Haplotype Diversity Research Articles

Colletotrichum (Sordariomycetes, Glomerellaceae) species associated with Citrus in Guangdong Province, China

ABSTRACT Colletotrichum species have diverse lifestyles, which can change from endophytic to pathogenic and other lifestyles such as saprobic. However, the exact mechanism of lifestyle changes is unknown. Over 20 Colletotrichum species cause citrus anthracnose worldwide and are also associated with the various Citrus species as endophytes in leaves, shoots, and fruits. The objective of this study was to explore the endophytic diversity associated with four species (Citrus reticulata, Citrus tachibana, Citrus nobilis Lour. Gonggan, and Citrus maxima (Burm.) Merr. cv. Shatian Yu) in Guangdong Province. This study collected 96 leaf and immature fruit samples from four Citrus species. In total, 183 Colletotrichum isolates were obtained, and based on multigene phylogenetic analysis of ITS, act, chs-1, gapdh and tub2 with morphology, nine known species viz. C. citricola, C. fructicola, C. gigasporum, C. gloeosporioides, C. karsti, C. plurivorum, C. siamense, C. tropicicola, and C. truncatum were identified. Herein, we report seven new hosts and six new geographical records. Among these, C. karsti and C. gloeosporioides are the most isolated species. Based on the diversity data analysis, C. gloeosporioides shows more than 0.5 haplotype diversity in the act, chs-1, ITS, and combined data sets. However, C. karsti showed a low haplotype diversity (Hd < 0.5) for single gene regions (ITS, act, chs-1, gapdh and tub2) and combined analysis (ITS + act + chs-1 + gapdh + tub2). Six Colletotrichum species were isolated from Citrus maxima and Citrus nobilis, respectively, five Colletotrichum species were isolated from Citrus tachibana, and three Colletotrichum species were isolated from Citrus reticulata. Our study reflects the rich Colletotrichum diversity associated with Citrus species in China. Furthermore, we emphasise that it is necessary to understand the intra-species diversity of Colletotrichum taxa while introducing new species in the future.

Chimeric CYP21A1P/CYP21A2 Genes in 21-Hydroxylase Deficiency Detected by Long-Read Sequencing and Phenotypes Correlation.

21-Hydroxylase deficiency (21-OHD) is caused by pathogenic variants in CYP21A2. High homology between CYP21A2 and its pseudogene CYP21A1P causes mismatches, leading to deletions and CYP21A1P/CYP21A2 chimeras. To detect chimeric CYP21A1P/CYP21A2 in 21-OHD patients using long-read sequencing (LRS) and analyze genotype-phenotype correlations. From 2015 to 2023, 869 21-OHD patients were enrolled at Peking Union Medical College Hospital, with 113 identified harboring CYP21A2 large deletion. Long-range PCR and LRS were used to identify the types of CYP21A1P/CYP21A2 chimeric. Haplotype analysis explored founder effects, and in vitro assays assessed the functional impact of novel mutations. Clinical data were retrospectively collected and patients were classified into 4 groups based on genotypes and residual enzyme activity to study genotype-phenotype correlations. Ten types of chimeric CYP21A1P/CYP21A2 genes were identified across 119 alleles, including a novel type, CH-10. The most common, CH-1, accounted for 50.4% of all types. Haplotype analysis of 24 SNPs within CYP21A1P/CYP21A2 CH-1 revealed 25 haplotypes, with haplotype 11 being the most prevalent. Variants p.L100P and p.L301V of CYP21A2 showed enzyme activities of 1.36 ± 0.44% or 1.63 ± 0.19% for 17-hydroxyprogesterone to 11-deoxycortisol, and 1.36 ± 0.58% or 3.99 ± 1.09% for progesterone to 11-deoxycorticosterone, respectively, linked to the simple virilizing type. Genotype-phenotype consistency rates were 78.6% to 84% across the 4 groups. LRS is a comprehensive genetic testing method for 21-OHD patients, effectively detecting both CYP21A2 gene variants and CYP21A1P/CYP21A2 chimeric gene types. This study expands the CYP21A2 variant spectrum by identifying a novel chimera. Haplotype analysis revealed diverse haplotypes for each chimeric gene type, suggesting the absence of a common founder effect. The strong genotype-phenotype correlation aids genetic counseling and supports personalized treatment.

