Nucleotide Diversity Indices Research Articles

Distribution pattern and driving factors of genetic diversity of passerine birds in the Mountains of Southwest China

Genetic diversity is one of the three dimensions of biodiversity and fundamental to various life forms on the Earth. Understanding the distribution pattern of genetic diversity and its driving forces has been an important topic in ecology, biogeography and conservation biology since the last decade. We investigated the genetic diversity pattern of passerine birds in the Mountains of Southwest China, a global biodiversity hotspot with the highest species richness of birds in the entire Eurasia, and explored the influencing forces of environmental variables on genetic diversity. We compiled 1189 Cytochrome b sequences of 27 passerine species from 152 geographic sites, covering the range of Mountains of Southwest China and its adjoining areas. We generated genetic diversity distribution maps using a grid-cell method based on nucleotide diversity and haplotype diversity indices. We further analyzed the variation pattern of the two indices along latitudinal, longitudinal, and elevational gradients. The correlations between the two indices and environmental variables were also evaluated. The nucleotide diversity hotspots were mostly located in the southern Hengduan Mountains, while for haplotype diversity, three hotspots were detected: the southeast edge of the Qinghai-Tibetan Plateau, the southern Hengduan Mountains and the Qinling Mountains. There was no monotonic increasing or decreasing pattern in nucleotide diversity or haplotype diversity along latitudinal, longitudinal or elevational gradients except for altitudinal range. Correlation and model selection analyses detected multiple environmental variables in driving genetic diversity patterns, including temperature, precipitation, vegetation, human influence, longitude and altitude range. Similar to the pattern of species richness, the nucleotide diversity pattern of passerine birds in the Mountains of Southwest China presents a decreasing trend from southwest to northeast, while the haplotype diversity pattern is more likely decreased from west to east. Our results indicate that the distribution pattern of genetic diversity may be derived from the complex topography and diverse microclimates in the Mountains of Southwest China.

Genome-wide selective detection of Mile red-bone goat using next-generation sequencing technology.

The ecotype population of goats (Capra hircus) was created by long‐term artificial selection and natural adaptation. Mile red‐bone goat is an indigenous breed with visible red bones, and its special bone structure has received extensive attention. This study aimed to identify genetic variants and candidate genes associated with specific bone phenotypes using next‐generation sequencing technology (NGS). The results revealed that 31,828,206 single nucleotide polymorphisms (SNPs) were obtained from 72 goats (20 Mile red‐bone goats and 52 common goats) by NGS. A total of 100 candidate genes were identified on the basis top 1% window interaction from nucleotide diversity (π), π ratio (π A/π B), and pairwise fixation index (F ST). Exactly 77 known signaling pathways were enriched. Specifically, three coding genes (NMNAT2, LOC102172983, and PNLIP) were annotated in the vitamin metabolism signaling pathways, and NCF2 was annotated to the osteoclast (OC) differentiation pathway. Furthermore, 5862 reliable copy number variations (CNVs) were obtained, and 14 and 24 genes were annotated with the top 1‰ CNV based on F ST (>0.490) and V ST (>0.527), respectively. Several pathways related to bone development and metabolism of exogenous substances in vivo, including calcium signaling pathway, OC differentiation, and glycerophospholipid metabolism, were annotated. Specifically, six genes from 19 candidate CNVs, which were obtained by interaction of the top 1‰ CNVs with F ST and V ST, were annotated to mucin‐type O‐glycan biosynthesis and metabolic pathways. Briefly, the results implied that pseudopurpurin and specific genetic variants work together to contribute to the red‐bone color and specific bone structure of Mile red‐bone goat. This study is helpful to understanding the genetic basis of the unique bone phenotype of Mile red‐bone goats.

