbaria Phalaris specimens did not produce new SNPs (single nucleotide polymorphisms) not present in extant specimens. Diagnostic SNPs were identified in 8/12 (66.6%) Phalaris species. This study demonstrates the use of herbaria tissue for barcoding as a means for improved species identification of Phalaris herbaria specimens. No significant correlation between specimen age and genomic DNA concentration was found. Phalaris arundinacea showed high SNP variation within its clade, with the North American being distinctly different than other USA and most Eurasian types, potentially allowing for future identification of specific SNPs to geographic origin.ConclusionsWhile not as efficient as extant specimens to obtain DNA, Phalaris herbaria specimens can produce high quality ITS sequences to evaluate historic genetic resources and facilitate identification of new species-specific barcodes. No correlation between DNA concentration and age of historic samples (119 year range) occurred. Considerable polymorphism was exhibited in the P. arundinacea clade with several N. American accessions being distinct from Eurasian types. Further development of within species- and genus-specific barcodes could contribute to designing PCR primers for efficient and accurate identification of N. American P. arundinacea. Our finding of misidentified Phalaris species indicates the need to exercise stringent quality control measures on newly generated sequence data and to approach public sequence databases in a critical way.

Characterization of the complete mitochondrial genomes of six horseflies (Diptera: Tabanidae).

The family Tabanidae (Insecta: Diptera) is one of the economically most important group of haematophagous insects, causing millions of livestock deaths per year. However, current knowledge on the mitochondrial genomes (mitogenomes) from this family is limited. Additional tabanid mitogenomes characterization is of utmost importance for their identification, epidemiologic and phylogenetic studies. We sequenced the mt genomes of six horseflies with an Illumina platform and their phylogenetic relationship was conducted with other infraorder Tabanomorpha members with available mt genome datasets. All six newly sequenced mitogenomes were typical 37-gene circular structures retaining the gene order of Tabanomorpha. The trnQ, trnM and trnA were highly conserved among the six mitogenomes (identity=100%). The TΨC arm and variable loop regions were relatively more variable compared to the amino acid receptor arm, anticodon arm and DHU arm of the tRNAs. Among 13 protein-coding genes (PCGs) of tabanids mitogenomes, the highest nucleotide diversity was detected in atp8, cox1, cox3, nad6 and cytb (0.1 for each). In addition, atp8 genes exhibited the highest evolutionary rate (ω=0.24) among 13 PCGs. The interspecies K2P genetic distances among some Tabanus spp. across the mitogenome was greater (0.08) than intergeneric genetic distance between T. amaenus and Atylotus miser (0.07). Phylogenetic analyses revealed non-monophyletic relationships among horseflies of the genus Tabanus. The present study showed mt gene order is highly conserved within Tabanus species. Our mito-phylogenomic analysis supports the paraphyly of the genus Tabanus. The new data provide novel genetic markers for studies of population genetics and systematics of horseflies.

Mitochondrial DNA D-loop sequence analysis reveals high variation and multiple maternal origins of indigenous Tanzanian goat populations.

The Small East African (SEA) goat are widely distributed in different agro‐ecological zones of Tanzania. We report the genetic diversity, maternal origin, and phylogenetic relationship among the 12 Tanzanian indigenous goat populations, namely Fipa, Songwe, Tanga, Pwani, Iringa, Newala, Lindi, Gogo, Pare, Maasai, Sukuma, and Ujiji, based on the mitochondrial DNA (mtDNA) D‐loop. High haplotype (H d = 0.9619–0.9945) and nucleotide (π = 0.0120–0.0162) diversities were observed from a total of 389 haplotypes. The majority of the haplotypes (n = 334) belonged to Haplogroup A which was consistent with the global scenario on the genetic pattern of maternal origin of all goat breeds in the world. Haplogroup G comprised of 45 haplotypes drawn from all populations except the Ujiji goat population while Haplogroup B with 10 haplotypes was dominated by Ujiji goats (41%). Tanzanian goats shared four haplotypes with the Kenyan goats and two with goats from South Africa, Namibia, and Mozambique. There was no sharing of haplotypes observed between individuals from Tanzanian goat populations with individuals from North or West Africa. The indigenous goats in Tanzania have high genetic diversity defined by 389 haplotypes and multiple maternal origins of haplogroup A, B, and G. There is a lot of intermixing and high genetic variation within populations which represent an abundant resource for selective breeding in the different agro‐ecological regions of the country.