Spatial and Genetic Diversity of Clinical Isolates of Blastocystis in Italy: A Network Analysis

Blastocystis is a common intestinal protist with a global distribution, frequently found in humans and various animals. Despite its prevalence, its role in human health remains debated, oscillating between being a harmless commensal and a potential pathogen. It has also been associated with gastrointestinal disorders such as irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). In Italy, the genetic and spatial diversity of Blastocystis remains understudied, despite the country’s diverse urbanized and environmental landscapes. This study investigates the haplotypic and spatial diversity of clinical isolates of Blastocystis across two different Italian regions, with an emphasis on subtype distribution and genetic variation. Using a network-based haplotype analysis, the study reveals a heterogeneous subtype distribution, with subtype ST4 (47.3%) being the most prevalent, followed by ST3 (20%), ST1 (16.4%), ST2 (12.7%), ST6 (1.8%) and ST7 (1.8%). The overall infection rate detected from symptomatic patients is 9.75%. Notably, ST4 shows limited haplotypic variation, suggesting a more stable population structure that is potentially linked to a human-adapted lineage. In contrast, ST1 and ST2 exhibit greater haplotypic diversity, likely due to ongoing zoonotic transmission. These findings enhance our understanding of the epidemiology of Blastocystis in Italy and underscore the need for further research on its pathogenic potential and transmission dynamics.

Genetic Diversity of Sand Fly (Phlebotomus papatasi) in Al‐Madinah Al‐Munawarah Region of Saudi Arabia

ABSTRACTSand flies called Phlebotomus papatasi are the primary vector of cutaneous leishmaniasis, which is an endemic disease in Al‐Madinah Al‐Munawarah, Saudi Arabia. The molecular characterization of sand fly species is a helpful tool because genetic variability and population structure within and between populations might influence vectoral capability, necessitating the assessment of management strategies to control the spread of cutaneous leishmaniasis. Therefore, in this study, the structure of the P. papatasi population in Al‐Madinah region was investigated. The samples of P. papatasi were collected from Al‐Madinah region, identified, and subjected to mitochondrial cytochrome b (Cytb) gene sequencing (n = 45). Analysis of the sequences revealed 13 substitutions. There were 12 different haplotypes identified. Nucleotide diversity and haplotype diversity were low estimated to be 0.0017 and 0.574, respectively. The neutrality indices determined using Tajima's D and Fu and Li's F* were all negative and statistically significant. This indicated that the population has an excess of singletons and low‐frequency variations. Network analysis showed one main haplotype and shared haplotypes at different nodes. According to this study, the P. papatasi population in the Al‐Madinah region is homogeneous. The knowledge obtained in this study contributes to a better understanding of the genetic geographic distribution of P. papatasi populations in relation to the location of Leishmania major foci, which could aid in the development of control strategies.

Taenia asiatica: Mitochondrial signatures based analysis of an emerging public health threat in India.

Taenia asiatica is a zoonotic tapeworm, commonly known as Asian Taenia. It is an emerging sister species of T. saginata with pigs as intermediate hosts. The present study aimed at genetic characterization and population structure analysis of T. asiatica metacestodes in slaughtered pigs in Haryana, north India. In total, the vital organs of 253 slaughtered pigs were screened for the presence of T. asiatica metacestodes. The molecular identification and phylogenetics were performed targeting the mitochondrial NADH dehydrogenase subunit 1 (nad1) and cytochrome C oxidase subunit 1 (cox1) genes. The median-joining haplotype network and population structure analyses were performed with the sequences generated herein and GenBank-archived T. asiatica sequences for both mitochondrial signatures. Out of 253 pigs screened, the liver of only one animal showed the presence of T. asiatica metacestodes. The sequences generated herein exhibited 99.60% and 98.85% similarity to the GenBank-archived sequences of T. asiatica corresponding to the nad1 and cox1 genes, respectively. Overall, 2 and 6 haplotypes for the overall data set with low nucleotide (0.00399±0.00237 and 0.00095±0.00042) and low haplotype (0.400±0.237 and 0.131±0.054) diversities were recorded for the nad1 and cox1 genes, respectively. The negative values recorded for the neutrality indices exhibited deviations from neutrality and hence, propounded recent population expansion or purifying selection or selective sweep. The findings of the present study are of significant medical importance considering an emerging global public health threat of the neglected tapeworm T. asiatica.