Genetic diversity and variation of seven Chinese grass shrimp (Palaemonetes sinensis) populations based on the mitochondrial COI gene

BackgroundChinese grass shrimp (Palaemonetes sinensis) is an important species widely distributed throughout China, which is ecologically relevant and possesses ornamental and economic value. These organisms have experienced a sharp decline in population due to overfishing. Therefore interest in P. sinensis aquaculture has risen in an effort to alleviate fishing pressure on wild populations. Therefore, we investigated the genetic diversity and variation of P. sinensis to verify the accuracy of previous research results, as well as to assess the risk of diversity decline in wild populations and provide data for artificial breeding.MethodsPalaemonetes sinensis specimens from seven locations were collected and their genetic variability was assessed based on mitochondrial COI gene segments. DNA sequence polymorphisms for each population were estimated using DNASP 6.12. The demographic history and genetic variation were evaluated using Arlequin 3.11. At last, the pairwise genetic distance (Ds) values and dendrograms were constructed with the MEGA 11 software package.ResultsOur study obtained sequences from 325 individuals, and 41 haplotypes were identified among the populations. The haplotype diversity (Hd) and nucleotide diversity (π) indices ranged from 0.244 ± 0.083 to 0.790 ± 0.048 and from 0.0004 ± 0.0001 to 0.0028 ± 0.0006, respectively. Haplotype network analyses identified haplotype Hap_1 as a potential maternal ancestral haplotype for the studied populations. AMOVA results indicated that genetic variations mainly occurred within populations (73.07%). Moreover, according to the maximum variation among groups (FCT), analysis of molecular variance using the optimal two-group scheme indicated that the maximum variation occurred among groups (53.36%). Neutrality and mismatch distribution tests suggested that P. sinensis underwent a recent population expansion. Consistent with the SAMOVA analysis and haplotype network analyses, the Ds and FST between the population pairs indicated that the JN population was distinctive from the others.ConclusionsOur study conducted a comprehensive characterization of seven wild P. sinensis populations, and our findings elucidated highly significant differences within populations. The JN population was differentiated from the other six populations, as a result of long-term geographical separation. Overall, the present study provided a valuable basis for the management of genetic resources and a better understanding of the ecology and evolution of this species.

Genetic Diversity and Relationships of Phalaenopsis Based on the rbcL and trnL-F Markers: In Silico Approach

In silico is the more comprehensive and applicable approach in supporting, both conservation and breeding programs of germplasm. The study aimed to analyze and determine the genetic diversity and relationships of 24 species of Phalaenopsis using two DNA barcoding markers, namely the rbcL and trnL-F, by in silico approach. All sequences of these markers were collected randomly from the NCBI website and analyzed using several softwares and methods, such as ClustalW and MultAlin for multiple sequence alignments and MEGA-X to determine its genetic diversity and relationships. Specifically, the genetic diversity was determined using a nucleotide diversity index and their relationships by the Maximum Likelihood method. The results showed that Phalaenopsis has a low genetic diversity of 0.24, 0.32, and 0.19, respectively. The phylogenetic analysis revealed that this orchid separated into five (for the rbcL), six (trnL-F), and seven clades (a combined one), where the closest relationship is shown by P. amboinensis vs. P. venosa, whereas the farthest by P. gibbosa vs. P. doweryensis, P. stuartiana vs. P. micholitzii, and P. celebensis vs. P. pulchra. The results have novel information on the diversity and relationships of Phalaenopsis on the in silico approach. Thus, our findings might be used in supporting the conservation and breeding program of Phalaenopsis, both locally and globally.

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.

Mitochondrial Genetic Diversity among Farmed Stocks of Oreochromis spp. (Perciformes, Cichlidae) in Madagascar

The fast development of aquaculture over the past decades has made it the main source of fish protein and led to its integration into the global food system. Mostly originating from inland production systems, aquaculture has emerged as strategy to decrease malnutrition in low-income countries. The Nile tilapia (Oreochromis niloticus) was introduced to Madagascar in the 1950s, and is now produced nationally at various scales. Aquaculture mostly relies on fry harvested from wild populations and grow-out in ponds for decades. It has recently been diversified by the introduction of several fast-growing strains. Little is known how local genetic diversity compares to recently introduced strains, although high and comparable levels of genetic diversity have previously been observed for both wild populations and local stocks. Our study compares DNA barcode genetic diversity among eight farms and several strains belonging to three species sampled. DNA-based lineage delimitation methods were applied and resulted in the detection of six well differentiated and highly divergent lineages. A comparison of DNA barcode records to sequences on the Barcode of Life Data System (BOLD) helped to trace the origin of several of them. Both haplotype and nucleotide diversity indices highlight high levels of mitochondrial genetic diversity, with several local strains displaying higher diversity than recently introduced strains. This allows for multiple options to maintain high levels of genetic diversity in broodstock and provides more options for selective breeding programs.

