DNA sequence polymorphism analysis using DnaSP

Dissection of the Genetic Basis for Total γ-Oryzanol and Its Components in Whole Grain Brown Rice through Genome-Wide Association Study

Antioxidants detain the onset and progression of several noncommunicable diseases. γ-oryzanol (GOZ), a major antioxidant in rice grain, is a mixture of steryl esters of ferulic acid and caffeic acid. The present study was conducted with the objective of assessing the natural genetic variation for GOZ and its components in Indian rice cultivars and further identify the genomic regions associated with it. A panel of 174 Indian rice accessions depicted significant genetic variation for GOZ concentration, which ranged from 78.96 to 765.43 mg kg-1 of brown rice. 24-Methylenecycloartanyl ferulate was the major constituent (23.99-317.82 mg kg-1), followed by campesteryl ferulate (13.86-117.56 mg kg-1) and cycloartenyl ferulate (7.18-207.50 mg kg-1). Further, a genome-wide association study (GWAS) conducted using 32,712 single nucleotide polymorphism (SNP) markers with BLINK and FarmCPU models identified 19 significant marker-trait associations (MTAs) for GOZ and its components. These significant MTAs could explain the phenotypic variation ranging from 0.001 to 48.875% and have enormous potential in marker-assisted breeding programs aiming at the development of nutrient-dense rice varieties.

Genetic and Population Diversity of Temnocephalids Associated with the Invasive Crayfish Cherax quadricarinatus in Malaysia

PURPOSE

A previous study revealed that temnocephalids Diceratocephala boschmai, Craspedella pedum, and Decadidymus sp. were highly prevalent in Cheraq quadricarinatus in Melaka and Johor, Malaysia.

METHODS

Herein, study was conducted to extract temnocephalids from C. quadricarinatus and identified using a molecular approach via two DNA markers: 28S ribosomal DNA and mitochondrial cytochrome c oxidase subunit I (CO1). Thereafter, the population diversity of D. boschmai in Malaysia using the CO1 DNA marker was analysed to visualize the genetic associations among populations.

RESULTS

The analysis of 16 variable (segregating) sites in the CO1 gene alignment of sequence from D. boschmai revealed a calculated haplotype diversity of 0.1266 among populations which indicates genetic variation within the studied groups. Additionally, the determination of nucleotide diversity (II) yielded a value of 0.0035, and Tajima's D neutrality test yielded a negative value for all populations, suggesting no significant departure from neutral evolution.

CONCLUSION

AMOVA analysis indicated that the genetic variation or polymorphism is primarily contributed within populations (95%) compared to between populations (4%).

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.

Plasmodium falciparum surf4.1 in clinical isolates: From genetic variation and variant diversity to in silico design immunopeptides for vaccine development

SURFINs protein family expressed on surface of both infected red blood cell and merozoite surface making them as interesting vaccine candidate for erythrocytic stage of malaria infection. In this study, we analyze genetic variation of Pfsurf4.1 gene, copy number variation, and frequency of SURFIN4.1 variants of P. falciparum in clinical isolates. In addition, secondary structure prediction and immunoinformatic were employed to identify immunogenic epitopes in humoral response as proposed vaccine candidates. Overall, our data demonstrate extensive polymorphism of SURFIN4.1 in both genetic and protein level. The surf4.1 gene showed extensive genetic variation with total of 447 polymorphic sites with maximum of three variants as well as singlet/triplet bases indels and mini/microsatellites in the coding sequence. The exon1 encoding extracellular region exhibited higher variation compared to exon2 which coding for intracellular domain. Interestingly, selective pressure was detected on both extracellular region (Var1 and Var2) as well as intracellular region (WRD2 and WRD3). Importantly, extensive full gene analysis suggests adenosine insertion at three key points nucleotide bases (nt 2409/2410, 3809/3810, and 4439/4440) of exon2 could lead to frameshift mutation resulted in four different SURFIN4.1 variants (TMs, WD1, WD2 and WD3). The SURFIN4.1 variant TMs was the most observed type with 67% frequency (51/76). Along with more than one copy number of surf4.1 gene was observed with frequency of 13% (9/70). Despite substantial polymorphism, analysis of relatedness within P. falciparum population using full coding sequence was able to group SURFIN4.1 protein into five distinct clades and reduced into four clades when using only exon1 coding sequence. Also, predicted secondary structure revealed conserved structure of five helix domains of extracellular region which similar among four SURFIN4.1 variant types. In addition, in silico design eight immunopeptides derived from SURFIN4.1, four of which are highly conserved and four of dimorphic epitopes, as potential vaccine candidates.

Genome-Wide Dissection of Selection on microRNA Target Genes Involved in Rice Flower Development

Although genome-wide studies have identified a number of candidate regions evolving under selection in domesticated animals and cultivated plants, few attempts have been made, from the point of a definite biological process, to assess sequence variation and characterize the regimes of the selection on miRNA-associated motifs. Here, we performed a genome-wide dissection of nucleotide variation and selection of miRNA targets associated with rice flower development. By sampling and resequencing 26 miRNA targets for globally diverse representative populations of Asian cultivated rice and wild relatives, we found that purifying selection has reduced genetic variation at the conserved miRNA binding sites on the whole, and highly conserved miRNA binding sequences were maintained in the studied rice populations. Conversely, non-neutral evolution of positive and/or artificial selection accelerates the elevated variations at nonconserved binding sites in a population-specific behavior which may have contributed to flower development-related phenotypic variation. Taken together, our results elucidate that miRNA targets involved in flower development are under distinctive selection regimes during rice evolution.

Identification and characterization of sulphotransferase (SOT) genes for tolerance against drought and heat in wheat and six related species

BACKGROUND

Sulphotransferase (SOT) enzyme (encoded by a conserved family of SOT genes) is involved in sulphonation of a variety of compounds, through transfer of a sulphuryl moiety from 3'phosphoadenosine- 5'phosphosulphate (PAPS) to a variety of secondary metabolites. The PAPS itself is derived from 3'adenosine-5'phosphosulphate (APS) that is formed after uptake of sulphate ions from the soil. The process provides tolerance against abiotic stresses like drought and heat in plants. Therefore, a knowledge of SOT genes in any crop may help in designing molecular breeding methods for improvement of tolerance for drought and heat.

METHODS

Sequences of rice SOT genes and SOT domain (PF00685) of corresponding proteins were both used for identification of SOT genes in wheat and six related species (T. urartu, Ae. tauschii, T. turgidum, Z. mays, B. distachyon and Hordeum vulgare), although detailed analysis was conducted only in wheat. The wheat genes were mapped on individual chromosomes and also subjected to synteny and collinearity analysis. The proteins encoded by these genes were examined for the presence of a complete SOT domain using 'Conserved Domain Database' (CDD) search tool at NCBI.

RESULTS

In wheat, 107 TaSOT genes, ranging in length from 969 bp to 7636 bp, were identified and mapped onto individual chromosomes. SSRs (simple sequence repeats), microRNAs, long non-coding RNAs (lncRNAs) and their target sites were also identified in wheat SOT genes. SOT proteins were also studied in detail. An expression assay of TaSOT genes via wheat RNA-seq data suggested engagement of these genes in growth, development and responses to various hormones and biotic/abiotic stresses.

CONCLUSIONS

The results of the present study should help in further functional characterization of SOT genes in wheat and other related crops.

Genome wide identification of the NPR1 gene family in plant defense mechanisms against biotic stress in chili (Capsicum annuum L.)

Chili pepper cultivation in the Indian subcontinent is severely affected by viral diseases, prompting the need for environmentally friendly disease control methods. To achieve this, it is essential to understand the molecular mechanisms of viral resistance in chili pepper. The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) genes are known to provide broad-spectrum resistance to various phytopathogens by activating systemic acquired resistance (SAR). An in-depth understanding of NPR1 gene expression during begomovirus infection and its correlation with different biochemical and physiological parameters is crucial for enhancing resistance against begomoviruses in chili pepper. Nevertheless, limited information on chili CaNPR genes and their role in biotic stress constrains their potential in breeding for biotic stress resistance. By employing bioinformatics for genome mining, we identify 5 CaNPR genes in chili. The promoter regions of 1,500 bp of CaNPR genes contained cis-elements associated with biotic stress responses, signifying their involvement in biotic stress responses. Furthermore, these gene promoters harbored components linked to light, development, and hormone responsiveness, suggesting their roles in plant hormone responses and development. MicroRNAs played a vital role in regulating these five CaNPR genes, highlighting their significance in the regulation of chili genes. Inoculation with the begomovirus "cotton leaf curl Khokhran virus (CLCuKV)" had a detrimental effect on chili plant growth, resulting in stunted development, fibrous roots, and evident virus symptoms. The qRT-PCR analysis of two local chili varieties inoculated with CLCuKV, one resistant (V1) and the other susceptible (V2) to begomoviruses, indicated that CaNPR1 likely provides extended resistance and plays a role in chili plant defense mechanisms, while the remaining genes are activated during the early stages of infection. These findings shed light on the function of chili's CaNPR in biotic stress responses and identify potential genes for biotic stress-resistant breeding. However, further research, including gene cloning and functional analysis, is needed to confirm the role of these genes in various physiological and biological processes. This in-silico analysis enhances our genome-wide understanding of how chili CaNPR genes respond during begomovirus infection.