Allelic and haplotype diversity of 12 X-chromosomal short tandem repeats in Koreans, with an analysis of anomalous profiles.

Owing to the unique inheritance pattern of theXchromosome, X-chromosomal short tandem repeat (X-STR) analysis represents a valuable tool in forensic DNA examination-particularly in complex kinship cases, missing person investigations, and disaster victim identification. We analyzed buccal swabs from 429 unrelated Korean males for forensic statistical parameters of 12 X-STRs. Among the 427 individuals analyzed (2 were excluded), DXS10135 was the most informative marker (polymorphism information content [PIC]=0.9131) and DXS7423 the least informative (PIC=0.4250). When analyzed based on the four linkage groups (LGs), each individual had unique 12 X-STR haplotypes, with LG1 showing the highest haplotype diversity (0.9968) and the most common haplotype frequency (0.0164). LG1 was also the most informative (PIC=0.9945), followed by LG3, LG4, and LG2 (with haplotype diversities of 0.9882-0.9968). Our analysis shows that Koreans clustered with East Asians, displayed strong genetic similarity, but differed significantly from Emirati Arabs, Brazilians, Argentinians, and Europeans, forming three distinct clusters influenced by historical and geographical factors. Within the examined X-STR haplotypes, biallelic patterns were identified in two instances: one involved a duplication at DXS10146, as indicated by relative peak height and normalized peak height ratio analysis, and the other encompassed eight loci, where balanced peak heights (72.51%) and anXpeak height imbalance at the amelogenin locus (59.69%) were indicative of Klinefelter syndrome with sex chromosome aneuploidy. The 12 X-STR loci are informative and discriminatory in the Korean population, providing critical insights for forensic applications and genetic research.

Several variants on chromosome 10 are associated with coarse hair diameter in Dazu black goats (Capra hircus).

Goats typically have double coats, with the outermost coarse hairs providing protection against mechanical and radiation damage. While much attention has been paid to cashmere due to its status as a high-end textile material, there is limited information available on coarse hair. This study aimed to identify genomic variants, such as single nucleotide polymorphisms (SNPs) and insertion/deletions (indels), associated with coarse hair diameter using a genome-wide association study (GWAS). Coarse hairs and blood samples were collected from 263 adult female goats. The diameter of coarse hairs was measured using an inverted microscope, and whole genome sequencing was conducted on the blood samples. After reads mapping, variants calling, and quality control, totals of 11 322 006 SNPs and 863 734 indels were included for SNP-GWAS and indel-GWAS analyses. Eight significant SNPs (p < 8.98e-8) and three significant indels (p < 1.16e-6) were identified. Among those, one SNP was located on Chromosome 4 and near the genes COL28A1 and C1GALT1. Seven significant SNPs were found in the region chr10_96664101-96670958, with the genes CDO1 and TMED7 located upstream and downstream, respectively. Haplotype analysis revealed that the diverse haplotypes of these seven SNPs presented varying values for coarse hair diameter. Notably, the only consistently significant insertion (chr10_96665085, GTA>G) was also located within the region chr10_96664101-96670958, further highlighting the importance of this genomic region in influencing coarse hair diameter. These significant variants and genomic regions provide valuable insights for investigating the genetic mechanisms underlying the variation in fiber diameter.

Buckwheat UDP-Glycosyltransferase FtUGT71K6 and FtUGT71K7 Tandem Repeats Contribute to Drought Tolerance by Regulating Epicatechin Synthesis.

Glycosyltransferase genes are organised as tandem repeats in the buckwheat genome, yet the functional implications and evolutionary significance of duplicated genes remain largely unexplored. In this study, gene family analysis revealed that FtUGT71K6 and FtUGT71K7 are tandem repeats in the buckwheat genome. Moreover, GWAS results for epicatechin suggested that this tandem repeat function was associated with epicatechin content of Tartary buckwheat germplasm, highlighting variations in the promoter haplotypes of FtUGT71K7 influenced epicatechin levels. FtUGT71K6 and FtUGT71K7 were shown to catalyse UDP-glucose conjugation to cyanidin and epicatechin. Furthermore, overexpression of FtUGT71K6 and FtUGT71K7 increased total antioxidant capacity and altered metabolite content of the epicatechin biosynthesis pathway, contributing to improved drought tolerance, while overexpression of FtUGT71K6 significantly improved salt stress tolerance. However, overexpression of these two genes did not contribute to resistance against Rhizoctonia solani. Evolutionary selection pressure analysis suggested positive selection of a critical amino acid ASP-53 in FtUGT71K6 and FtUGT71K7 during the duplication event. Overall, our study indicated that FtUGT71K6 and FtUGT71K7 play crucial roles in drought stress tolerance via modulating epicatechin synthesis in buckwheat.