Genome-wide selection signal analysis of Australian Boer goat reveals artificial selection imprinting on candidate genes related to muscle development.

As one of the best-known commercial goat breeds in the world, Boer goat has undergone long-term artificial selection for nearly 100years, and its excellent growth rate and meat production performance have attracted considerable worldwide attention. Herein, we used single nucleotide polymorphisms (SNPs) called from the whole-genome sequencing data of 46 Australian Boer goats to detect polymorphisms and identify genomic regions related to muscle development in comparison with those of 81 non-specialized meat goat individuals from Europe, Africa, and Asia. A total of 13795202 SNPs were identified, and the whole-genome selective signal screen with a π ratio of nucleotide diversity (πcase /πcontrol ) and pairwise fixation index (FST ) was analyzed. Finally, we identified 1741 candidate selective windows based on the top 5% threshold of both parameters; here, 449 candidate genes were only found in 727 of these regions. A total of 433 genes out of the 449 genes obtained were annotated to 2729 gene ontology terms, of which 51 were directly linked to muscle development (e.g., muscle organ development, muscle cell differentiation) by 30 candidate genes (e.g., JAK2, KCNQ1, PDE5A, PDLIM5, TBX5). In addition, 246 signaling pathways were annotated by 178 genes, and two pathways related to muscle contraction, including vascular smooth muscle contraction (ADCY7, PRKCB, PLA2G4E, ROCK2) and cardiac muscle contraction (CACNA2D3, CASQ2, COX6B1), were identified. The results could improve the current understanding of the genetic effects of artificial selection on the muscle development of goat. More importantly, this study provides valuable candidate genes for future breeding of goats.

Genetic differentiation of dengue vector Aedes aegypti in the small geographical scale of Banyumas District, Indonesia based on Cytochrome Oxidase I

Abstract. Mohammed MA, Nuryanto A, Kusmintarsih ES. 2021. Genetic differentiation of dengue vector Aedes aegypti in the small geographical scale of Banyumas District, Indonesia based on Cytochrome Oxidase I. Biodiversitas 22: 675-683. Aedes aegypti (Linnaeus, 1762) is a major vector of arboviruses. Currently, Ae. aegypti is spreading throughout the Banyumas District, Central Java, Indonesia and there is little information regarding the genetic variation of this species, yet the information is essential to develop effective vector control measures. The aims of this study was to evaluate the genetic differentiation of Ae. aegypti populations in South Purwokerto and Cilongok subdistricts. Mosquito larvae were collected using oviposition traps inside houses in South Purwokerto and Cilongok (Jastaba village). Twenty larvae of Ae. aegypti, ten from each location were identified and used for genetic analysis. Analysis of mitochondrial cytochrome Oxidase I (mtCOI) produced around 600 bp fragments, detecting ten haplotypes. The haplotype diversity and nucleotide diversity indices were higher in South Purwokerto samples. Tajima and Fu’s statistics indicated that the sampled populations were in genetic equilibrium. Indices of demographic history were fit for a spatial expansion model. Higher genetic variation was observed within the population compared to between the populations. Furthermore, strong genetic difference was detected between the two populations, with highly significant FS (p < 0.0001). Weak haplotype sharing occurred between the two populations assuming that the gene flow was facilitated by human transportation. All haplotypes were a cluster of single clades and closely related to haplotypes generated from previous studies in Central Java.

Genetic Mapping and Nucleotide Diversity of Two Powdery Mildew Resistance Loci in Melon (Cucumis melo).