Prevalence and Genetic Diversity of Viruses Associated with Rugose Wood Complex in Greek Vineyards.

Rugose wood is one of the most important disease syndromes of grapevine, and it has been associated with at least three viruses: grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine virus A (GVA), and grapevine virus B (GVB). All three viruses show a worldwide distribution pattern, and their genetic composition has been the focus of extensive research in past years. Despite their first record in Greece almost 20 years ago, there is a lack of knowledge on the distribution and genetic variability of their populations in Greek vineyards. In this context, we investigated the distribution of GRSPaV, GVA, and GVB in rootstocks, self-rooted vines, and grafted grapevine cultivars originating from different geographic regions that represent important viticultural areas of Greece. Three new reverse transcription-PCR assays were developed for the reliable detection of GRSPaV, GVA, and GVB. Our results indicated that GVA is the most prevalent in Greek vineyards, followed by GRSPaV and GVB. However, virus incidence differed among self-rooted and grafted grapevine cultivars or rootstocks tested. Selected isolates from each virus were further molecularly characterized to determine their phylogenetic relationships. All three viruses exhibited high nucleotide diversity, which was depicted in the constructed phylogenetic trees. Isolates from Greece were placed in various phylogroups, reinforcing the scenario of multiple introductions of GVA, GVB, and GRSPaV in Greece and highlighting the effect of different transmission modes in the evolutionary course of the three viruses.

Assessing Genomic Diversity and Productivity Signatures in Dianzhong Cattle by Whole-Genome Scanning.

Dianzhong cattle is a classic Chinese indigenous cattle breed with historical records dating back to 200 BC. But with its genomic differences having not been clearly elucidated, the quest for genomic characterization will be an essential step towards understanding the genomic basis of productivity and adaptation to survival under Chinese farming systems. Here we compared 10 Dianzhong cattle (four newly sequenced and six downloaded) with 29 published genomes of three underlying ancestral populations (Chinese zebu, Indian zebu, and Yanbian cattle) to characterize the genomic variations of Dianzhong cattle. Dianzhong cattle has a high nucleotide diversity (0.0034), second only to Chinese zebu. Together with analyses of linkage disequilibrium decay and runs of homozygosity, Dianzhong cattle displayed higher genomic diversity and weaker artificial selection compared with Yanbian cattle. From a selective sweep analysis by four methods (Fst, π-ratio, XP-CLR, and XP-EHH), the positive selective signals were mainly manifested in candidate genes and pathways related to heat resistance, growth and development, fat deposition, and male reproduction. Missense mutations were detected in candidate genes, SDS (c.944C > A and p.Ala315Glu), PDGFD (c.473A > G and p.Lys158Arg), and DDX4 (rs460251486, rs722912933, and rs517668236), which related to heat resistance, fat deposition, and spermatogenesis, respectively. Our findings unravel, at the genome-wide level, the unique diversity of Dianzhong cattle while emphasizing the opportunities for improvement of livestock productivity in further breeding programs.

Geography-Driven Evolution of Potato Virus A Revealed by Genetic Diversity Analysis of the Complete Genome.

Potato virus A (PVA), a member of the genus Potyvirus, is an important potato pathogen that causes 30%–40% yield reduction to global potato production. Knowledge on the genetic structure and the evolutionary forces shaping the structure of this pathogen is limited but vital in developing effective management strategies. In this study, we investigated the population structure and molecular evolution of PVA by analyzing novel complete genomic sequences from Chinese isolates combined with available sequences from Europe, South America, Oceania, and North America. High nucleotide diversity was discovered among the populations studied. Pairwise FST values between geographical populations of PVA ranged from 0.22 to 0.46, indicating a significant spatial structure for this pathogen. Although purifying selection was detected at the majority of polymorphic sites, significant positive selection was identified in the P1, NIa, and NIb proteins, pointing to adaptive evolution of PVA. Further phylogeny–trait association analysis showed that the clustering of PVA isolates was significantly correlated with geographic regions, suggesting that geography-driven adaptation may be an important determinant of PVA diversification.