Genetic diversity of Plasmodium falciparum reticulocyte binding protein homologue-5, which is a potential malaria vaccine candidate: baseline data from areas of varying malaria endemicity in Mainland Tanzania

BackgroundThe limited efficacy of the two recently approved malaria vaccines, RTS,S/AS01 and R21/Matrix- M™, highlights the need for alternative vaccine candidate genes. Plasmodium falciparum Reticulocyte Binding Protein Homologue 5 (Pfrh5) is a promising malaria vaccine candidate, given its limited polymorphism, its essential role in parasite survival, a lack of immune selection pressure and higher efficacy against multiple parasites strains. This study evaluated the genetic diversity of Pfrh5 gene among parasites from regions with varying malaria transmission intensities in Mainland Tanzania, to generate baseline data for this potential malaria vaccine candidate.MethodsThis study utilized secondary data of 697 whole-genome sequences which were generated by the MalariaGEN Community Network. The samples which were sequenced to generated the data were collected between 2010 and 2015 from five districts within five regions of Mainland Tanzania, with varying endemicities (Morogoro-urban district in Morogoro region, Muheza in Tanga, Kigoma-Ujiji in Kigoma, Muleba in Kagera, and Nachingwea district in Lindi region). Wright's fixation index (FST), Wright’s inbreeding coefficient (Fws), Principal component analysis (PCA), nucleotide diversity (π), haplotype network, haplotype diversity (Hd), Tajima's D, and Linkage disequilibrium (LD) were used to assess the diversity of the gene.ResultsOf the sequences used in this study, 84.5% (n = 589/697) passed quality control and 313 (53.1%) were monoclonal (contained infections from a single strain of P. falciparum) and were used for haplotype diversity and haplotype network analysis. High within-host diversity (Fws < 0.95) was reported in Kigoma-Ujiji (60.7%), Morogoro-urban (53.1%), and Nachingwea (50.8%), while Muleba (53.9%) and Muheza (61.6%) had low within-host diversity (Fws ≥ 0.95). PCA did not show any population structure and the mean FST value was 0.015. Low nucleotide diversity values were observed across the study sites (mean π = 0.00056). A total of 27 haplotypes were observed among the 313 monoclonal samples and under-fives exhibited higher haplotype counts. The Pf3D7 was detected as Hap_1, which occurred in 16/313 (5.1%) monoclonal sequences. Negative Tajima's D values were observed among the parasite populations in all the study sites.ConclusionLow levels of polymorphism in the pfrh5 gene were observed based on low nucleotide and haplotype diversity, a lack of population structure and negative Tajima’s D values. This study provides essential data on the diversity of the Pfrh5 gene indicating that it can be considered in the development of the next generation malaria vaccines. Robust and intensive studies of this and other candidate genes are crucial to support the prioritization of the Pfrh5 gene for potential inclusion in a broadly cross-protective malaria vaccine.

Intraspecific identification and genetic diversity analysis of Paeonia lactiflora based on chloroplast genes rpoB and psbK-psbI.

Paeonia lactiflora Pall., a member of Paeoniaceae family, is a medicinal herb widely used in traditional Chinese medicine. Chloroplasts are multifunctional organelles containing distinct genetic material. This study provides a foundation for identifying P. lactiflora, protecting and utilizing germplasm resources, and supporting molecular breeding efforts. In this study, five complete chloroplast genome sequences of P. lactiflora samples originating from different regions in China were sequenced using the Illumina NovaSeq 4000 platform. All five P. lactiflora chloroplasts had a typical cyclic tetrameric structure with 130 genes annotated. Comparative genomic analysis indicated that rpoB and psbK-psbI function as thepotential specific DNA barcodes for intraspecific identification of P. lactiflora. PCR amplification of rpoB and psbK-psbI was performed on 246 samples from 7 production areas, achieving 100% amplification efficiency. Sequence analysis revealed that 5 and 10 haplotypes were identified based on rpoB and psbK-psbI, respectively. The joint analysis of two sequences identified 15 haplotypes named Hap1 ~ Hap15. Hap5 emerged as the most prevalent and geographically widespread haplotype across China. Haplotypic diversity (Hd) was 0.786, and nucleotide diversity was 0.00281, suggesting that P. lactiflora had high genetic diversity at the species level. The Neighbor-Joining tree showed that the 15 haplotypes were clustered into two branches, indicating extensive genetic exchange between clusters. The introduction of new individuals or rare genes into different clusters through gene flow increased genetic variation within clusters, enriching P. lactiflora genetic diversity.