Powdery mildew (PM) significantly and negatively affects the yield and quality of melon (Cucumis melo) worldwide. Race 2F is the predominant physiological race of the pathogen Podosphaera xanthii in many regions. We used accessions PMR 6 (P1; resistant to PM) and M1-7 (P2; susceptible to PM) to analyze the inheritance of resistance to PM (race 2F). The ratio between resistant and susceptible individuals fits a Mendelian segregation ratio of 13:3 in a total of 256 F2 individuals and 1:1 in BC1P2. The resistance to PM in PMR 6 was governed by two genes: a dominant (AA) gene with an epistatic effect and a recessive gene (bb). Only individuals with aaBB or aaBb genotypes were susceptible to PM. Two PM resistance loci, Pm2.1 and pm12.1, were mapped on chromosomes 2 and 12 by bulked segregant analysis and secondary mapping by quantitative trait loci analysis with 18 markers. A new marker-assisted selection system to identify melon genotypes resistant or susceptible to PM was developed and tested in 93 melon accessions. Nucleotide diversity (π) and fixation index (Fst) for the two PM resistance loci were estimated using resequencing data of 336 melons from three groups: C. melo subsp. agrestis, Cucumis melo subsp. melo, and the intermediate type. The lowest π was observed in C. melo ssp. agrestis, and the highest Fst value was between C. melo ssp. agrestis and C. melo ssp. melo. The findings provide a promising tool that can be used to accelerate breeding for durable resistance to PM.

Comprehensive analysis of mitochondrial DNA based genetic diversity in Indian goats.

Thirty four distinct breeds and many non-descript populations represent the caprine diversity of India. Genetic characterization of breeds is an essential element in designing breeding strategies and preserving genetic diversity. Considering the popularity of mitochondrial DNA for phylogeographical studies, this study involved an extensive analysis of population structure and genetic diversity of 28 defined breeds and 5 lesser known populations representing all four major agro-climatic zones of India using mitochondrial DNA markers. Analysis of hypervariable region 1 of mtDNA control region in 443 goats together with 22 reference sequences, delineated 341 distinct haplotypes belonging to four maternal haplogroups; A, B, C and D, with haplogroup A representing 90% of the individuals. The haplotype and nucleotide diversity indices of Indian goats were 0.998±0.001 and 0.028±0.001, respectively indicating abundant genetic variability. Estimates of population demographic parameters from mismatch analysis suggested a relatively good fit to the model of either spatial or demographic expansion of Indian goats. AMOVA analysis and topology of MJ network suggested lack of phylogeographic structure in domestic goats, which can be attributed to unstructured animal breeding, dwindling pastures and nomadic pastoralism. Genetic differentiation between goats from different agro-ecological regions was in accordance with their geographical propinquity.

Genome scan detection of selective sweeps among biotypes of the soybean aphid, Aphis glycines, with differing virulence to resistance to A. glycines (Rag) traits in soybean, Glycine max

Multiple biotypes of soybean aphid, Aphis glycines, occur in North America adapted for survival (virulence) on soybean, Glycine max, with one or more different resistance to A. glycines (Rag) traits. The degree of genome-wide variance between biotypes and the basis of virulence remains unknown, but the latter is hypothesized to involve secreted effector proteins. Between 167,249 and 217,750 single nucleotide polymorphisms (SNPs) were predicted from whole genome re-sequencing of A. glycines avirulent biotype 1 (B1) and virulent B2, B3 and B4 colony-derived iso-female lines when compared to the draft B1 genome assembly, Ag_bt1_v6.0. Differences in nucleotide diversity indices (π) estimated within 1000 bp sliding windows demonstrated that 226 of 353 (64.0%) regions most differentiated between B1 and ≥ 2 virulent biotypes, representing < 0.1% of the 308 Mb assembled genome size, are located on 15 unordered scaffolds. Furthermore, these 226 intervals were coincident and show a significant association with 326 of 508 SNPs with significant locus-by-locus FST estimates between biotype populations (r = 0.6271; F1,70 = 45.36, P < 0.001) and genes showing evidence of directions selection (πN/πS > 2.0; r = 0.6233; F1,70 = 50.20, P < 0.001). A putative secreted effector glycoprotein is encoded in proximity to genome intervals of low estimated π (putative selective sweep) within avirulent B1 compared to all three virulent biotypes. Additionally, SNPs are clustered in or in proximity to genes putatively involved in intracellular protein cargo transport and the regulation of secretion. Results of this study indicate that factors on a small number of scaffolds of the A. glycines genome may contribute to variance in virulence towards Rag traits in G. max.