Population Genetic Structure of the Invasive Spotted Alfalfa Aphid Therioaphis trifolii (Hemiptera: Aphididae) in China Inferred From Complete Mitochondrial Genomes

Biological invasions represent a natural rapid evolutionary process in which invasive species may present a major threat to biodiversity and ecosystem integrity. Analyzing the genetic structure and demographic history of invaded populations is critical for the effective management of invasive species. The spotted alfalfa aphid (SAA) Therioaphis trifolii is indigenous in the Mediterranean region of Europe and Africa and has invaded China, causing severe damages to the alfalfa industry. However, little is known about its genetic structure and invasion history. In this study, we obtained 167 complete mitochondrial genome sequences from 23 SAA populations across China based on high-throughput sequencing and performed population genetic and phylogenomic analyses. High haplotype diversity and low nucleotide diversity were found in SAA populations in China with distinct genetic structures, i.e., all populations diverged into three phylogenetic lineages. Demographic history analyses showed a recent expansion of the SAA population, consistent with the recent invasion history. Our study indicated that SAA may have invaded through multiple introduction events during commercial trades of alfalfa, although this needs further validation by nuclear markers.

Spread beyond the border: Small Scale genetic structure of the introduced Banggai cardinalfish (Pterapogon kauderni) population in the Bali Strait

The living marine aquarium trade has been known to mediate various aquatic invaders to spread and established a new population outside of their natural home range. In most cases, the introduce species cause a cascaded effect which harm the native species and their ecosystem. The successful of the invasion event often related to the genetic properties of the introduced species. Therefore, using a molecular approach based on a mitochondrial DNA marker, the present work aimed to evaluate the population genetic structure of the introduced P. kauderni population in Bali Strait. Samples were collected from four sites in Gilimanuk Bay, Bali Strait. Our results showed a high haplotype diversity and low nucleotide diversity that might be a signal of a bottleneck. Overall, we found five haplotypes comprising two unique haplotypes and three shared haplotypes. Genetic structure was detected in some localities, which indicates Pterapogon kauderni might originated from various genetically distinct populations. However, we could not conclusively determine the observed patterns of the genetic structure within each site. These patterns are likely related to the multiple introduction event of P. kauderni in Bali Strait. Additional samples from both side (introduced and native habitat) combined with more rapidly evolving markers may describe the structure more clearly.

Balancing selection and wild gene pool contribute to resistance in global rice germplasm against planthopper.

Interactions and co-evolution between plants and herbivorous insects are critically important in agriculture. Brown planthopper (BPH) is the most severe insect of rice, and the biotypes adapt to feed on different rice genotypes. Here, we present genomics analyses on 1,520 global rice germplasms for resistance to three BPH biotypes. Genome-wide association studies identified 3,502 single nucleotide polymorphisms (SNPs) and 59 loci associated with BPH resistance in rice. We cloned a previously unidentified gene Bph37 that confers resistance to BPH. The associated loci showed high nucleotide diversity. Genome-wide scans for trans-species polymorphisms revealed ancient balancing selection at the loci. The secondarily evolved insect biotypes II and III exhibited significantly higher virulence and overcame more rice varieties than the primary biotype I. In response, more SNPs and loci evolved in rice for resistance to biotypes II and III. Notably, three exceptional large regions with high SNP density and resistance-associated loci on chromosomes 4 and 6 appear distinct between the resistant and susceptible rice varieties. Surprisingly, these regions in resistant rice might have been retained from wild species Oryza nivara. Our findings expand the understanding of long-term interactions between rice and BPH and provide resistance genes and germplasm resources for breeding durable BPH-resistant rice varieties.