Redescription and molecular analysis of Corynosoma pseudohamanni Zdzitowiecki, 1984 (Acanthocephala: Polymorphidae) juveniles from Notothenia coriiceps Richardson in the water area of Argentine Islands, West Antarctica.

Corynosoma pseudohamanni Zdzitowiecki, 1984 (Polymorphidae) was described from the intestinal tract of 5 species of seals including the type and main host, the Weddell seal Leptonycotes weddellii (Lesson) in the South Shetlands, West Antarctica. Notothenia coriiceps was the primary paratenic host of 14 fish hosts reported in the original description. We describe excysted juveniles from the body cavity of the major paratenic host, Notothenia coriiceps Richardson collected off Galindez Island, Argentine Islands, West Antarctica for the first time. The original description was not "based on material collected from the final hosts (seals) and paratenic hosts (fish)" as stated since no description of juveniles was given then. Our excysted juveniles were generally smaller than reported adults and many of the other measurements were comparable to those of the adults in the original description. We added many of the incomplete measurements of adults in the original description especially those of the underdeveloped reproductive structures. We compared our morphometric description with the only other one available for juveniles collected from three paratenic fish hosts from Prince Gustav Channel, Antarctica. We have added informative optical microscopy images and SEM images of internal and external structures, previously missed in the original description. Energy Dispersive X-ray analysis revealed the highest levels of calcium in all hooks and hook roots compared to sulfur and phosphorus. We also provide a molecular characterization of the species for the first time. Newly generated sequences of the mitochondrial cytochrome c oxidase subunit 1 (mtcox1) gene from isolates of C. pseudohamanni cystacanths were compared with sequences of other acanthocephalans available in GenBank. Phylogenetic analyses based on maximum likelihood (ML) and Bayesian inference (BI) methods of the cox1 dataset placed all the species of Corynosoma in a single clade, with strong support. The mt cox1 sequences of C. pseudohamanni formed a strongly supported individual clade with the published sequences of Corynosoma nortmeri and Corynosoma magdaleni from the North Sea, Germany. We have determined the genetic diversity ofC. pseudohamanni and compare it with other Corynosoma species haplotype diversity and distribution.

Prevalence and diversity of Aphanomyces astaci in cambarid crayfish of Pennsylvania: where native and introduced hosts meet.

The crayfish plague pathogen Aphanomyces astaci (Oomycota: Saprolegniales) is native to North America but expanded with its crayfish hosts to other regions. In most of its invaded range, A. astaci haplotypes are associated with specific American crayfish, probably due to introduction bottlenecks, but haplotype diversity is higher and clear host-specific associations are lacking in its native range. However, little is known about the infection rate and load of this pathogen in North America. We investigated the distribution, prevalence and genetic variation of A. astaci in Pennsylvania (eastern USA), where multiple native and introduced crayfish species (family Cambaridae) occur. We used A. astaci-specific quantitative PCR to screen 533 individuals representing 8 crayfish species (2 Cambarus and 6 Faxonius) from 49 sites. Faxonius limosus, an American species first introduced to Europe and carrier of A. astaci genotype group E, was of particular interest. We confirmed A. astaci infections in 76% of sites in all but 1 host taxon, with the pathogen infection rate and load comparable to established populations of North American crayfish studied in Europe and Japan. Despite the absence of highly infected hosts, we genotyped A. astaci from 14 sites. We only detected 2 mitochondrial haplotypes, but nuclear markers indicated the presence of at least 4 distinct pathogen genotypes, none documented from invaded areas in Europe or Asia. Genotype group E was not detected in F. limosus, possibly due to limited spatial distribution of the original strain. Our results highlight both benefits and limitations of combining multiple pathogen genotyping methods.