Purifying selection shaping the evolution of the Toll-like receptor 2 TIR domain in brown hares (Lepus europaeus) from Europe and the Middle East

Toll-like receptors (TLRs) are transmembrane proteins of the innate immune system, composed of the ectodomain involved in pathogen recognition and the intracellular Toll/interleukin-1 receptor (TIR) domain important for downstream signal transduction. Here, we analyze the genetic variability of TIR nucleotide and amino-acid sequences of the TLR2 gene in 243 brown hares from Europe and the Middle East and tested for the presence of selection signals and spatial structuring. TLR2 TIR domain sequences were PCR amplified and sequenced, while genotyping was performed by phasing. Genetic diversity indices were calculated in DnaSP and Arlequin, while presence of selection signals was tested using MEGA and the Datamonkey web server. The presence of spatial patterns in TIR sequence distribution was tested by spatial Principal Component Analysis (sPCA) in adegenet. A total of 13 haplotypes were revealed with haplotype diversity of 0.424, and nucleotide diversity (π) of 0.00138. Two spatial clusters were revealed: "Anatolia/Middle East" and "Europe". In Anatolia the two most prevalent amino-acid variants, A and B (the latter being the most ancestral) were maintained at similar frequencies; but in Europe a shift in genotype frequencies was observed as well as a higher number of nonsynonymous substitutions giving rise to novel amino-acid protein variants originating from the evolutionarily younger protein variant. Molecular diversity (haplotype and nucleotide diversity) indices were significantly higher in the "Anatolia/Middle East" cluster. A signal of purifying selection was detected acting on the TIR sequences.

Genotyping and Genetic Diversity Analysis of 47 Flowering Cherry (&lt;I&gt;Cerasus&lt;/i&gt;) Germplasms

In order to provide a theoretical basis for conservation and utilization of excellent flowering cherry germplasms, genetic diversity and genotype were analyzed based on single nucleotide polymorphism (SNP) molecular markers. A total of 47 germplasms were sequenced using&nbsp;restriction site-associated DNA sequencing (RAD-Seq) method, and highly consistent SNP sites have been identified for genetic diversity analysis and genotyping. The RAxML program was used for phylogenetic tree construction, based on the maximum likelihood (ML) method. The ADMIXTURE software was used to analyze genetic structure. The GCTA software was used for principal component analysis. Genetic diversity parameters, includes nucleotide diversity (&pi; value), expected heterozygosity (exp &nbsp;He ) and genetic differentiation index ( F ST ), were carried out using the PopGenome and Arlequin 3.0 software. A total of 79 667 highly consistent SNPs were obtained, after genotype integrity filtering and closely linked sites screening. According to the phylogenetic, principal components and population structure analysis results, the 47 germplasms could be divided into eight genetic clusters. The &pi; and&nbsp;exp &nbsp;He &nbsp;value of each cluster was as follows: I: 0.128 19, 0.119 94; II: 0.139 64, 0.130 55; III: 0.21 55, 0.164 73; IV: 0.086 82, 0.061 22; V: 0.095 49, 0.069 73; VI: 0.191 22, 0.10 61; VII: 0.16 85, 0.158 78; VIII: 0.290 98, 0.183 43. The cluster IV and V presented the largest genetic differentiation, with an&nbsp; F ST value of 0.4612 89, followed by IV and VI, with an&nbsp; F ST &nbsp;value of 0.456 958; the lowest genetic differentiation existed between the cluster VII and VIII, with an&nbsp; F ST &nbsp;value of 0.0976 13. Except for cluster VII and VIII, the genetic differentiation among the other clusters was at or above the medium level. The results of genotyping showed that there were 29 individuals (61.70 %) with single genetic component, and 18 individuals (38.30 %) with two or three genetic components. Based on the results of genetic components analysis, there were four potential interspecific hybridizations. There was a high genetic diversity among 47 flowering cherry germplasms, obvious genetic differentiation among the eight clusters. The genetic components of natural hybrid individuals and artificial hybrid cultivars were revealed, and their parents were inferred, based on the genotyping results.&nbsp

Mitochondrial DNA reveals low genetic diversity in Ecuadorian Andean bears

Few studies have analyzed the genetics of Andean bear (Tremarctos ornatus) populations through the use of the hypervariable D-Loop mitochondrial region. This approach can be useful for the assessment of genetic diversity and ancestral lineages. In the present study we evaluate the genetic status of an Andean bear population in northern Ecuador using D-loop mtDNA sequence polymorphisms. For this purpose, DNA from individuals sampled in the Metropolitan District of Quito was used to amplify and sequence a fragment of the hypervariable D-loop region. Our results show remarkably low levels of genetic diversity, based on haplotype (H) and nucleotide (π) diversity indices, and low pairwise genetic distances between haplotypes. Phylogenetic analyses suggest that these haplotypes are clustered into a single monophyletic group. These diversity indices are among the lowest reported for any bear population, suggesting a need to establish or revise the current conservation strategies in the region.