Exploring the genomic resources and analysing the genetic diversity and population structure of Chinese indigenous rabbit breeds by RAD-seq

BackgroundChinese indigenous rabbits have distinct characteristics, such as roughage resistance, stress resistance and environmental adaptability, which are of great significance to the sustainable development of the rabbit industry in China. Therefore, it is necessary to study the genetic diversity and population structure of this species and develop genomic resources.ResultsIn this study, we used restriction site-associated DNA sequencing (RAD-seq) to obtain 1,006,496 SNP markers from six Chinese indigenous rabbit breeds and two imported rabbit breeds. Jiuyishan and Fujian Yellow rabbits showed the highest nucleotide diversity (π) and decay of linkage disequilibrium (LD), as well as higher observed heterozygosity (Ho) and expected heterozygosity (He), indicating higher genetic diversity than other rabbits. The inbreeding coefficient (FIS) of New Zealand rabbits and Belgian rabbits was higher than that of other rabbits. The neighbour-joining (NJ) tree, principal component analysis (PCA), and population structure analysis of autosomes and Y chromosomes showed that Belgian, New Zealand, Wanzai, Sichuan White, and Minxinan Black rabbits clustered separately, and Fujian Yellow, Yunnan Colourful, and Jiuyishan rabbits clustered together. Wanzai rabbits were clearly separated from other populations (K = 3), which was consistent with the population differentiation index (FST) analysis. The selection signature analysis was performed in two populations with contrasting coat colours. With Sichuan White and New Zealand rabbits as the reference populations and Minxinan Black and Wanzai rabbits as the target populations, 408, 454, 418, and 518 genes with a selection signature, respectively, were obtained. Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed on the genes with a selection signature. The results showed that the genes with a selection signature were enriched in the melanogenesis pathway in all four sets of selection signature analyses.ConclusionsOur study provides the first insights into the genetics and genomics of Chinese indigenous rabbit breeds and serves as a valuable resource for the further effective utilization of the species.

GENETIC DIVERSITY OF BROILER CHICKEN BRANDS RAISED IN ARID AND SEMI-ARID ZONES OF NORTHERN NIGERIA USING MITOCHONDRIAL DNA

A sector of broiler production is growing very fast to meet the high demand of meat in Nigeria. However, high mortality rates among the broilers especially during the hot dry season in arid and semi-arid zones is worrisome. There is a need for molecular genetics study that could aid in management, conservation and sustainable exploitation of this species. To evaluate the genetic diversity of broilers raised in these regions, a total of forty-six broilers were randomly sampled from eight different brands (Agrited, Amo, Chi, Fol-hope, Obasanjo, Olam, Yammfy and Zatech) for mitochondrial DNA analysis. Four haplotypes were detected among all the samples used that belong to the four strains. The sequences of mitochondrial regions revealed high haplotype diversity (0.78600) and low nucleotide diversity (0.00286). Lower genetic diversity observed may increase the chances of rapid disease infection and distribution during any disease outbreak. Introduction of new strains of broilers with high genetic diversity is highly recommended. Future study should be conducted on the performance of these strains during the extremely hot temperature period in arid and semi-arid zones of Nigeria. This is to provide reliable information for the sake of local broiler farmer’s benefit who invests largely on this sector. The study will also help the geneticists from these brands to develop a strain that could survive and perform excellently under severe climatic conditions of the rural areas of arid and semi-arid zones of Nigeria

Unraveling the genetics of tomato fruit weight during crop domestication and diversification

Key MessageSix novel fruit weight QTLs were identified in tomato using multiple bi-parental populations developed from ancestral accessions. Beneficial alleles at these loci arose in semi-domesticated subpopulations and were likely left behind. This study paves the way to introgress these alleles into breeding programs.The size and weight of edible organs have been strongly selected during crop domestication. Concurrently, human have also focused on nutritional and cultural characteristics of fruits and vegetables, at times countering selective pressures on beneficial size and weight alleles. Therefore, it is likely that novel improvement alleles for organ weight still segregate in ancestral germplasm. To date, five domestication and diversification genes affecting tomato fruit weight have been identified, yet the genetic basis for increases in weight has not been fully accounted for. We found that fruit weight increased gradually during domestication and diversification, and semi-domesticated subpopulations featured high phenotypic and nucleotide diversity. Columella and septum fruit tissues were proportionally increased, suggesting targeted selection. We developed twenty-one F2 populations with parents fixed for the known fruit weight genes, corresponding to putative key transitions from wild to fully domesticated tomatoes. These parents also showed differences in fruit weight attributes as well as the developmental timing of size increase. A subset of populations was targeted for QTL-seq, leading to the identification of six uncloned fruit weight QTLs. Three QTLs, located on chromosomes 1, 2 and 3, were subsequently validated by progeny testing. By exploring the segregation of the known fruit weight genes and the identified QTLs, we estimated that most beneficial alleles in the newly identified loci arose in semi-domesticated subpopulations from South America and were not likely transmitted to fully domesticated landraces. Therefore, these alleles could be incorporated into breeding programs using the germplasm and genetic resources identified in this study.