Leveraging a phased pangenome for haplotype design of hybrid potato.

The tetraploid genome and clonal propagation of the cultivated potato (Solanum tuberosum L.)1,2 dictate a slow, non-accumulative breeding mode of the most important tuber crop. Transitioning potato breeding to a seed-propagated hybrid system based on diploid inbred lines has the potential to greatly accelerate its improvement3. Crucially, the development of inbred lines is impeded by manifold deleterious variants; explaining their nature and finding ways to eliminate them is the current focus of hybrid potato research4-10. However, most published diploid potato genomes are unphased, concealing crucial information on haplotype diversity and heterozygosity11-13. Here we develop a phased potato pangenome graph of 60 haplotypes from cultivated diploids and the ancestral wild species, and find evidence for the prevalence of transposable elements in generating structural variants. Compared with the linear reference, the graph pangenome represents a broader diversity (3,076 Mb versus 742 Mb). Notably, we observe enhanced heterozygosity in cultivated diploids compared with wild ones (14.0% versus 9.5%), indicating extensive hybridization during potato domestication. Using conservative criteria, we identify 19,625 putatively deleterious structural variants (dSVs) and reveal a biased accumulation of deleterious single nucleotide polymorphisms (dSNPs) around dSVs in coupling phase. Based on the graph pangenome, we computationally design ideal potato haplotypes with minimal dSNPs and dSVs. These advances provide critical insights into the genomic basis of clonal propagation and will guide breeders to develop a suite of promising inbred lines.

Genetic diversity and phylogeography of the global Theileria orientalis isolates inferred from MPSP gene sequences.

Theileria orientalis is a non-transforming Theileria species infecting cattle and water buffaloes. Several outbreaks of oriental theileriosis accompanied by considerable economic loss were documented in Asia, Australia, and New Zealand. The major piroplasm surface protein (MPSP) gene has frequently been used to molecularly characterize T. orientalis isolates worldwide. Various MPSP genotypes were detected with significant virulence variations. The present study provides the first in silico analysis for all globally published T. orientalis MPSP isolates to evaluate their phylogeny, diversity, and population structure. All studies that tested T. orientalis isolates using PCR-MPSP protocols were systematically collected from various databases. Theileria orientalis MPSP-sequenced isolates on the GenBank were collected and the sequences were tested for their phylogenetic relatedness, genetic diversity, recombination, natural selection, and population structure using various software. The collected T. orientalis-MPSP isolates (n = 795) were clustered into 12 genotypes, including types 1 (Chitose), 2 (Ikeda), 3 (Buffeli), 4, 5, 7, 8, and N1-N5. The previously identified type 6 belonged to a separate species (Theileria sinensis). The previously identified type 9 was transferred to type 4. Two unidentified isolates from water buffaloes in India were clustered into a new suggested genotype "type N5". Of the 12 genotypes, Ikeda (type 2) is the most virulent in cattle. However, a few clinical cases have also been linked to types 1 (Chitose) and 7. In water buffaloes, T. orientalis outbreaks have been linked to genotypes N2 and N5. Geographic mapping of various genotypes revealed the dispersal of types 1 and 3 worldwide. Overall, the 795 isolates comprised 532 haplotypes and displayed very high nucleotide (π = 0.14) and haplotype (Hd = 0.995) diversities. As a result, a very low sequence conservation value (C = 0.207) was determined. The twelve genotypes displayed comparable haplotype diversities accompanied by statistically significant negative Tajima's D and Fu's Fs values suggesting population expansion. A high value for the minimum number of recombination events (Rm = 65) was estimated for the 795 isolates, and this value varied from 0 to 23 at the genotype level. Most types also displayed significant positive selection (dn/ds ratio > 1). This suggests that both recombination and positive selection occur in T. orientalis MPSP gene, which could explain the very high genetic diversity among various T. orientalis types. Different patterns were detected for the gene flow among T. orientalis populations from various hosts and geographies; however, there is evidence for the genetic relatedness between populations from neighbouring countries. The high genetic polymorphism and different associated pathogenicity in T. orientalis-MPSP genotypes highlight the need for further investigations employing whole genome sequencing technology to provide accurate comparative gene-level analyses and help further understand their pathogenicity.