Haemonchus contortus, an obligatory haematophagus worm infection in small ruminants: Population genetics and genetic diversity

Haemonchus contortus, a stomach worm, is prevalent in ruminants worldwide. They particularly hamper profitable small ruminant production. Here, we estimate the genetic variation of H. contortus collected from slaughtered goats and sheep from various geographic zones of Bangladesh using multiple genes. To perform this, adult parasites were isolated from the abomasum of slaughtered animals (sheep and goats). Among them, 79 male H. contortus were identified by microscopy. Following the extraction of DNA, ITS-2 and cox1 genes were amplified and subsequently considered for sequencing. After alignment and editing, sequences were analyzed to find out sequence variation, diversity pattern of genes, and population genetics of isolates. Among the sequence data, the analyses identified 19 genotypes of ITS-2 and 77 haplotypes of cox1 genes. The diversity of nucleotides was 0.0103 for ITS-2 and 0.029 for cox1 gene. The dendogram constructed by the genotype and haplotype sequences of H. contortus revealed that two populations were circulating in Bangladesh without any demarcation of host and geographic regions. Analysis of population genetics demonstrated a high flow of genes (89.2 %) within the population of the worm in Bangladesh. The Fst value showed very little amount of genetic difference among the worm populations of Bangladesh but marked genetic variation between different continents. The findings are expected to help explain the risks of anthelmintic resistance and the transmission pattern of the parasite, and also provide a control strategy against H. contortus.

Dataset on evaluation of intra-specific genetic diversity and phylogenetic relationship of Launaea taraxacifolia (Willd.) Amin ex C. Jeffrey in southwest Nigeria using rbcL gene maker

Launaea taraxacifolia (Willd.) Amin Ex C. Jeffrey (Asteraceae) popularly known as "African wild lettuce" is a neglected, underutilized, and sometimes classified as a weed in West and Central Africa. The plant has been naturalized in numerous regions of the world, including Asia, North America, Europe, and North Africa. This highly nutritional and medicinal leafy vegetable is endemic to some states in southwest, Nigeria. People who utilize the species still depend largely on its spontaneous appearance in the wild, except for some herbalists who cultivate it for therapeutic uses. Its domestication and cultivation are still at infant stage. Without the intervention of breeders, the full potential of this species would remain untapped. The inadequate information about the genetic diversity of L. taraxacifolia hinders its improvement through breeding programme and for conservation purposes, hence this dataset. A total of fifteen (15) accessions of L. taraxacifolia were collected from Oyo, Osun and Ogun states in Nigeria. The accessions were partitioned into three populations according to their collection states and subjected to DNA extraction, polymerase chain reaction amplification and Sanger sequencing using ribulose-1,5-carboxylase/oxygenase large subunit gene (rbcL). The dataset composed of partial rbcL gene sequences which provides information on L. taraxacifolia distribution in southwest, Nigeria, its genetic diversity, single nucleotide polymorphic information, codon usage bias and amino acids molecular weight profile. The dataset recorded a relatively low number of segregating sites (3), total number of haplotypes (4), and nucleotide diversity (0.298) with a high gene diversity (0.667) and average number of nucleotide differences (0.895). A significant low level of genetic differentiation (Fst) was recorded for the population in the decreasing order of 0.103 (Ogun and Oyo populations), 0.000 (Ogun and Osun populations) and -0.222 (Oyo and Osun populations). The unweighted pair group method with arithmetic mean revealed the genetic diversity and phylogenetic relationships of L. taraxacifolia accessions which could be explored for its domestication, cultivation, genetic improvement and conservation in Nigeria.

Comparison of the first time detected Oesophagostomum asperum with Oesophagostomum columbianum in sheep and goats in Bangladesh based on the trinity: Morphology, morphometry and genetic diversity

Oesophagostomum spp. (Family: Chabertiidae) is keeping a low profile in terms of severity in Bangladesh while maintaining economic loss through disguise within sheep and goats. The study was performed to identify prevalence, confirmation of species through morphology and morphometry followed by phylogeny using ITS2 and COX1 genes. In total 384 slaughterhouse-sourced small and large intestines were pooled from Mymensingh, Kishoreganj, Netrokona, Sherpur and Tangail districts of Mymensingh division. Followed by isolation, O. columbianum and O. asperum were identified following their key morphological features. Notably, O. asperum was first time detected in Bangladesh. The overall prevalence of Oesophagostomum spp. was found 60.93%. The prevalence of O. columbianum (64.95%) was almost double than that of O. asperum (35.04%). Among several characters, only the distance between anus to tail tip showed a significant morphological disparity in female. The Neighbor-joining (NJ) phylogenic trees based on ITS2 and COX1 genes confirmed the study species. The first time identified O. asperum along with morphometry and phylogeny will add value to the fact that nematodes are invisibly present with high prevalence in this country. This study will help to draw specific attention to command a practical control strategy for intervening in economic loss.

A. B. D. A, Abbas K, Hussain T, Ramasamy S, Manomohan V, Tapsoba ASR, Pichler R, Babar ME, Periasamy K. Indigenous cattle of Sri Lanka: Genetic and phylogeographic relationship with Zebu of Indus Valley and South Indian origin

The present study reports the population structure, genetic admixture and phylogeography of cattle breeds of Sri Lanka viz. Batu Harak, Thawalam and White cattle. Moderately high level of genetic diversity was observed in all the three Sri Lankan zebu cattle breeds. Estimates of inbreeding for Thawalam and White cattle breeds were relatively high with 6.1% and 7.2% respectively. Genetic differentiation of Sri Lankan Zebu (Batu Harak and White cattle) was lowest with Red Sindhi among Indus Valley Zebu while it was lowest with Hallikar among the South Indian cattle. Global F statistics showed 6.5% differences among all the investigated Zebu cattle breeds and 1.9% differences among Sri Lankan Zebu breeds. The Sri Lankan Zebu cattle breeds showed strong genetic relationships with Hallikar cattle, an ancient breed considered to be ancestor for most of the Mysore type draught cattle breeds of South India. Genetic admixture analysis revealed high levels of breed purity in Lanka White cattle with >97% Zebu ancestry. However, significant taurine admixture was observed in Batu Harak and Thawalam cattle. Two major Zebu haplogroups, I1 and I2 were observed in Sri Lankan Zebu with the former predominating the later in all the three breeds. A total of 112 haplotypes were observed in the studied breeds, of which 50 haplotypes were found in Sri Lankan Zebu cattle. Mismatch analysis revealed unimodal distribution in all the three breeds indicating population expansion. The sum of squared deviations (SSD) and raggedness index were non-significant in both the lineages of all the three breeds except for I1 lineage of Thawalam cattle (P<0.01) and I2 lineage of Batu Harak cattle (P<0.05). The results of neutrality tests revealed negative Tajima's D values for both the lineages of Batu Harak (P>0.05) and White cattle (P>0.05) indicating an excess of low frequency polymorphisms and demographic expansion. Genetic dilution of native Zebu cattle germplasm observed in the study is a cause for concern. Hence, it is imperative that national breeding organizations consider establishing conservation units for the three native cattle breeds to maintain breed purity and initiate genetic improvement programs.

The G2-Like gene family in Populus trichocarpa: identification, evolution and expression profiles

The Golden2-like (GLK) transcription factors are plant-specific transcription factors (TFs) that perform extensive and significant roles in regulating chloroplast development. Here, genome-wide identification, classification, conserved motifs, cis-elements, chromosomal locations, evolution and expression patterns of the PtGLK genes in the woody model plant Populus trichocarpa were analyzed in detail. In total, 55 putative PtGLKs (PtGLK1-PtGLK55) were identified and divided into 11 distinct subfamilies according to the gene structure, motif composition and phylogenetic analysis. Synteny analysis showed that 22 orthologous pairs and highly conservation between regions of GLK genes across P. trichocarpa and Arabidopsis were identified. Furthermore, analysis of the duplication events and divergence times provided insight into the evolutionary patterns of GLK genes. The previously published transcriptome data indicated that PtGLK genes exhibited distinct expression patterns in various tissues and different stages. Additionally, several PtGLKs were significantly upregulated under the responses of cold stress, osmotic stress, and methyl jasmonate (MeJA) and gibberellic acid (GA) treatments, implying that they might take part in abiotic stress and phytohormone responses. Overall, our results provide comprehensive information on the PtGLK gene family and elucidate the potential functional characterization of PtGLK genes in P. trichocarpa.

Evolution and biogeography of apple stem grooving virus

BACKGROUND

Apple stem grooving virus (ASGV) has a wide host range, notably including apples, pears, prunes and citrus. It is found worldwide.

METHOD

In this study, two near complete genomes, and seven coat protein (CP) sequences of Iranian isolates from apple were determined. Sequences added from GenBank provided alignments of 120 genomic sequences (54 of which were recombinant), and 276 coat protein genes (none of them recombinant).

RESULT

The non-recombinant genomes gave a well supported phylogeny with isolates from diverse hosts in China forming the base of the phylogeny, and a monophyletic clade of at least seven clusters of isolates from around the world with no host or provenace groupings among them, and all but one including isolates from China. The six regions of the ASGV genome (five in one frame, one - 2 overlapping) gave significantly correlated phylogenies, but individually had less statistical support. The largest cluster of isolates contained those from Iran and had isolates with worldwide provenances, and came from a wide range of mono- and dicotyledonous hosts. Population genetic comparisons of the six regions of the ASGV genome showed that four were under strong negative selection, but two of unknown function were under positive selection.