Insights into the effect of human civilization on Malus evolution and domestication.

The evolutionary history of the Malus genus has not been well studied. In the current study, we presented genetic evidence on the origin of the Malus genus based on genome sequencing of 297 Malus accessions, revealing the genetic relationship between wild species and cultivated apples. Our results demonstrated that North American and East Asian wild species are closer to the outgroup (pear) than Central Asian species, and hybrid species including natural (separated before the Pleistocene, about 2.5 Mya) and artificial hybrids (including ornamental trees and rootstocks) are between East and Central Asian wild species. Introgressions from M. sylvestris in cultivated apples appeared to be more extensive than those from M. sieversii, whose genetic background flowed westward across Eurasia and eastward to wild species including M. prunifolia, M. × asiatica, M. × micromalus, and M. × robust. Our results suggested that the loss of ancestral gene flow from M. sieversii in cultivated apples accompanied the movement of European traders around the world since the Age of Discovery. Natural SNP variations showed that cultivated apples had higher nucleotide diversity than wild species and more unique SNPs than other apple groups. An apple ERECTA‐like gene that underwent selection during domestication on 15th chromosome was identified as a likely major determinant of fruit length and diameter, and an NB‐ARC domain‐containing gene was found to strongly affect anthocyanin accumulation using a genome‐wide association approach. Our results provide new insights into the origin and domestication of apples and will be useful in new breeding programmes and efforts to increase fruit crop productivity.

Determinants of Persistent Patterns of Pepino Mosaic Virus Mixed Infections.

Pepino mosaic virus (PepMV) has become a pandemic virus in tomato crops, causing important economic losses worldwide. In Spain, isolates of the EU and CH2 strains co-circulate, with PepMV-EU predominantly found in mixed infections. Simultaneous in planta mixed infections result in an asymmetric antagonism against PepMV-CH2, but the outcome of over-infections has never been tested. PepMV-EU and PepMV-CH2 time-lagged inoculations were performed, and viral accumulation was measured 10 days after challenge inoculation. PepMV-EU had a protective effect over PepMV-CH2; in contrast, the accumulation of PepMV-EU increased in plants pre-inoculated with PepMV-CH2 as compared to single infections. We also studied the effect of the type of infection on viral transmission. Independently of the nature of the infection (single or mixed), we observed a strong positive correlation between virus accumulation in the source plant and transmission, excluding mixed infection effects different than modulating viral accumulation. Finally, in order to determine the genetic variability of PepMV strains in single and mixed infections, a 430 nucleotide region was RT-PCR amplified from samples from a serial passages experiment and deep-sequenced. No significant differences were found in the number of nucleotide substitutions between single and mixed infections for PepMV-EU; in contrast, significant differences were found for PepMV-CH2, which was more variable in single than in mixed infections. Comparing PepMV-EU with PepMV-CH2, a higher nucleotide diversity was found for PepMV-CH2. Collectively, our data strongly suggest that PepMV mixed infections can impact the virus epidemiology by modulating in planta virus strain accumulation and diversification.

Genetic diversity and haplotypes of paediatric hydatid cyst isolates and first occurrence of E. canadensis (G6/G7) in paediatric cases in Turkey.

Cystic echinococcosis (CE) is a neglected zoonotic tropical disease caused by Echinococcus granulosus sensu lato. The aim of this study was to investigate the genetic variation of hydatid cyst isolates obtained from surgically confirmed paediatric cases originating from two different regions in eastern Turkey. Seventeen paediatric cases aged between 6 and 16 were operated by open surgery, and the germinal layers of their cysts were obtained for further molecular analyses. After genomic DNA isolation, 875 bp mt-CO1 gene fragments were amplified in all samples by PCR. Then, the unidirectional sequence analyses of the PCR products were carried out. According to the BLAST analyses of 17 sequences, 16 of these sequences were matched with E. granulosus sensu stricto, while one sequence was identified as E. canadensis (G6/G7) for the first time in paediatric cases in Turkey. High haplotype diversity and low nucleotide diversity were observed in the E. granulosus s.s. sequences.

