Genetic Characteristics of the Baikal Seal Pusa sibirica Population

Nucleotide sequence diversity in two mtDNA loci (the cytochrome b gene and the control region) was for the first time studied in the Baikal seal Pusa sibirica with the use of several spatiotemporal samples. The population was found to be evolutionarily young and to be in the stage of demographic expansion.

Morphological and molecular characteristics of Plasmodium juxtanucleare in layer chicken from three districts of Yogyakarta, Indonesia

Background and Aim

Blood parasite infections in poultry, such as Plasmodium, are a serious threat to the poultry industry due to their potential to cause economic losses. To date, there has been inadequate research on the morphological and molecular detection of the different Plasmodium species that infect poultry in Indonesia. Therefore, this study aimed to analyze the morphological and molecular characteristics of Plasmodium spp. and the several predisposing factors for Plasmodium infection in layer chickens from three districts of Yogyakarta, Indonesia.

Materials and Methods

One hundred and five blood samples from layer chickens were collected from 13 farms located in three districts of Yogyakarta (Sleman, Bantul, and Kulon Progo) between September and November 2022. Blood samples were subjected to microscopic and polymerase chain reaction (PCR) analyses. Sequencing was performed using basic local alignment search tools to identify the nucleotide structure of cytochrome b. Phylogenetic analysis of Plasmodium was performed using the MEGA-X software.

Results

Microscopic examination revealed that 17/105 positives (16.19%) were positive for blood parasite infection. Trophozoites, erythrocytic meronts, and microgametocytes of Plasmodium were found in blood samples. Based on the morphological examination, the species found in the samples was close to Plasmodium juxtanucleare. Polymerase chain reaction examination revealed that 21/60 samples were positive for Plasmodium (35%). The Plasmodium species identified from the sequenced samples were proven to be P. juxtanucleare. The P. juxtanucleare from Thailand was closely related to samples (99.64%-100%) with a genetic distance of 0%-1%. In addition, age, population, and cage type were not significantly associated with Plasmodium infection.

Conclusion

Based on microscopic and PCR examinations, the Plasmodium species found in the three districts of Yogyakarta was P. juxtanucleare. The genetic distance between samples from the three districts of Yogyakarta was closely related (0%-1%) to P. juxtanucleare from Thailand and Japan. There was no correlation between Plasmodium infection and age, cage type, or population.

Molecular Epidemiology of Theileria annulata in Cattle from Two Districts in Punjab (Pakistan)

Simple Summary

Pakistan is a tropical country where climate is favourable for tick growth and hence its incidence of tick-borne diseases is high, affecting the output of the livestock sector. In the present study the infection rate of Theileria annulata, the causative agent of bovine theileriosis, was compared in apparently healthy cattle enrolled from two different regions in Pakistan. Parasite prevalence was found to be higher in Dera Ghazi Khan District than in Lodhran. The infection rate was higher in cattle that were infested with ticks and in those animals that were housed indoors at dairy farms with other animals. This prophylactic detection of parasite will help to design strategies to control tick and tick-borne diseases in study areas.

Abstract

The present study was designed to report the molecular prevalence of T. annulata in cattle blood samples collected from Punjab in Pakistan. A total of 428 cattle blood samples were collected from Districts Lodhran (n = 218) and Dera Ghazi Khan (n = 210). The prevalence of T. annulata was determined by the amplification of a fragment from its cytochrome b gene and parasite prevalence was significantly higher (p = 0.03) in the blood samples of cattle collected from Dera Ghazi Khan (70/210; 33%) as compared to Lodhran (52/218; 24%). Presence of T. annulata was also confirmed by the amplification of a fragment from their 30 kDa gene. The amplified PCR products of both genes were confirmed by DNA sequencing and these partial DNA sequences were submitted to GenBank. Phylogenetic analysis revealed that amplified partial gene sequences resembled previously reported T. annulata sequences in cattle from India, China, Iran, Tunisia, Turkey and Egypt. The incidence of T. annulata infection was higher in Sahiwal cattle (p = 0.04) than the other enrolled cattle breed from Dera Ghazi Khan. Female cattle from Lodhran (p = 0.02), while males (p = 0.02), animals housed in close compounds (p = 0.04), animals with a tick burden (p = 0.005) and farms with only cattle (p = 0.01) in Dear Ghazi Khan were found to be more susceptible to T. annulata infection. We recommend that large-scale tick and tick-borne disease control strategies be implemented in both districts under investigation, especially in Dera Ghazi Khan.