CONCLUSION

ASGV most likely originated and spread in East Asia in one or more of various plant species, but not in Eurasia; the ASGV population of China had the greatest overall nucleotide diversity and largest number of segregating sites.

Comparative Genome Analysis of Old World and New World TYLCV Reveals a Biasness toward Highly Variable Amino Acids in Coat Protein

Begomoviruses, belonging to the family Geminiviridae and the genus Begomovirus, are DNA viruses that are transmitted by whitefly Bemisia tabaci (Gennadius) in a circulative persistent manner. They can easily adapt to new hosts and environments due to their wide host range and global distribution. However, the factors responsible for their adaptability and coevolutionary forces are yet to be explored. Among BGVs, TYLCV exhibits the broadest range of hosts. In this study, we have identified variable and coevolving amino acid sites in the proteins of Tomato yellow leaf curl virus (TYLCV) isolates from Old World (African, Indian, Japanese, and Oceania) and New World (Central and Southern America). We focused on mutations in the coat protein (CP), as it is highly variable and interacts with both vectors and host plants. Our observations indicate that some mutations were accumulating in Old World TYLCV isolates due to positive selection, with the S149N mutation being of particular interest. This mutation is associated with TYLCV isolates that have spread in Europe and Asia and is dominant in 78% of TYLCV isolates. On the other hand, the S149T mutation is restricted to isolates from Saudi Arabia. We further explored the implications of these amino acid changes through structural modeling. The results presented in this study suggest that certain hypervariable regions in the genome of TYLCV are conserved and may be important for adapting to different host environments. These regions could contribute to the mutational robustness of the virus, allowing it to persist in different host populations.

Genetic Diversification of Starch Branching Enzymes during Maize Domestication and Improvement

Elucidating the genetic basis of starch pasting and gelatinization properties is crucial for enhancing the quality of maize and its utility as feed and industrial raw material. In maize, ZmSBE genes encode important starch branching enzymes in the starch biosynthesis pathway. In this study, we re-sequenced the genomic sequences of ZmSBEI, ZmSBEIIa, ZmSBEIIb, and ZmSBEIII in three lines called 335 inbred lines, 68 landrace lines, and 32 teosinte lines. Analyses of nucleotide polymorphisms and haplotype diversity revealed differences in the selection patterns of ZmSBEI, ZmSBEIIa, ZmSBEIIb, and ZmSBEIII during maize domestication and improvement. A marker-trait association analysis of inbred lines detected 22 significant loci, including 18 SNPs and 4 indels significantly associated with three maize starch physicochemical properties. The allele frequencies of two variants (SNP17249C and SNP5055G) were examined in three lines. The frequency of SNP17249C in ZmSBEIIb was highest in teosinte lines, followed by landrace lines, and inbred lines, whereas there were no significant differences in the frequency of SNP5055G in ZmSBEIII among the three lines. These results suggest that ZmSBE genes play an important role in the phenotypic variations in the starch physicochemical properties in maize. The genetic variants detected in this study may be used to develop functional markers for improving maize starch quality.

Hypothalamic GnRH expression and pulsatility depends on a balance of prolactin receptors in the plains vizcacha, Lagostomus maximus

In mammals, gestation is considered a physiological hyperprolactinemia status. Prolactin (PRL) is one of the modulators of gonadotropin-releasing hormone (GnRH) neurons function. The South American plains vizcacha (Lagostomus maximus) is a unique model to study the regulation of hypothalamic GnRH neurons by direct and indirect steroid-dependent pathways. The aim was to characterize the hypothalamic expression of endocrine markers in vizcacha during gestation as well as their response to experimental induced hyperprolactinemia. The possible involvement of PRL regulatory pathways on GnRH in the context of hypothalamic and pituitary reactivation in mid-gestating vizcachas was discussed. Using two in vivo approaches, we determined changes in the hypothalamic expression and distribution of prolactin receptor (PRLR), tyrosine hydroxylase (TH), and dopamine type 2 receptor. A significant increment in the number of tuberoinfundibular dopaminergic (TIDA) neurons was determined in the arcuate nucleus from early to term pregnancy. On the other hand, at preoptic area, the number of both TH+PRLR+ and GnRH+PRLR+ double-labeled neurons significantly decreased at mid-pregnancy probably allowing the recovery of GnRH expression indicating that both types of neurons may represent the key points of PRL indirect and direct pathways modulating GnRH. Moreover, in a model of induced hyperprolactinemic vizcachas, the inhibitory effect of PRL on GnRH at both expression and delivery levels were confirmed. These results suggest the concomitant participation of both PRL regulatory pathways on GnRH modulation and pinpoint the key role of PRL on GnRH expression enabling the recovery of the hypothalamic activity during the gestation in this species.

The Impact of Variation in the Toll-like Receptor 3 Gene on Epizootic Hemorrhagic Disease in Illinois Wild White-Tailed Deer (Odocoileus virginianus)

Epizootic hemorrhagic disease (EHD) leads to high mortality in white-tailed deer (Odocoileus virginianus) and is caused by a double-stranded RNA (dsRNA) virus. Toll-like receptor 3 (TLR3) plays a role in host immune detection and response to dsRNA viruses. We, therefore, examined the role of genetic variation within the TLR3 gene in EHD among 84 Illinois wild white-tailed deer (26 EHD-positive deer and 58 EHD-negative controls). The entire coding region of the TLR3 gene was sequenced: 2715 base pairs encoding 904 amino acids. We identified 85 haplotypes with 77 single nucleotide polymorphisms (SNPs), of which 45 were synonymous mutations and 32 were non-synonymous. Two non-synonymous SNPs differed significantly in frequency between EHD-positive and EHD-negative deer. In the EHD-positive deer, phenylalanine was relatively less likely to be encoded at codon positions 59 and 116, whereas leucine and serine (respectively) were detected less frequently in EHD-negative deer. Both amino acid substitutions were predicted to impact protein structure or function. Understanding associations between TLR3 polymorphisms and EHD provides insights into the role of host genetics in outbreaks of EHD in deer, which may allow wildlife agencies to better understand the severity of outbreaks.

Characterization of the Complete Mitochondrial Genome of the Spotted Catfish Arius maculatus (Thunberg, 1792) and Its Phylogenetic Implications

The spotted catfish, Arius maculatus (Siluriformes), is an important economical aquaculture species inhabiting the Indian Ocean, as well as the western Pacific Ocean. The bioinformatics data in previous studies about the phylogenetic reconstruction of Siluriformes were insufficient and incomplete. In the present study, we presented a newly sequenced A. maculatus mitochondrial genome (mtDNA). The A. maculatus mtDNA was 16,710 bp in length and contained two ribosomal RNA (rRNA) genes, thirteen protein-coding genes (PCGs), twenty-two transfer RNA (tRNA) genes, and one D-loop region. The composition and order of these above genes were similar to those found in most other vertebrates. The relative synonymous codon usage (RSCU) of the 13 PCGs in A. maculatus mtDNA was consistent with that of PCGs in other published Siluriformes mtDNA. Furthermore, the average non-synonymous/synonymous mutation ratio (Ka/Ks) analysis, based on the 13 PCGs of the four Ariidae species, showed a strong purifying selection. Additionally, phylogenetic analysis, according to 13 concatenated PCG nucleotide and amino acid datasets, showed that A. maculatus and Netuma thalassina (Netuma), Occidentarius platypogon (Occidentarius), and Bagre panamensis (Bagre) were clustered as sister clade. The complete mtDNA of A. maculatus provides a helpful dataset for research on the population structure and genetic diversity of Ariidae species.

Morphometry and genetic diversity pattern of Cysticercus tenuicollis, an important food-borne taeniid metacestode in goats in Bangladesh

Cysticercus tenuicollis is a larval stage of Taenia hydatigena resulting in cysticercosis, and responsible for enormous economic loses, especially in livestock production. Here, we planned to determine the prevalence and explore genetic variation of C. tenuicollis isolated from goats based on small subunit ribosomal RNA (rrnS) and cytochrome oxidase subunit 1 (cox1). To do this, samples were collected from different slaughter houses of municipal areas such as Bramhapalli slaughterhouse, Jubileeghat slaughterhouse and Mesuabazar slaughterhouse at Mymensingh sadar, and tentatively identified by morphological and morphometrical analysis. To study genetic variation, DNA was extracted from C. tenuicollis, and amplified rrnS and cox1 genes using specific primers, and were sequenced. Among 1372 examined animals, 177 (12.9%) were infected with C. tenuicollis. Cysts were recovered from peritoneum (7.9%), liver (4.4%) and urinary bladder (0.6%) of the infected animals. Females (18.9%) and adults (20.7%) were significantly more susceptible than male (8.8%) and young (9.3%), respectively. Genetic analysis defined 8 distinct rrnS genotypes and 9 unique cox1 haplotypes among 20 C. tenuicollis isolates. The nucleotide diversities were 0.00283 and 0.00434 for rrnS and cox1 genes, respectively. Neighbor joining (NJ) trees of rrnS and cox1 gene were constructed and the studied sequences were clustered with reference sequences of T. hydatigena with strong nodal support (100%). To compare Bangladeshi isolates, a median joining network was constructed with the population from other geographical regions and hosts. This led to a clustering pattern, but the clusters were not built with unique geographical regions or hosts. In conclusion, this is the first study that describes the genetic variation of T. hydatigena population and suggests the existence of host-specific variants. Therefore, it is fundamental to dispose infected viscera, restrict dog movement and proper management of slaughter house for the prevention and control of cysticercosis.