Phylogeography, Population Structure, and Historical Demography of Black Drum in North America

AbstractThe Black Drum Pogonias cromis is an abundant estuarine‐dependent fish that supports recreational and commercial fisheries. We examined the phylogeography and historical demography of the Black Drum along the Atlantic and Gulf of Mexico coasts of the United States using mitochondrial DNA sequences and nuclear DNA microsatellites. Black Drum exhibited high haplotype diversity and low nucleotide diversity across its range. We observed 249 haplotypes that resolved into two haplogroups: haplogroup 1 was most abundant along the Texas coast, and haplogroup 2 was more abundant in the Atlantic Ocean and the eastern Gulf of Mexico. Analysis of molecular variance, pairwise estimates of genetic differentiation, assessment of isolation by distance, Bayesian clustering, and multivariate ordination indicated that most population structure within Black Drum was associated with a western Gulf of Mexico versus Atlantic–eastern Gulf of Mexico split. However, analysis of molecular variance, haplotype diversity, and measures of genetic differentiation provided evidence of weak population structure on the Texas coast, perhaps due to a of combination of isolation by distance and limited emigration into and dispersal from the upper and lower Laguna Madre on the lower coast. Mismatch distributions, neutrality tests, and Bayesian skyline plots suggest that haplogroup 1 underwent rapid demographic and range expansion approximately 15,000 years ago, whereas the demographic and range expansion of haplogroup 2 was more gradual and began earlier (circa 25,000–30,000 years ago). Our results suggest that Black Drum may benefit from being managed as two stocks: (1) western Gulf of Mexico and (2) Atlantic Ocean plus eastern Gulf of Mexico. Additionally, weak but significant genetic divergence in the Laguna Madre coincides with known life history divergence in this region. Caution should be used regarding the management of Black Drum in Texas as a single demographic unit.

Using Genealogical Concordance and Coalescent-Based Species Delimitation to Assess Species Boundaries in the Diaporthe eres Complex.

DNA sequence analysis has been of the utmost importance to delimit species boundaries in the genus Diaporthe. However, the common practice of combining multiple genes, without applying the genealogical concordance criterion has complicated the robust delimitation of species, given that phylogenetic incongruence between loci has been disregarded. Despite the several attempts to delineate the species boundaries in the D. eres complex, the phylogenetic limits within this complex remain unclear. In order to bridge this gap, we employed the Genealogical Phylogenetic Species Recognition principle (GCPSR) and the coalescent-based model Poisson Tree Processes (PTPs) and evaluated the presence of recombination within the D. eres complex. Based on the GCPSR principle, presence of incongruence between individual gene genealogies, i.e., conflicting nodes and branches lacking phylogenetic support, was evident. Moreover, the results of the coalescent model identified D. eres complex as a single species, which was not consistent with the current large number of species within the complex recognized in phylogenetic analyses. The absence of reproductive isolation and barriers to gene flow as well as the high haplotype and low nucleotide diversity indices within the above-mentioned complex suggest that D. eres constitutes a population rather than different lineages. Therefore, we argue that a cohesive approach comprising genealogical concordance criteria and methods to detect recombination must be implemented in future studies to circumscribe species in the genus Diaporthe.