Genetic diversity and population structure of malaria vector mosquitoes Anopheles subpictus, Anopheles peditaeniatus, and Anopheles vagus in five districts of Sri Lanka

BackgroundAlthough Sri Lanka is considered as a malaria-free nation, the threat of re-emergence of outbreaks still remains due to the high prevalence and abundance of malaria vectors. Analysis of population genetic structure of malaria vectors is considered to be one of the vital components in implementing successful vector control programmes. The present study was conducted to determine the population genetic structure of three abundant malaria vectors; Anopheles subpictus sensu lato (s.l.), Anopheles peditaneatus and Anopheles vagus from five administrative districts in two climatic zones; intermediate zone (Badulla and Kurunegala districts) and dry zone (Ampara, Batticoloa and Jaffna districts) of Sri Lanka using the mitochondrial gene, cytochrome c oxidase subunit I (COI).MethodsAdult mosquitoes of An. subpictus s.l., An. peditaeniatus, and An. vagus were collected from five study sites located in five districts using cattle baited traps and backpack aspirators. Representative samples of each species that were morphologically confirmed were selected from each locality in generating COI sequences (> 6 good quality sequences per species per locality).ResultsAnopheles subpictus s.l. specimens collected during the study belonged to two sibling species; An. subpictus ‘A’ (from all study sites except from Jaffna) and An. subpictus ‘B’ (only from Jaffna). The results of haplotype and nucleotide diversity indices showed that all the three species are having high genetic diversity. Although a high significant pairwise difference was observed between An. subpictus ‘A’ and ‘B’ (Fst> 0.950, p < 0.05), there were no significant genetic population structures within An. peditaeniatus, An. vagus and An. subpictus species A (p > 0.05), indicating possible gene flow between these populations.ConclusionsGene flow among the populations of An. peditaeniatus, An. vagus and An. subpictus species A was evident. Application of vector control measures against all mosquito species must be done with close monitoring since gene flow can assist the spread of insecticide resistance genes over a vast geographical area.

Global sequence diversity of the lactate dehydrogenase gene in Plasmodium falciparum

BackgroundAntigen-detecting rapid diagnostic tests (RDTs) have been recommended by the World Health Organization for use in remote areas to improve malaria case management. Lactate dehydrogenase (LDH) of Plasmodium falciparum is one of the main parasite antigens employed by various commercial RDTs. It has been hypothesized that the poor detection of LDH-based RDTs is attributed in part to the sequence diversity of the gene. To test this, the present study aimed to investigate the genetic diversity of the P. falciparum ldh gene in Thailand and to construct the map of LDH sequence diversity in P. falciparum populations worldwide.MethodsThe ldh gene was sequenced for 50 P. falciparum isolates in Thailand and compared with hundreds of sequences from P. falciparum populations worldwide. Several indices of molecular variation were calculated, including the proportion of polymorphic sites, the average nucleotide diversity index (π), and the haplotype diversity index (H). Tests of positive selection and neutrality tests were performed to determine signatures of natural selection on the gene. Mean genetic distance within and between species of Plasmodium ldh was analysed to infer evolutionary relationships.ResultsNucleotide sequences of P. falciparum ldh could be classified into 9 alleles, encoding 5 isoforms of LDH. L1a was the most common allelic type and was distributed in P. falciparum populations worldwide. Plasmodium falciparum ldh sequences were highly conserved, with haplotype and nucleotide diversity values of 0.203 and 0.0004, respectively. The extremely low genetic diversity was maintained by purifying selection, likely due to functional constraints. Phylogenetic analysis inferred the close genetic relationship of P. falciparum to malaria parasites of great apes, rather than to other human malaria parasites.ConclusionsThis study revealed the global genetic variation of the ldh gene in P. falciparum, providing knowledge for improving detection of LDH-based RDTs and supporting the candidacy of LDH as a therapeutic drug target.