Update: Assessing the evolutionary trajectory of the Apaporis caiman (Caiman crocodilus apaporiensis, Medem 1955) via mitochondrial molecular markers

The spectacled caiman (Caiman crocodilus) is currently considered to be a species complex due to the relatively high morphological and molecular diversity expressed across its range. One of the populations of interest, inhabiting the Apaporis River (Colombia), was described based on skull features as an incipient species (C. c. apaporiensis) and has been treated by some authors as a full species. Recent molecular work challenged this hypothesis, because relatively low mitochondrial molecular differentiation was found between the morphologically described Apaporis caiman and C. crocodilus (s.s.) Amazonian populations. Here, we present an update on the topic based on a larger molecular sample size and on analysis of expanded geometric morphometric data that include six newly collected skulls. Morphometric data support the existence of previously recognized morphotypes within the complex in Colombia and demonstrate that the newly collected material can be assigned to the classic Apaporis caiman morphotype. However, our expanded genetic analysis fails to find appreciable mitochondrial molecular divergence of the Apaporis caiman population from the C. c. crocodilus population (COI-CytB: Amazon Peru 0.17 ± 0.06%, CytB-only: Caquetá River Colombia 0.08 ± 0.07%). The Apaporis caiman is interpreted to be a phenotypically distinct member of the cis-Andean C. crocodilus metapopulation that has not yet achieved (or may not be undergoing at all) appreciable genetic differentiation. Thus, it should not be considered a fully independent evolutionary lineage, nor given full species rank.

Genetic deletions and high diversity of Plasmodium falciparum histidine-rich proteins 2 and 3 genes in parasite populations in Ghana

Rapid diagnostic tests (RDTs) are used to diagnose malaria in Ghana and other malaria endemic countries. Plasmodium falciparum histidine-rich protein 2 (PFHRP2) based RDTs are widely used, however the occurrence of deletions of the pfhrp2 gene in some parasites have resulted in false negative test results. Monoclonal antibodies of PFHRP2 cross reacts with PFHRP3 because they share structural similarities and this complements the detection of the parasites by RDT. These two genes were investigated in Ghanaian P. falciparum parasite population to detect deletions and the polymorphisms in exon 2 of the pfhrp2 and pfhrp3 genes. Parasite isolates (2,540) from children ≤ 12 years with uncomplicated malaria from 2015 to 2020 transmission seasons were used. Both genes were amplified using nested PCR and negative results indicated the presence of the deletion of genes. Amplified genes were sequenced for the detection of the amino acid repeats. Deletions were observed in 30.7% (780/2,540) and 17.2% (438/2,540) of the samples for pfhrp2 and pfhrp3 respectively with increasing trends over the three time periods (χ2 -10.305, p = 0.001). A total of 1,632 amplicons were sequenced for each gene, analysis was done on 1,124 and 1,307 good quality sequences for pfhrp2 and pfhrp3 respectively. Pfhrp2 repeat polymorphisms were dominantly of types 2 (AHHAHHAAD) and 7 (AHHAAD) with large numbers of variants. A novel variant of type 14 (AHHANHATD) was seen for pfhrp2. For the pfhrp3 repeat types, 16 (AHHAAN), 17 (AHHDG) and 18 (AHHDD) were the dominant types observed. Variants of type 16 (AHHAAH) and (AHHASH) were also dominant. Repeat types 1, 2, 3, 4, 5, 6, 7, 8, 11, 13, 15, 16, and 19 were observed be shared by both genes. The haplotype diversity of both genes ranged between 0.872 and 1 indicating high diversity of the polymorphisms in the isolates. The implication of the findings of the frequencies of the pfhrp2 and pfhrp3 deletions as well as the variants of the main epitopes of the monoclonal antibodies for the RDT (types 2 and 7) in our isolates is an indication of decreased sensitivity of the RDTs in diagnosing malaria infections in Ghana.

Genome-Wide Identification and Characterization of G2-Like Transcription Factor Genes in Moso Bamboo (Phyllostachys edulis)

G2-like (GLK) transcription factors contribute significantly and extensively in regulating chloroplast growth and development in plants. This study investigated the genome-wide identification, phylogenetic relationships, conserved motifs, promoter cis-elements, MCScanX, divergence times, and expression profile analysis of PeGLK genes in moso bamboo (Phyllostachys edulis). Overall, 78 putative PeGLKs (PeGLK1–PeGLK78) were identified and divided into 13 distinct subfamilies. Each subfamily contains members displaying similar gene structure and motif composition. By synteny analysis, 42 orthologous pairs and highly conserved microsynteny between regions of GLK genes across moso bamboo and maize were found. Furthermore, an analysis of the divergence times indicated that PeGLK genes had a duplication event around 15 million years ago (MYA) and a divergence happened around 38 MYA between PeGLK and ZmGLK. Tissue-specific expression analysis showed that PeGLK genes presented distinct expression profiles in various tissues, and many members were highly expressed in leaves. Additionally, several PeGLKs were significantly up-regulated under cold stress, osmotic stress, and MeJA and GA treatment, implying that they have a likelihood of affecting abiotic stress and phytohormone responses in plants. The results of this study provide a comprehensive understanding of the moso bamboo GLK gene family, as well as elucidating the potential functional characterization of PeGLK genes.

Identification and genetic diversity analysis of Rickettsia in Dermacentor nuttalli within inner Mongolia, China

Background

The genus Rickettsia contains the lineages spotted fever group (SFG), typhus group (TG), and transitional group (TRG). The spotted fever group Rickettsia (SFGR) is transmitted by ticks. The tick species Dermacentor nuttalli is considered the main vector carrying SFGR in Inner Mongolia. Studying the genetic diversity and population structure of Rickettsia is essential for developing effective control strategies and predicting evolutionary trends of Rickettsia.

Methods

In 2019 we collected 408 D. nuttalli in the Inner Mongolia Autonomous Region, detected the percentage of Rickettsia-positive specimens, and characterized the haplotypes. From the Rickettsia-positive ticks, the gltA and ompA genes were extracted, amplified, and sequenced.

Results

Ten haplotypes of the gltA gene and 22 haplotypes of the ompA gene were obtained. The phylogenetic analysis showed that the haplotypes G1–G7 and G9 of the gltA gene cluster with Rickettsia raoultii, while G8 and G10 cluster with Rickettsia sibirica. Haplotypes O1–O15, O18 and O20–O22 of the ompA gene cluster with R. raoultii, while O16 and O19 cluster with R. sibirica. The average haplotype diversity was 0.3 for gltA and 0.7 for ompA. The average nucleotide diversity was greater than 0.05. Neutrality tests were nonsignificant for Tajima’s D results and Fu’s Fs results. The fixation index values (FST) showed that the degree of genetic differentiation between most sampled populations was small (FST < 0.05), whereas some populations showed a medium (FST > 0.05) or large (FST > 0.15) degree of differentiation. Analysis of molecular variance (AMOVA) revealed that the variation within populations was greater than that between populations. The mismatch analysis of Rickettsia showed double peaks.

Conclusions

We found two Rickettsia spp. (R. raoultii and R. sibirica). The high genetic disparity of Rickettsia allows for easy adaption to different environments. Genetic differentiation between populations is small, and Rickettsia populations do not show a geographically differentiated structure. The high rates of retention and infection of Rickettsia in D. nuttalli together with the animal husbandry exchange in Inner Mongolia gradually led to the harmonization of genetic characteristics of Rickettsia across various regions. Overall, the significant genetic diversity and geographical structure of Rickettsia in D. nuttalli are critical for SFGR control.

Graphical Abstract

An In Silico Analysis of Malaria Pre-Erythrocytic-Stage Antigens Interpreting Worldwide Genetic Data to Suggest Vaccine Candidate Variants and Epitopes

Failure to account for genetic diversity of antigens during vaccine design may lead to vaccine escape. To evaluate the vaccine escape potential of antigens used in vaccines currently in development or clinical testing, we surveyed the genetic diversity, measured population differentiation, and performed in silico prediction and analysis of T-cell epitopes of ten such Plasmodium falciparum pre-erythrocytic-stage antigens using whole-genome sequence data from 1010 field isolates. Of these, 699 were collected in Africa (Burkina Faso, Cameroon, Guinea, Kenya, Malawi, Mali, and Tanzania), 69 in South America (Brazil, Colombia, French Guiana, and Peru), 59 in Oceania (Papua New Guinea), and 183 in Asia (Cambodia, Myanmar, and Thailand). Antigens surveyed include cell-traversal protein for ookinetes and sporozoites, circumsporozoite protein, liver-stage antigens 1 and 3, sporozoite surface proteins P36 and P52, sporozoite asparagine-rich protein-1, sporozoite microneme protein essential for cell traversal-2, and upregulated-in-infectious-sporozoite 3 and 4 proteins. The analyses showed that a limited number of these protein variants, when combined, would be representative of worldwide parasite populations. Moreover, predicted T-cell epitopes were identified that could be further explored for immunogenicity and protective efficacy. Findings can inform the rational design of a multivalent malaria vaccine.