Genetic diversity and transmission patterns of Echinococcus granulosussensu stricto among domestic ungulates of Sardinia, Italy

Cystic echinococcosis (CE), a parasitic zoonosis of public health and economic concern, is highly endemic in Sardinia, Italy. The study involved examining the intraspecific variability and demographic structure of Echinococcus granulosussensu stricto (s.s.) in common hosts of this parasite. Molecular surveillance included the fragment amplification of a partial mitochondrial gene, cox1 (750 bp), for a total of 69 isolates derived from sheep (n = 52), cattle (n = 11), pigs (n = 4), and goats (n = 2). It was ascertained that E. granulosus s.s. was the primary agent of infection among these ungulates and G1 genotype was highly prevalent (79.71%). Considerable intraspecific variation was found, revealing the existence of 22 haplotypes with relatively high haplotype (0.8555 ± 0.033) and low nucleotide diversities (0.00281 ± 0.00030). Population demographics indicated an expanding parasitic population signifying negative deviation from neutrality indices. Little genetic differentiation was found between the subpopulations of E. granulosus s.s. in the island. Moreover, the geographic dispersal of genotypes G1 and G3 also indicated similarity between Sardinian and mainland Echinococcus granulosus s.s. populations reaffirming the sympatric occurrence and efficient transmission of G1 and G3 genotypes. Molecular survey of CE has the potential to yield baseline information on the infective genotypes among the intermediate hosts and helps in devising suitable control strategies for curtailing the disease.

Forensic Genetic Analysis of Mitochondrial DNA Hypervariable Region III Sequences in Muslims from South India

The absence of recombination, high rate of mutation, and maternal inheritance of the mitochondrial DNA (mtDNA) genome makes it a valuable tool in many fields including evolutionary anthropology, genetic genealogy, population history, and forensic science. The mtDNA genome can be separated into two parts: a large coding region and a smaller fragment called the control region or non-coding region that generally referred to as displacement loop (D loop). The mtDNA D-loop region was highly polymorphic and has proven a precious marker in forensic identification. The study aims to examine and suggests polymorphism of the HVRIII region as a power marker along with HVRI and HVRII in forensic investigations. Within the control region of the mtDNA genome, the sequences of hypervariable region III (HVR III) (nucleotide position 438-574) were obtained from 60 unrelated Muslims of Shrirangapattana town, located in Karnataka state of South India. The complete mtDNA control region was amplified and sequenced by the Sanger sequencing method. The study provided the identification of 18 different haplotypes and 17 polymorphic nucleotide positions. The most common haplotype (H.18) was consistent with the Anderson sequence which occurred fourteen times. The distribution of nucleotide substitutions, insertions, and deletions was computed and determined that transitions made up the majority of the variations (58%) in this region. The genetic diversity was estimated at 0.89939 and the random match probability at 0.1155. The power of discrimination was found to be 0.8844 and the rest of the statistical parameters such as the mean of pair-wise differences and nucleotide diversity were established as 2.255932 ± 1.25884 and 0.010071± 0.00623, respectively. Consequently, the discovery of high genetic, haplotype, and nucleotide diversity, and high power of discrimination impart the use of hypervariable region III (HVR III) as an important marker in forensic investigations.

High genetic diversity of Giardia duodenalis assemblage E in Chinese dairy cattle.

Giardia duodenalis is a common protozoan parasite that can infect humans and animals. Although previous studies demonstrated that the assemblage E of G. duodenalis is prevalent in cattle, studies on its genetic diversity were mostly based on single loci and very few involved multilocus analysis. To better understand the genetic variability and structure of G. duodenalis assemblage E in Chinese dairy cattle, 651 multilocus sequences derived from nine provinces (Gansu, Guangdong, Henan, Jiangsu, Ningxia, Shaanxi, Shanghai, Sichuan and Xinjiang) of China were analyzed in this study. Results showed that a total of 220 haplotypes were identified in the G. duodenalis assemblage E, with a high haplotype diversity (Hd=0.97225) and low nucleotide diversity (π=0.00259). The genetic differentiation index (FST) and gene flow (Nm) results indicated low degree of genetic differentiation, implying frequent genetic communication. Combined with the analysis of molecular variance (AMOVA), genetic variation within populations (81.7%) was higher than that among populations (18.3%), indicating low degree of genetic differentiation between populations. Such low rates of gene differentiation supported no significant correlations with geographical divisions. Moreover, both negative Tajima's D and Fu's FS values of neutrality tests and unimodal curve of mismatch distribution analyses indicated that G. duodenalis assemblage E population in Chinese dairy cattle had experienced demographic expansion. Overall, these findings contribute to an improved understanding of the population genetics and evolutionary biology of G. duodenalis assemblage E and assist in its control in cattle.