Genetic and Haplotype Diversity of Hoplolaimus (Nematoda: Hoplolaimidae) Through Analysis of COI of mtDNA

Lance nematodes (Hoplolaimus spp.) feed on the roots of various plants, including key horticultural products. An investigation of the genetic diversity and structure of six Hoplolaimus species, utilizing the cytochrome c oxidase I (COI) of the mtDNA gene, was based on 174 sequences available on the NCBI. Based on the COI of mtDNA, the haplotype analysis revealed 44 haplotypes. Nucleotide diversity was low among all species of Hoplolaimus, except for H. magnistylus (π = 0.04915) and H. stephanus (π = 0.06746). In contrast, haplotype diversity (Hd) was high, especially for H. stephanus (Hd = 0.89) and H. pararobustus (Hd = 0.90). Phylogenetic analysis grouped the various populations into eight clades, and the result showed that H. magnistylus was placed in three different clades, which showed high variability in haplotype supported by the haplotype network. Neutrality tests and mismatch distribution based on the mtDNA supported the hypothesis of a constant population with no expansion in Hoplolaimus, except for H. concaudajuvencus (Tajima (D) = −0.84971) and H. columbus (Tajima (D) = −0.87674). In conclusion, genetic analysis showed a neutral evolution amongst the Hoplolaimus species. The result of the present study provides a better insight into the Hoplolaimus species toward species delimitation and managing this plant-parasitic nematode in various crops.

CAYSS: Package for Automatic Cytometry Analysis of Yeast Spore Segregation.

Meiotic recombination is a powerful source of haplotypic diversity, and thus plays an important role in the dynamics of short-term adaptation. However, high-throughput quantitative measurement of recombination parameters is challenging because of the large size of offspring to be genotyped. One of the most efficient approaches for large-scale recombination measurement is to study the segregation of fluorescent markers in gametes. Applying this to yeast spores by flow cytometry has already been proved to be highly efficient, but manual analyses of distributions of signal intensities is time-consuming and produces nonperfectly reproducible results. Such analyses are required to identify events corresponding to spores and to assign each of them to a genotypic class depending on their fluorescence intensity. The CAYSS package automatically reproduces the manual process that we've been developing to analyze yeast recombination for years, including Maximum-Likelihood estimation of fluorescence extinction (Raffoux et al. 2018a). When comparing the results of manual versus CAYSS automatic analyses of the same cytometry data, recombination rates and interference were on average very similar, with less than 3% differences on average and strong correlations (R2 > 0.9). In conclusion, as compared to manual analysis, CAYSS allows to save a lot of human time and produces totally reproducible results.

Molecular epidemiology and genetic diversity of disappearing Plasmodium vivax in southern Thailand

The evolution of genetic diversity and population structure of Plasmodium vivax as malaria elimination approaches remains unclear. This study analyzed the genetic variation and molecular epidemiology of P. vivax from Yala Province in southern Thailand, an area in the pre-elimination phase. Seventy P. vivax isolates, collected between 2017 and 2020, were genotyped for domain II of pvdbp and the 42-kDa region of pvmsp1 using amplicon deep sequencing. Data from Yala province were compared to published data from Tak province, where transmission was higher. Key analyses included nucleotide diversity (π), haplotype diversity (Hd), natural selection, recombination rates, and complexity of infection (COI). Genetic diversity in Yala was relatively low (π = 0.008dbp and 0.014msp1; Hd = 0.774dbp and 0.407msp1) compared to Tak (π = 0.012dbp and 0.027msp1; Hd = 0.849dbp and 0.962msp1). In Yala, polyclonal infections were found in 53.7% of pvdbpII and 47.8% of pvmsp142 isolates, with average COI of 1.6 and 1.7. Both genes were under balancing selection. Distinct genetic differences were found between Yala and Tak in pvmsp142, providing a local genotypic profile useful for tracing parasite origins.

Genetic insights into the first detection of Paracoccus marginatus (Hemiptera: Pseudococcidae) in Australia.