Novel pfk13 polymorphisms in Plasmodium falciparum population in Ghana

The molecular determinants of Plasmodium falciparum artemisinin resistance are the single nucleotide polymorphisms in the parasite’s kelch propeller domain, pfk13. Validated and candidate markers are under surveillance in malaria endemic countries using artemisinin-based combination therapy. However, pfk13 mutations which may confer parasite artemisinin resistance in Africa remains elusive. It has therefore become imperative to report all observed pfk13 gene polymorphisms in malaria therapeutic efficacy studies for functional characterization. We herein report all novel pfk13 mutations observed only in the Ghanaian parasite population. In all, 977 archived samples from children aged 12 years and below with uncomplicated malaria from 2007 to 2017 were used. PCR/Sanger sequencing analysis revealed 78% (763/977) of the samples analyzed were wild type (WT) for pfk13 gene. Of the 214 (22%) mutants, 78 were novel mutations observed only in Ghana. The novel SNPs include R404G, P413H, N458D/H/I, C473W/S, R529I, M579T/Y, C580R/V, D584L, N585H/I, Q661G/L. Some of the mutations were sites and ecological zones specific. There was low nucleotide diversity and purifying selection at the pfk13 locus in Ghanaian parasite population. With increasing drug pressure and its consequent parasite resistance, documenting these mutations as baseline data is crucial for future molecular surveillance of P. falciparum resistance to artemisinin in Ghana.

Phylogenetic analysis of Eimeria tenella isolated from the litter of different chicken farms in Mymensingh, Bangladesh

Background

Eimeria tenella is the most pathogenic intracellular protozoan parasite of seven Eimeria species causing chicken coccidiosis around the world. This species is particularly responsible for caecal coccidiosis leading to serious morbidity–mortality and financial loss in poultry production.

Methods

The present study explored the genetic diversity of E. tenella. Litter slurry was collected from 18 broiler farms located in Mymensingh district, Bangladesh. Litter samples were processed for oocyst isolation–identification using parasitological techniques followed by genomic DNA extraction from sporulated oocysts. For molecular analysis, the internaltranscribedspacer1 gene of E. tenella was amplified using species‐specific primers and sequenced. After editing and alignment, 263 bp sequences were used for analysis.

Results

Genetic analysis showed seven distinct genotypes and detected six single nucleotide polymorphisms among the 18 E. tenella isolates. The nucleotide and genotype diversity were 0.00507 and 0.8235, respectively. A phylogenetic tree was constructed with 66 sequences (seven studied genotypes and 59 reference sequences from GenBank database). The neighbour‐joining tree represented that the studied E. tenella isolates were grouped with reference E. tenella isolates with strong nodal support (100%) and the nucleotide sequences of E. tenella, E. necatrix, E. acervulina, E. brunetti, E. maxima, E. mitis and E. praecox formed separate clusters without any geographical boundaries.

Conclusions

This is the first study on the genetic analysis of E. tenella from Mymensingh district, Bangladesh. These findings will provide baseline data on the species conformation and genetic variations of E. tenella. Further extensive investigation will be needed to reveal the population genetic structure of this parasite and thus will facilitate the planning of effective control strategies.

Disjunction and Vicariance Between East and West Asia: A Case Study on Euonymus sect. Uniloculares Based on Plastid Genome Analysis

Scientists have long been captivated by biogeographic disjunctions, and disjunctions between East Asia and North America have been particularly well-studied at the genus and family levels. By contrast, disjunctions between eastern and western Asia have received less attention. Euonymus L. is taxonomically divided into two sections based on the number of cells in anthers as follows: E. sect. Uniloculares has one-celled anthers and occurs mainly in Asia, whereas E. sect. Biloculares has two-celled anthers and is distributed globally. We used Illumina sequencing to investigate the genomes of four species in sect. Uniloculares. The chloroplast (cp) genomes are highly conserved (157,290-158,094 bp). Pseudogenisation of ndhF and intron loss in rps16 was detected. Based on the cp genomes of the four species of E. sect. Uniloculares, we propose a novel hypothesis of disjunction between eastern and western Asia. Biogeographic reconstruction and molecular dating revealed that sect. Uniloculares separated from its sect. Biloculares forebears 4.0 Mya during the Pliocene era. The radial diversification of sect. Uniloculares from East Asia and the establishment of the western Asian clade during the Pleistocene era (1.9 Mya) were the results of both dispersal and vicariance, making the section the youngest diverged clade conforming to age estimation. The centre of origin of sect. Uniloculares was determined to be in East Asia. Disjunctions and diversification between eastern and western Asia in sect. Uniloculares are thought to have been caused by changes in monsoon patterns, temperature variations, and the emergence of the Gobi Desert.

MC1R diversity and its role in skin pigmentation variation in West Maharashtra, India

OBJECTIVES

MC1R polymorphisms have been reported to be under a selective constraint in populations inhabiting high UVR regions such as Africans; however, these patterns are not consistent. Here we analyze the MC1R gene in West Maharashtra, India to see if sequence diversity corresponds to their diverse pigmentary profiles and if MC1R is constrained in dark skinned tribal as compared to lighter skinned caste populations.

METHODS

A 2648 bp region of this gene was sequenced in 102 individuals and the data was compared for π, ϴ diversity indices. Tajima's D was assessed for signatures of purifying selection and MC1R variants were associated with MI measures using the additive, dominant, and recessive models. Pairwise F_ST was tested among study populations and between study populations and 1000 Genomes regional samples.

RESULTS

MC1R diversity was not uniquely patterned among castes and tribes. Non-synonymous variants rs2228479A, rs1805007_T, and rs885479_A showed low variability in these populations. Selection tests did not indicate any constraint on MC1R and pairwise F_ST were also low among the study populations (-0.0163 to 0.06112). The SNP rs3212359 was significantly associated with MI measures when tested using different association models.

CONCLUSIONS

We do not find evidence of a selective constraint on MC1R. The presence of a large number of unique haplotypes and low F_ST values at this locus suggests that MC1R polymorphisms may not be influencing pigmentation variation among castes and tribes in this region. Observed associations between rs3212359 and MI measures need to be validated through studies on larger samples and in-vitro functional studies.

Phylogenetics and Evolution of Potato Virus V: Another Potyvirus that Originated in the Andes

Potato virus V (PVV) causes a disease of potato (Solanum tubersosum) in South and Central America, Europe, and the Middle East. We report here the complete genomic sequences of 42 new PVV isolates from the potato's Andean domestication center in Peru and of eight historical or recent isolates from Europe. When the principal open reading frames of these genomic sequences together with those of nine previously published genomic sequences were analyzed, only two from Peru and one from Iran were found to be recombinant. The phylogeny of the 56 nonrecombinant open reading frame sequences showed that the PVV population had two major phylogroups, one of which formed three minor phylogroups (A1 to A3) of isolates, all of which are found only in the Andean region of South America (Peru and Colombia), and the other formed two minor phylogroups, a basal one of Andean isolates (A4) that is paraphyletic to a crown cluster containing all the isolates found outside South America (World). This suggests that PVV originated in the Andean region, with only one minor phylogroup spreading elsewhere in the world. In minor phylogroups A1 and A3, there were two subclades on long branches containing isolates from S. phureja evolving more rapidly than the others, and these interfered with dating calculations. Although no temporal signal was directly detected among the dated nonrecombinant sequences, PVV and potato virus Y (PVY) are from the same potyvirus lineage and are ecologically similar, so "subtree dating" was done via a single maximum likelihood phylogeny of PVV and PVY sequences, and PVY's well-supported 157 ce "time to most common recent ancestor" was extrapolated to date that of PVV as 29 bce. Thus the independent historical coincidences supporting the datings of the PVV and PVY phylogenies are the same; PVV arose ≥2,000 years ago in the Andes and was taken to Europe during the Columbian Exchange, where it diversified around 1853 ce, soon after the European potato late blight pandemic. PVV is likely to be more widespread than currently realized and is of biosecurity relevance for world regions that have not yet recorded its presence.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Morphological and molecular characterization of Castniidae (Lepidoptera) associated to sugarcane in Colombia

The giant sugarcane borer, Telchin licus, has been reported as an economically important sugarcane pest in Colombia; however, its taxonomic status has been scarcely investigated and previous reports offer an ambiguous characterization of both the immature and adult stages. The objective of this work is to identify Telchin species affecting sugarcane and alternative hosts in different departments of the country by integrating molecular analysis and conventional morphology. To date, T. licus has been found in the departments of Caquetá, Casanare, and Meta, while T. atymnius has been found in Antioquia, Caldas, Nariño, and Valle del Cauca. Sugarcane, Musaceae, and Heliconiaceae have been found to be hosts to both species. Additionally, the species T. cacica has also been registered in the department of Nariño, affecting heliconias and plantains. Genetic variation within the species allowed differentiation at the molecular level of subspecies of T. licus and T. atymnius, confirming that the subspecies present in Colombia are T. licus magdalena, T. atymnius humboldti, and T. atymnius atymnius. The haplotype diversity of populations is closely related to their geographical distribution, indicating low gene flow between populations and possible speciation inside the country. Analysis of genetic variance showed significant differences among and within T. atymnius populations, which may suggest a high genetic structure along the regions where it is found and the possible presence of additional subspecies to those previously reported. To understand the geographical and environmental conditions that determine the pest's distribution in Colombia, this information needs to be complemented with ecological considerations of possible geographical isolation and association of alternative hosts.