Genetic diversity of six silver carp ( Hypophthalmichthys molitrix ) geographical populations based on mitochondrial COI sequences

PDF HTML阅读 XML下载 导出引用 引用提醒 基于COI序列的长江中上游鲢6个地理群体遗传多样性分析 DOI: 作者: 作者单位: 1. 中国水产科学研究院长江水产研究所, 湖北 武汉 430223;2. 农业农村部水生动物基因组学重点实验室, 湖北 武汉 430223 作者简介: 沙航(1991-),男,硕士,研究方向为水产动物种质资源与遗传育种.E-mail:ikriss@163.com 通讯作者: 中图分类号: S917 基金项目: 科技部科技基础性工作专项（2013FY110700）；中国水产科学研究院基本科研业务费项目（2014A11，2016HY-JC03）；现代农业产业技术体系建设专项（CARS-46-01）. Genetic diversity of six silver carp (Hypophthalmichthys molitrix) geographical populations based on mitochondrial COI sequences Author: Affiliation: 1. Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China;2. Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Wuhan 430223, China Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:为了对长江中上游鲢（）种质资源现状进行监测和评价，本研究利用线粒体细胞色素C氧化酶I（cytochrome c oxidase subunit I）基因（COI）对长江中上游宜宾、忠县、万州、石首、监利、湘江6个鲢群体进行了遗传多样性分析。结果表明，在648 bp的COI序列中共检测到42个变异位点，其中单变异位点14个，简约信息位点28个。6个群体123个个体共定义了26个单倍型，单倍型多样性为0.0476~0.0945，核苷酸多样性为0.00196~0.00982。6个鲢群体总体遗传多样性丰富，万州群体单倍型多样性和核苷酸多样性均最高，忠县群体单倍型多样性最低，核苷酸多样性最低的为石首群体。遗传变异主要来自群体内个体间，单倍型网络图和系统进化树显示各群体的单倍型没有形成明显的地理格局。此外，上游宜宾群体和万州群体与中游的石首、监利和湘江群体具有明显的遗传分化，中游的监利群体与石首群体和湘江群体也有一定的遗传分化，上游群体和中游群体应该分属于长江水系两个不同的种群。 Abstract:The silver carp (), one of the four major Chinese carps, is widely distributed in the Yangtze, Pearl, and Heilongjiang River Basins of China. The wild silver carp populations in the Yangtze River, with an excellent production performance, is an important germplasm resource for artificial farming and breeding. Because of overfishing, habitat fragmentation, and water pollution, the natural carp populations have been continuously declining in recent years. The basic genetic background analysis of the silver carp would be theoretically and practically important for the conservation of germplasm resources and genetic improvement. In this study, mitochondrial cytochrome C oxidase subunit I gene (COI) was sequenced to determine the genetic diversity and variation of six geographical silver carp populations:Yibin, Zhongxian, Wanzhou, Shishou, Jianli, and Xiangjiang. The amplified fragment was 648 bp in length, and a total of 26 haplotypes were defined among 123 sequences of COI from the six silver carp populations. The haplotype and nucleotide diversity index of the six populations ranged from 0.0476 to 0.0945, and from 0.00196 to 0.00982, respectively. The six groups exhibited a high genetic diversity, of which the Wanzhou population showed the highest haplotype and nucleotide diversities; the lowest haplotype and nucleotide diversities were observed in the Zhongxian and Shishou populations, respectively. The molecular variance (AMOVA) analysis showed that the variation within populations (accounting for 88.72%) was the main source of variation, and only 11.28% of the variation was found among the groups. The haplotype network was radial, centering on the main haplotype. The neighbor-joining phylogenetic tree of haplotypes based on genetic distances were inconsistent with their geographical distances. According to the differentiation index (, there were high differences between the Yinbin, Wanzhou, and 3 populations from the middle reach ( < 0.05); meanwhile, the Jianli population showed a significant differentiation from the Shishou and Xiangjiang populations ( < 0.01). The results revealed that the upper-and middle-reach populations should have originated from different populations in the Yangtze River. This study could provide useful basic data for the scientific protection, and reasonable and sustainable utilization of this germplasm resource in the Yangtze River Basin. 参考文献 相似文献 引证文献