Species spread in a new environment is often associated with founders' effect, and reduced effective population size and genetic diversity. However, reduced genetic diversity does not necessarily translate to low establishment and spread potential. Paracoccus marginatus Williams and Granara de Willink is a polyphagous pest that has invaded 4 continents in around 34 years. It was first detected in the Northern Territory, Australia in July 2023. Following this, we collected 45 specimens from 20 suburbs across 3 regions. Using mitochondrial cytochrome oxidase I and nuclear ribosomal RNA genes (18S and 28S), we examined molecular diagnostics robustness, genetic diversity, haplotype network, and demographics (Tajima D) of the recently detected Australian population. We compared our samples with publicly available sequences deposited on GenBank. All 3 genes were suitable for molecular diagnosis with a 100% identity score. For all 3 genes, we found low nucleotide diversity, haplotype diversity, and negative Tajima D in the newly detected P. marginatus population, suggesting a recent single founder event by a few individuals. Comparing our study's sequences with global sequences showed low haplotype diversity, nucleotide diversity, and Tajima's D, suggesting that despite low genetic diversity at the 3 genes, P. marginatus has successfully invaded South America, Africa, Asia, and Oceania. Our study highlights the role of demographic and life history traits in the species' invasion success. We provide a baseline dataset from the first detection of P. marginatus in Australia. Further analysis of the spread can provide insights into invasive species' adaptation in a novel environment.

Population genetic structure of Uroteuthis edulis in the East China Sea based on the COI gene.

Uroteuthis edulis is a significant economic cephalopod resource utilized by mainland China, Taiwan, and Japan. Understanding the population genetic structure of U.edulis is essential to evaluate the changes of its resource abundance. In this study, we used the COI gene as a marker to evaluate the population structure of U.edulis. Molecular marker analysis indicated that the sampled individuals were categorized into three populations (ES1, ES2, and ES3). All populations exhibited high haplotype diversity indices (Hd) and low nucleotide diversity indices (Pi), with the ES2 population showing the lowest Hd and Pi values. Analysis of molecular variance (AMOVA) revealed that genetic variation among populations accounted for 89.06% of the total variation. The phylogenetic tree illustrated distinct lineage clustering, with each population forming a separate clade. Combined with the biological information, it was observed that the majority of female individuals were larger in size and exhibited high sexual maturity. Male individuals displayed notable differences across populations: ES1 individuals were primarily small to medium-sized with low sexual maturity, ES2 individuals were mainly medium-sized with a relatively even distribution of sexual maturity, and ES3 individuals were predominantly large-sized with high sexual maturity. The findings indicate substantial genetic differentiation and ecological variation among U.edulis. Strengthen monitoring of population resources and genetic diversity, long-term tracking of changes, and the timely formulation of scientifically sound conservation and management measures to ensure the sustainable development in future.

Range-wide understanding of genetic diversity and population structure of endangered Kashmir musk deer in North-Western Himalaya.

The endangered Kashmir musk deer (Moschus cupreus), native to high-altitude Himalayas, is an ecological significant and endangered ungulate, threatened by habitat loss and poaching for musk pod distributed in western Himalayan ranges of India, Nepal and Afghanistan. Despite its critical conservation status and ecological importance in regulating vegetation dynamics, knowledge gaps persist regarding its population structure and genetic diversity, hindering effective management strategies. We aimed to understand the population genetics of Kashmir musk deer in north-western Himalayas using two mitochondrial DNA (mtDNA) regions and 11 microsatellite loci. Total of 63 consensus sequences were analyzed, revealing 10 haplotypes with high haplotype diversity (Hd = 0.906 ± 0.031) and moderate nucleotide diversity (π = 0.00539 ± 0.004) at mitochondrial markers. Microsatellite analysis indicated moderate genetic variability, with observed heterozygosity (Ho = 0.445 ± 0.049) and expected heterozygosity (He = 0.764 ± 0.039), comparable to the forest musk deer but relatively lower than that observed in other ungulates. Population structure analysis identified three potential genetic clusters, with evidence of genetic admixture in the Lahaul Valley, possibly due to gene flow from neighboring areas. Historical demographic analyses using Bayesian skyline plots and mismatch distribution curves indicated stable population sizes in the past, followed by recent declines in maternal effective population size. Our findings highlight the necessity of preserving the genetic diversity of the Kashmir musk deer to ensure its long-term survival. We recommend expanding the geographic range of sampling to include regions such as Chamba and Kinnaur districts in Himachal Pradesh, potential areas in Jammu and Kashmir and Uttarakhand, for more comprehensive population-level analysis. Such efforts will be crucial for developing targeted conservation strategies and mitigating the impacts of human activities on this endangered species.