From the river to the ocean: mitochondrial DNA analyses provide evidence of spectacled caimans (Caiman crocodilus Linnaeus 1758) mainland–insular dispersal

There are few studies that have investigated the evolutionary history of large vertebrates on islands off the Caribbean coast of South America. Here we use the spectacled caiman (Caiman crocodilus) to investigate among- and within-population patterns of genetic diversity to understand connectivity between island and mainland populations. The spectacled caiman is naturally distributed across Central and South America including the islands of Trinidad and Tobago, which are considered to have the only natural insular populations of the species. Because of this apparent isolation, we sought to determine whether caimans on Trinidad and Tobago comprise a unique lineage and have reduced genetic diversity compared to mainland caimans. We test these hypotheses by using mitochondrial DNA variation to assess the phylogenetic and phylogeographical relationships of the C. crocodilus populations inhabiting these islands within the evolutionary context of the entire spectacled caiman complex. Phylogenetic analyses placed the Trinidad and Tobago samples together with samples from Colombia, Venezuela and Brazil into one well-supported clade, which corresponds to the defined Orinoco/upper Negro lineage. Interestingly, the majority of sequences from Trinidad and Tobago are similar or identical to haplotypes reported from Venezuela and Colombia, supporting the idea of a dispersal process from the Orinoco River to these islands. We discuss the implications of our findings for systematics and the conservation of the species and how these dispersal movements could shape the current phylogeographical structure depicted for C. crocodilus.

rbcL, a potential candidate DNA barcode loci for aconites: conservation of himalayan aconites

BACKGROUND

Aconitum heterophyllum Wall. ex Royle and Aconitum balfourii Stapf, are two highly important, threatened medicinal plants of the Indian Himalayan Region. Root-tubers of Aconites have occupied an important place in Indian pharmacopoeia from very ancient times. India is a hub of the wild-collected medicinal herbs industry in Asia and these two aconites are known to have been heavily traded from the region in illicit manner. Prosecution of these illegal trading crimes is hampered by lack of pharma-forensic expertise and tools.

METHODS AND RESULTS

Present study was conducted to evaluate the discriminatory potential of rbcL, a Chloroplast based DNA barcode marker for the authentication of these two Himalayan Aconites. Fresh plant samples were collected from their natural distributional range as well as raw materials were procured from herbal market and a total of 32 sequences were generated for the rbcL region. Analysis demonstrated that rbcL region can successfully be used for authentication and importantly, both the aconites, were successfully discriminated by rbcL locus with high bootstrap support (> 50%).

CONCLUSION

Molecular markers could certainly be relied upon morphological and chemical markers being tissue specific, having a higher discriminatory power and not age dependent. Phylogenetic analysis using Maximum Likelihood Method revealed that the rbcL gene could successfully discriminate Himalayan Aconites to species level and have potential to be used in pharma-forensic applications as well as to curb illicit trade of these invaluable medicinal plants.

Virulence effector SidJ evolution in Legionella pneumophila is driven by positive selection and intragenic recombination

Effector proteins translocated by the Dot/Icm type IV secretion system determine the virulence of Legionella pneumophila (L. pneumophila). Among these effectors, members of the SidE family (SidEs) regulate several cellular processes through a unique phosphoribosyl ubiquitination mechanism mediated by another effector, SidJ. Host-cell calmodulin (CaM) activates SidJ to glutamylate the SidEs of ubiquitin (Ub) ligases and to make a balanced Ub ligase activity. Given the central role of SidJ in this regulatory process, studying the nature of evolution of sidJ is important to understand the virulence of L. pneumophila and the interaction between the bacteria and its hosts. By studying sidJ from a large number of L. pneumophila strains and using various molecular evolution algorithms, we demonstrated that intragenic recombination drove the evolution of sidJ and contributed to sidJ diversification. Additionally, we showed that four codons of sidJ which are located in the N-terminal (NTD) (codons 58 and 200) and C-terminal (CTD) (codons 868 and 869) domains, but not in the kinase domain (KD) had been subjected to strong positive selection pressure, and variable mutation profiles of these codons were identified. Protein structural modeling of SidJ provided possible explanations for these mutations. Codons 868 and 869 mutations might engage in regulating the interactions of SidJ with CaM through hydrogen bonds and affect the CaM docking to SidJ. Mutation in codon 58 of SidJ might affect the distribution of main-chain atoms that are associated with the interaction with CaM. In contrast, mutations in codon 200 might influence the α-helix stability in the NTD. These mutations might be important to balance Ub ligase activity for different L. pneumophila hosts. This study first reported that intragenic recombination and positive Darwinian selection both shaped the genetic plasticity of sidJ, contributing to a deeper understanding of the adaptive mechanisms of this intracellular bacterium to different hosts.

Melatonin is involved in the modulation of the hypothalamic and pituitary activity in the South American plains vizcacha, Lagostomus maximus

Melatonin, the key messenger of photoperiodic information, is synthesized in the pineal gland by arylalkylamine N-acetyltransferase enzyme (AANAT). It binds to specific receptors MT₁ and MT₂ located in the hypothalamus and pituitary gland. Melatonin can modulate the reproductive axis affecting the secretion of gonadotropin-releasing hormone (GnRH) and luteinizing hormone (LH). The South American plains vizcacha, Lagostomus maximus, shows natural poliovulation of up to 800 oocytes per estrous cycle, a 154-day long pregnancy, and reactivation of the reproductive axis at mid-gestation with pre-ovulatory follicular recruitment, presence of active corpora lutea, and variations of the endocrine status. Here we analyzed the involvement of melatonin in the modulation of the hypothalamic and pituitary gland physiology of vizcacha thorough several approaches, including histological localization of melatoninergic system components, assessment of melatoninergic components expression throughout the reproductive cycle, and evaluation of the effect of melatonin on hypothalamic and pituitary activities during the follicular and luteal phases of the estrous cycle. AANAT and melatonin receptors were localized in the pineal gland and preoptic area of the hypothalamus. Increase in pineal AANAT and serum melatonin expression was observed as pregnancy progressed, with the lowest hypothalamic MT₁ and MT₂ levels at mid-pregnancy. Pulsatility assays demonstrated that melatonin induces GnRH and LH secretion at luteal phase. The melatoninergic system effects on hypothalamic and pituitary gland hormones secretion during pregnancy pinpoint to melatonin as a potential key factor underlying the reactivation of the reproductive axis activity at mid-gestation.

Iranian Strawberry crinkle cytorhabdovirus variation assessed using its movement protein (P3) gene

BACKGROUND

Strawberry crinkle virus (SCV) is a member of the genus Cytorhabdovirus, family Rhabdovirida, and order Mononegavirales. SCV affects the production of various strawberry cultivars. In this study we investigated the genetic diversity of SCV in strawberry fields based on P3 (movement protein) gene.

METHODS AND RESULTS

The samples were collected from strawberry fields in the Kurdistan Province, Iran. P3 gene from 20 SCV isolates, representing 18 nucleic acid haplotypes, is composed of 729 nucleotides, encoding a protein with 243 amino acids. SCV-P3 sequences shared 98.77%-99.86% nucleotide and 97.5%-100% amino acid sequence identity. Phylogenetic analyses of the new P3 sequences with two previously published SCV-P3 sequences from the Czech Republic showed that there are two major phylogroups (I and II) and three minor phylogroups in the body of the phylogeny, I-1, I-2, II-1. Comparisons of P3 gene sequences revealed a mutational bias, with more differences being transitions than transversions. The ratio of non-synonymous/synonymous nucleotide changes was < 1, indicating that SCV-P3 gene is under predominantly negative selection.

CONCLUSIONS

Phylogenetic and sequence identity analyses showed that SCV isolates from Iran are closely related and have not diverged more than 2% based on P3 gene despite geographical separation and strawberry cultivar. This is the first report of the genetic diversity of SCV worldwide.

The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces

Many fungi require specific growth conditions before they can be identified. Direct environmental DNA sequencing is advantageous, although for some taxa, specific primers need to be used for successful amplification of molecular markers. The internal transcribed spacer region is the preferred DNA barcode for fungi. However, inter- and intra-specific distances in ITS sequences highly vary among some fungal groups; consequently, it is not a solely reliable tool for species delineation. Ampelomyces, mycoparasites of the fungal phytopathogen order Erysiphales, can have ITS genetic differences up to 15%; this may lead to misidentification with other closely related unknown fungi. Indeed, Ampelomyces were initially misidentified as other pycnidial mycoparasites, but subsequent research showed that they differ in pycnidia morphology and culture characteristics. We investigated whether the ITS2 nucleotide content and secondary structure was different between Ampelomyces ITS2 sequences and those unrelated to this genus. To this end, we retrieved all ITS sequences referred to as Ampelomyces from the GenBank database. This analysis revealed that fungal ITS environmental DNA sequences are still being deposited in the database under the name Ampelomyces, but they do not belong to this genus. We also detected variations in the conserved hybridization model of the ITS2 proximal 5.8S and 28S stem from two Ampelomyces strains. Moreover, we suggested for the first time that pseudogenes form in the ITS region of this mycoparasite. A phylogenetic analysis based on ITS2 sequences-structures grouped the environmental sequences of putative Ampelomyces into a different clade from the Ampelomyces-containing clades. Indeed, when conducting ITS2 analysis, resolution of genetic distances between Ampelomyces and those putative Ampelomyces improved. Each clade represented a distinct consensus ITS2 S2, which suggested that different pre-ribosomal RNA (pre-rRNA) processes occur across different lineages. This study recommends the use of ITS2 S2s as an important tool to analyse environmental sequencing and unveiling the underlying evolutionary processes.