Mitochondrial Genetic Diversity and Phylogeography ofMus musculus castaneusin Northern Punjab, Pakistan

Regions of Iran, Afghanistan, Pakistan and northwestern India have been proposed as the place of origin of Mus musculus castaneus. But despite the fact that Pakistan encompasses an important part of its range, M. m. castaneus populations in Pakistan have not been the subject of intensive genetic and biogeographic studies, except for a very small number of samples included in past studies. We studied genetic variation in M. m. castaneus (CAS) from northern Punjab Province, Pakistan, by using cytochrome b (Cytb) analysis in a sample of 98 individuals. Median-joining network revealed four well differentiated CAS sub-lineages coexisting within a small geographical region; these had previously been thought to have largely non-overlapping geographic distributions. Moreover, haplotypes from Pakistan occupied a central position in the network and all identified global haplotypes were also present in Pakistan. All identified CAS sub-lineages proved to be highly diverse on the basis of haplotype and nucleotide diversity indices. Tajima's D test and Fu's Fs tests of neutrality suggest recent population expansions in all sub-lineages. Expansion times were estimated as 21,760-134,930, 10,800-64,400 and 4950-30,665 ybp using substitution rates of 2.5%, 5% and 11%, respectively. Our results support the hypothesis that northern Punjab Province in Pakistan is the most likely source area for M. m. castaneus, and that the CAS sub-lineages in this region have undergone rapid population expansion events at different time periods, which appear to have benefitted from human-mediated transport, although one of them clearly predates the establishment of human settlements in this region.

Genetic Diversity and Prevalence ofLeishmania mexicanainBichromomyia olmeca olmecain an Endemic Area of Mexico

Leishmaniases are endemic in southwestern Mexico, and different sand fly species are infected with Leishmania mexicana Biagi. One of the most abundant vectors and dominant species is Bichromomyia olmeca olmeca (Vargas and Diaz-Najera). We analyzed the genetic variability of Bichromomyia olmeca olmeca and the prevalence of Leishmania mexicana infections with an endemic focus: “the Ejido 20 de Junio” (Mancolona), Campeche, Mexico, where patients with leishmaniases are reported throughout the year. Genetic diversity analysis of 102 sequences of a 270-bp fragment of the 3´ end of mitochondrial cytochrome b (cyt b) gene of Bichromomyia olmeca olmeca revealed 17 haplotypes. The nucleotide diversity and nucleotide polymorphism index were low. The neutrality test and Mismatch test showed population expansion. Prevalence of Leishmania mexicana was 24.5% in 102 females analyzed. This is the first study showing the genetic diversity of Bichromomyia olmeca olmeca sand flies in the Campeche region of Mexico, and also provides novel information on the high infection rate of Bichromomyia olmeca olmeca by Leishmania mexicana. Our finding of high sand fly infection rates during the end of the dry and hot weather of July enriches the literature because high infection rates had been reported only during the rainy season (November) in the region.

A genome-wide survey with different rapeseed ecotypes uncovers footprints of domestication and breeding.

Rapeseed (Brassica napus L.) is an important oilseed crop. Despite a short period of domestication and breeding, rapeseed has formed three diverse ecotype groups, namely spring, winter, and semi-winter. However, the genetic changes among the three ecotype groups have remained largely unknown. To detect selective signals, a set of 327 accessions from a worldwide collection were genotyped using a Brassica array, producing 33 186 high-quality single nucleotide polymorphisms (SNPs). Linkage disequilibrium (LD) was unevenly distributed across the genome. A total of 705 (78.2%) weak LD regions were found in the A subgenome, whereas 445 (72.6%) strong LD regions were in the C subgenome. By calculating the nucleotide diversity and population differentiation indices, a total of 198 selective sweeps were identified across ecotype groups, spanning 5.91% (37.9 Mb) of the genome. Within these genome regions, a few known functional genes or loci were found to be in association with environmental adaptability and yield-related traits. In particular, all 12 SNPs detected in significant association with flowering time among accessions were in the selection regions between ecotype groups. These findings provide new insights into the structure of the B. napus genome and uncover the footprints of domestication and breeding.