Genetic differentiation and restricted gene flow in rice landraces from Yunnan, China: effects of isolation-by-distance and isolation-by-environment

BACKGROUND

Understanding and identifying the factors responsible for genetic differentiation is of fundamental importance for efficient utilization and conservation of traditional rice landraces. In this study, we examined the spatial genetic differentiation of 594 individuals sampled from 28 locations in Yunnan Province, China, covering a wide geographic distribution and diverse growing conditions. All 594 accessions were studied using ten unlinked target genes and 48 microsatellite loci, and the representative 108 accessions from the whole collection were sampled for resequencing.

RESULTS

The genetic diversity of rice landraces was quite different geographically and exhibited a geographical decline from south to north in Yunnan, China. Population structure revealed that the rice landraces could be clearly differentiated into japonica and indica groups, respectively. In each group, the rice accessions could be further differentiated corresponded to their geographic locations, including three subgroups from northern, southern and middle locations. We found more obvious internal geographic structure in the japonica group than in the indica group. In the japonica group, we found that genetic and phenotypic differentiation were strongly related to geographical distance, suggesting a pattern of isolation by distance (IBD); this relationship remained highly significant when we controlled for environmental effects, where the likelihood of gene flow is inversely proportional to the distance between locations. Moreover, the gene flow also followed patterns of isolation by environment (IBE) whereby gene flow rates are higher in similar environments. We detected 314 and 216 regions had been differentially selected between Jap-N and Jap-S, Ind-N and Ind-S, respectively, and thus referred to as selection signatures for different geographic subgroups. We also observed a number of significant and interesting associations between loci and environmental factors, which implies adaptation to local environment.

CONCLUSIONS

Our findings highlight the influence of geographical isolation and environmental heterogeneity on the pattern of the gene flow, and demonstrate that both geographical isolation and environment drives adaptive divergence play dominant roles in the genetic differentiation of the rice landraces in Yunnan, China as a result of limited dispersal.

Specialist versus generalist parasites: the interactions between host diversity, environment and geographic barriers in avian malaria

The specialist versus generalist strategies of hemoparasites in relation to their avian host, as well as environmental factors, can influence their prevalence, diversity and distribution. In this paper we investigated the influence of avian host species, as well as the environmental and geographical factors, on the strategies of Haemoproteus and Plasmodium hemoparasites. We determined prevalence and diversity by targeting their cytochrome b (Cytb) in a total of 2,590 passerine samples from 138 localities of Central and South America, and analysed biogeographic patterns and host-parasite relationships. We found a total prevalence of 23.2%. Haemoproteus presented a higher prevalence (15.3%) than Plasmodium (4.3%), as well as a higher diversity and host specificity. We determined that Plasmodium and Haemoproteus prevalences correlated positively with host diversity (Shannon index) and were significantly influenced by bird diversity, demonstrating a possible "amplification effect". We found an effect of locality and the avian family for prevalences of Haemoproteus and Plasmodium. These results suggest that Haemoproteus is more specialist than Plasmodium and could be mostly influenced by its avian host and the Andes Mountains.

Legacy of draught cattle breeds of South India: Insights into population structure, genetic admixture and maternal origin

The present study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The diversity of South Indian cattle was moderately high. A significantly strong negative correlation coefficient of -0.674 (P<0.05) was observed between the effective population size of different breeds and their estimated F_IS. The genetic structure analysis revealed the distinctness of Kangayam, Vechur and Punganur cattle from the rest of the zebu breeds. The results showed the influence of Hallikar breed in the development of most Mysore type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admixture (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former being predominant than the later. The pairwise differences among the I2 haplotypes of South Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results indicated the need for additional sampling and comprehensive analysis of mtDNA control region variations to unravel the probable location of origin and domestication of I2 zebu lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of endangerment due to small effective population size and high rate of inbreeding (ii) lack of sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in zebu cattle. Availability of purebred semen for artificial insemination, incorporation of genomic/molecular information to identify purebred animals and increased awareness among farmers will help to maintain breed purity, conserve and improve these important draught cattle germplasms of South India.

Demography reveals populational expansion of a recently extinct Iberian ungulate

Reconstructing the demographic history of endangered taxa is paramount to predict future fluctuations and disentangle the contributing factors. Extinct taxa or populations might also provide key insights in this respect by means of the DNA extracted from museum specimens. Nevertheless, the degraded status of biological material and the limited number of records may pose some constraints. For this reason, identifying all available sources, including private and public biological collections, is a crucial step forward. In this study, we reconstructed the demographic history based on cytochrome-b sequence data of the Pyrenean ibex (Capra pyrenaica pyrenaica), a charismatic taxon of the European wildlife that became extinct in the year 2000. Moreover, we built a database of the museum specimens available in public biological collections worldwide and genotyped a privately owned 140-year-old trophy from the Spanish Pyrenees to confirm its origin. We found that the population of the Pyrenean ibex underwent a recent expansion approximately 20,000 years ago, after which trophy hunting and epizootics triggered a relentless population decline. Our interpretations, based on the genetic information currently available in public repositories, provide a solid basis for more exhaustive analyses relying on all the new sources identified. In particular, the adoption of a genome-wide approach appears a fundamental prerequisite to disentangle the multiple contributing factors associated with low genetic diversity, including inbreeding depression, acting as extinction drivers.

Genome-wide identification and expression analysis of ADP-ribosylation factors associated with biotic and abiotic stress in wheat (Triticum aestivum L.)

The ARF gene family plays important roles in intracellular transport in eukaryotes and is involved in conferring tolerance to biotic and abiotic stresses in plants. To explore the role of these genes in the development of wheat (Triticum aestivum L.), 74 wheat ARF genes (TaARFs; including 18 alternate transcripts) were identified and clustered into seven sub-groups. Phylogenetic analysis revealed that TaARFA1 sub-group genes were strongly conserved. Numerous cis-elements functionally associated with the stress response and hormones were identified in the TaARFA1 sub-group, implying that these TaARFs are induced in response to abiotic and biotic stresses in wheat. According to available transcriptome data and qRT-PCR analysis, the TaARFA1 genes displayed tissue-specific expression patterns and were regulated by biotic stress (powdery mildew and stripe rust) and abiotic stress (cold, heat, ABA, drought and NaCl). Protein interaction network analysis further indicated that TaARFA1 proteins may interact with protein phosphatase 2C (PP2C), which is a key protein in the ABA signaling pathway. This comprehensive analysis will be useful for further functional characterization of TaARF genes and the development of high-quality wheat varieties.

Genetic diversity analysis of Dermacentor nuttalli within Inner Mongolia, China

Background

Ticks (Arthropoda, Ixodida), after mosquitoes, are the second most prevalent vector of infectious diseases. They are responsible for spreading a multitude of pathogens and threatening the health and welfare of animals and human beings. However, given the history of tick-borne pathogen infections in the Inner Mongolia Autonomous Region of China, surprisingly, neither the genetic diversity nor the spatial distribution of haplotypes within ticks has been studied.

Methods

We characterized the haplotype distribution of Dermacentor nuttalli in four main pastoral areas of the Inner Mongolia Autonomous Region, by sampling 109 individuals (recovered from sheep) in April–August 2019. The 16S rRNA gene, cytochrome c oxidase subunit I (COI), and the internal transcribed spacer 2 region (ITS2) were amplified and sequenced from extracted DNA.

Results

Twenty-six haplotypes were identified using 16S rRNA sequences, 57 haplotypes were identified with COI sequences, and 75 haplotypes were identified with ITS2 sequences. Among the three genes, total haplotype diversity was greater than 0.7, while total nucleotide diversity was greater than 0.06. Neutrality tests revealed a significantly negative Tajima’s D result, while Fu's Fs was not significantly positive. Fixation index values (F_ST) indicated that the degree of genetic differentiation among some sampled populations was small, while for others it was moderate. Analysis of molecular variance (AMOVA) revealed that the variation within populations was greater than that among populations. The mismatch analysis of D. nuttalli exhibited double peaks.

Conclusion

The genetic diversity of D. nuttalli populations in our region can likely adapt to different geographical environments, thereby leading to genetic diversity, and creating genetic differentiation among different populations. However, genetic differentiation is cryptic and does not form a pedigree geographical structure.

Prevention and Control of Pathogens Based on Big-Data Mining and Visualization Analysis

Morbidity and mortality caused by infectious diseases rank first among all human illnesses. Many pathogenic mechanisms remain unclear, while misuse of antibiotics has led to the emergence of drug-resistant strains. Infectious diseases spread rapidly and pathogens mutate quickly, posing new threats to human health. However, with the increasing use of high-throughput screening of pathogen genomes, research based on big data mining and visualization analysis has gradually become a hot topic for studies of infectious disease prevention and control. In this paper, the framework was performed on four infectious pathogens (Fusobacterium, Streptococcus, Neisseria, and Streptococcus salivarius) through five functions: 1) genome annotation, 2) phylogeny analysis based on core genome, 3) analysis of structure differences between genomes, 4) prediction of virulence genes/factors with their pathogenic mechanisms, and 5) prediction of resistance genes/factors with their signaling pathways. The experiments were carried out from three angles: phylogeny (macro perspective), structure differences of genomes (micro perspective), and virulence and drug-resistance characteristics (prediction perspective). Therefore, the framework can not only provide evidence to support the rapid identification of new or unknown pathogens and thus plays a role in the prevention and control of infectious diseases, but also help to recommend the most appropriate strains for clinical and scientific research. This paper presented a new genome information visualization analysis process framework based on big data mining technology with the accommodation of the depth and breadth of pathogens in molecular level research.

Population genetic structure of the highly endangered butterfly Coenonympha oedippus (Nymphalidae: Satyrinae) at its southern edge of distribution

The Slovenian False Ringlet Coenonympha oedippus populations are under serious threat, as in the last two decades have witnessed a sharp decline in population distribution and size due to destruction, fragmentation and/or habitat quality degradation through intensive agriculture, abandonment of use and urbanization. We investigated the genetic diversity and structure of C. oedippus from the entire range of the species in Slovenia. Our results showed that the genetic variation in the Slovenian C. oedippus populations agrees with the geographical structure and the ecotypes previously determined by morphological and ecological data. We confirmed the existence of four genetically divergent and spatially non-overlapping geographical groups (Istria, Karst, Gorica, Ljubljansko barje) and two ecotypes ("wet" and "dry"). Despite small sample sizes due to critically threatened species, the results indicated significant nuclear and mitochondrial genetic diversity within the spatial groups. By gaining new insights into the evolutionary history of the C. oedippus population, we have recommended to consider the Slovenian population as one Evolutionary Significant Unit, and four spatial populations as Management Units for conservation purposes.

MiR396 regulatory network and its expression during grain development in wheat

Wheat contains the largest number of miR396 family with 17 miR396 in Poaceae. MiR396 regulatory network underlying wheat grain development has not comprehensively been explored. Our results showed that precursor miR396 family in Poaceae exhibited not only conservativeness but also diversification especially in wheat. Five haplotypes were detected in Poaceae species, while 4 haplotypes in wheat with Hap-4 (miR396a) and Hap-5 (miR396n) unique to wheat. GO enrichment analysis of target genes showed that the first 20 enrichment functions of miR396a and miR396n are completely different from each other, and also completely different from miR396(b-g), miR396(h-m), and miR396(o-q). Functional annotation on the 18 target genes shared by miR396(b-g), miR396(h-m), and miR396(o-q) found that 11 of the 18 target genes are growth-regulating factor (GRF) genes. Our results indicated that, during the grain filling stage of wheat, miR396 is involved in the development of grains by regulating the expression of GRF genes (GRF1, GRF6, and GRF9). Although the enrichment function of miR396(b-g), miR396(h-m), and miR396(o-q) is the same, the gene functional networks they formed differ greatly. Our results indicated that polyploidization enriches not only the diversity of miR396 family and its target genes but also gene functional networks in wheat. These results laid foundation for further elucidating function of miR396 gene family underlying wheat grain development.

Chloroplast-based DNA barcode analysis indicates high discriminatory potential of matK locus in Himalayan temperate bamboos

The study was conducted to evaluate the discriminatory potential of selected chloroplast-based DNA barcode regions for identifying and resolving phylogeny of the Indian bamboos. Among 11 chloroplast markers screened, only four, namely matK, rbcL, psbK-I and rps16-trnQ showed successful amplification in 88 genotypes of 30 Indian bamboo taxa under Bambuseae and Arundinarieae tribes. A total of 244 sequences were generated for the four chloroplast regions. Tree-based analysis demonstrated that none of the tested regions successfully discriminated the taxa under Bambuseae tribe. Importantly, our highly concerned Himalayan temperate bamboo species under Arundinarieae tribe, were successfully discriminated by matK locus with high bootstrap support (>60%). Sequence comparisons revealed that the discriminatory power demonstrated by matK region actually lies in the few unique fixed nucleotides (UFNs) despite the overall DNA polymorphism. Although, rps16-trnQ region was found to be the most polymorphic and revealed high genetic divergence among different taxonomic levels, it could not successfully discriminated the taxa with strong statistical support. In a taxonomically difficult plant group like bamboos, whose genome is relatively more complex and has a slow rate of molecular evolution, it is difficult to get a universal marker. Further, highly variable barcode regions utilized in other species may not be informative, and thus, the development of DNA barcodes for different taxonomic levels, such as lineages or tribes could be a viable approach.

Genetic diversity of Listeria monocytogenes serotype 1/2a strains collected in Brazil by Multi-Virulence-Locus Sequence Typing

Listeria monocytogenes is an opportunistic pathogen with the ability to adapt to different environmental conditions, resulting in safety issues for food producers. Foods contaminated by L. monocytogenes can represent a risk if consumed by susceptible individuals such as elderly, pregnant women and the immunocompromised. The aim of this study was to evaluate the genetic diversity of a collection of L. monocytogenes isolated from different matrices in Brazil during the period of 1979-2015. A total of 51 L. monocytogenes serotype 1/2a strains isolated from clinical samples (n = 3) and food samples (n = 48) were characterized by Multi-Virulence-Locus Sequence Typing (MVLST). The strains were assigned to nine virulence types (VT): VT-11 (n = 3, 5·9%), VT-45 (n = 27, 52·9%), VT-59 (n = 11, 21·6%), VT-68 (n = 3, 5·9%), VT-94 (n = 2, 3·9%), VT-107 (n = 2, 3·9%), VT-184 (n = 1, 1·9%), VT-185 (n = 1, 1·9%) and VT-186 (n = 1, 1·9%); and four of them (VT-11, VT-45, VT-59 and VT-68) have already been associated with cases of listeriosis worldwide. The VT-11, VT-59 (Epidemic Clone V) and VT-186 were identified in blood culture samples, as well as in different classes of foods. It is recommended that the epidemiological surveillance agencies evaluate the risk that foods contaminated with L. monocytogenes VTs pose to susceptible populations.

Whole genome sequencing of Plasmodium vivax isolates reveals frequent sequence and structural polymorphisms in erythrocyte binding genes

Plasmodium vivax malaria is much less common in Africa than the rest of the world because the parasite relies primarily on the Duffy antigen/chemokine receptor (DARC) to invade human erythrocytes, and the majority of Africans are Duffy negative. Recently, there has been a dramatic increase in the reporting of P. vivax cases in Africa, with a high number of them being in Duffy negative individuals, potentially indicating P. vivax has evolved an alternative invasion mechanism that can overcome Duffy negativity. Here, we analyzed single nucleotide polymorphism (SNP) and copy number variation (CNV) in Whole Genome Sequence (WGS) data from 44 P. vivax samples isolated from symptomatic malaria patients in southwestern Ethiopia, where both Duffy positive and Duffy negative individuals are found. A total of 123,711 SNPs were detected, of which 22.7% were nonsynonymous and 77.3% were synonymous mutations. The largest number of SNPs were detected on chromosomes 9 (24,007 SNPs; 19.4% of total) and 10 (16,852 SNPs, 13.6% of total). There were particularly high levels of polymorphism in erythrocyte binding gene candidates including merozoite surface protein 1 (MSP1) and merozoite surface protein 3 (MSP3.5, MSP3.85 and MSP3.9). Two genes, MAEBL and MSP3.8 related to immunogenicity and erythrocyte binding function were detected with significant signals of positive selection. Variation in gene copy number was also concentrated in genes involved in host-parasite interactions, including the expansion of the Duffy binding protein gene (PvDBP) on chromosome 6 and MSP3.11 on chromosome 10. Based on the phylogeny constructed from the whole genome sequences, the expansion of these genes was an independent process among the P. vivax lineages in Ethiopia. We further inferred transmission patterns of P. vivax infections among study sites and showed various levels of gene flow at a small geographical scale. The genomic features of P. vivax provided baseline data for future comparison with those in Duffy-negative individuals and allowed us to develop a panel of informative Single Nucleotide Polymorphic markers diagnostic at a micro-geographical scale.

Genetic diversity in natural range remnants of the critically endangered hirola antelope

The hirola antelope (Beatragus hunteri) is considered to be the most endangered antelope in the world. In the ex situ translocated population at Tsavo East National Park, calf mortality and the critically low population numbers might suggest low genetic diversity and inbreeding depression. Consequently, a genetic study of the wild population is pivotal to gain an understanding of diversity and differentiation within its range before designing future translocation plans to increase the genetic diversity of the ex situ population. For that purpose, we assessed 55 individuals collected across five localities in eastern Kenya, covering its entire natural range. We used the complete mitochondrial DNA control region and microsatellite genotyping to estimate genetic diversity and differentiation across its range. Nuclear genetic diversity was moderate in comparison to other endangered African antelopes, with no signals of inbreeding. However, the mitochondrial data showed low nucleotide diversity, few haplotypes and low haplotypic differentiation. Overall, the inferred low degree of genetic differentiation and population structure suggests a single population of hirola across the natural range. An overall stable population size was inferred over the recent history of the species, although signals of a recent genetic bottleneck were found. Our results show hope for ongoing conservation management programmes and that there is a future for the hirola in Kenya.