Multiple species-specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats

Large carnivore feeding ecology plays a crucial role for management and conservation for predators and their prey. One of the keys to this kind of research is to identify the species composition in the predator diet, for example, prey determination from scat content. DNA-based methods applied to detect prey in predators' scats are viable alternatives to traditional macroscopic approaches, showing an increased reliability and higher prey detection rate. Here, we developed a molecular method for prey species identification in wolf (Canis lupus) scats using multiple species-specific marker loci on the cytochrome b gene for 18 target species. The final panel consisted of 80 assays, with a minimum of four markers per target species, and that amplified specifically when using a high-throughput Nanofluidic array technology (Fluidigm Inc.). As a practical example, we applied the method to identify target prey species DNA in 80 wolf scats collected in Sweden. Depending on the number of amplifying markers required to obtain a positive species call in a scat, the success in determining at least one prey species from the scats ranged from 44% to 92%. Although we highlight the need to evaluate the optimal number of markers for sensitive target species detection, the developed method is a fast and cost-efficient tool for prey identification in wolf scats and it also has the potential to be further developed and applied to other areas and large carnivores as well.

[Genetic diversity and genetic structure of Sorex isodon in Northeast China]

A total of 64 haplotypes were obtained from the complete Cytochrome b gene (Cyt b) of 77 Sorex isodon collected from three populations (Daxing'anling, Xiaoxing'anling, and Changbai Mountains) in Northeast China. The haplotype diversity was 0.9920 and the nucleotide diversity was 0.0105, indicating high genetic diversity. The genetic diversity of Changbai Mountains population was significantly higher than that of Daxing'anling and Xiaoxing'anling populations. The F-statistics, the number of migrants per generation and the genetic distance results showed that the genetic distances among the populations and among the sampling sites were generally consistent with geographical distance. Analysis of molecular variance showed that the differentiation among populations, among sampling sites, and within sampling site accounted for 33.4%, 10.2% and 56.4% of total variation, respectively. The analysis of population history showed that S. isodon in Northeast China experienced no population expansion. The reported complete sequence of Cyt b gene of S. isodon (GenBank) of Europe and other parts of Asia was downloaded to examine the genetic structure of S. isodon. The phylogenetic tree was divided into two large branches. One branch consisted mainly of Daxing'anling and Xiaoxing'anling samples. The other branch was departed into two sub-branches. Median-joining network analysis showed that there were three lineages: one lineage mainly consisted of haplotypes from Daxing'anling and Xiaoxing'anling, and also four haplotypes of Changbai Mountains, while the other lineage included a few haplotypes of three populations in Northeast China, and those from Baikal Lake, Russia and Finland. The last lineage was entirely composed of haplotypes from Changbai Mountains. The results of genetic diversity, phylogenetic tree and median-joining network all suggested that the Changbai Mountains was the refuge for S. isodon during last glacial.

Rapid chromosomal evolution in enigmatic mammal with XX in both sexes, the Alay mole vole Ellobiusalaicus Vorontsov et al., 1969 (Mammalia, Rodentia)

Evolutionary history and taxonomic position for cryptic species may be clarified by using molecular and cytogenetic methods. The subterranean rodent, the Alay mole vole Ellobiusalaicus Vorontsov et al., 1969 is one of three sibling species constituting the subgenus Ellobius Fischer, 1814, all of which lost the Y chromosome and obtained isomorphic XX sex chromosomes in both males and females. E.alaicus is evaluated by IUCN as a data deficient species because their distribution, biology, and genetics are almost unknown. We revealed specific karyotypic variability (2n = 52-48) in E.alaicus due to different Robertsonian translocations (Rbs). Two variants of hybrids (2n = 53, different Rbs) with E.tancrei Blasius, 1884 were found at the Northern slopes of the Alay Ridge and in the Naryn district, Kyrgyzstan. We described the sudden change in chromosome numbers from 2n = 50 to 48 and specific karyotype structure for mole voles, which inhabit the entrance to the Alay Valley (Tajikistan), and revealed their affiliation as E.alaicus by cytochrome b and fragments of nuclear XIST and Rspo1 genes sequencing. To date, it is possible to expand the range of E.alaicus from the Alay Valley (South Kyrgyzstan) up to the Ferghana Ridge and the Naryn Basin, Tien Shan at the north-east and to the Pamir-Alay Mountains (Tajikistan) at the west. The closeness of E.tancrei and E.alaicus is supported, whereas specific chromosome and molecular changes, as well as geographic distribution, verified the species status for E.alaicus. The case of Ellobius species accented an unevenness in rates of chromosome and nucleotide changes along with morphological similarity, which is emblematic for cryptic species.

The phylogenetics of Leucocytozoon caulleryi infecting broiler chickens in endemic areas in Indonesia

Aim

The objective of this research was to determine the species and strains of Leucocytozoon caulleryi and study the phylogenetics of L. caulleryi of broiler chickens in endemic areas in Indonesia.

Materials and Methods

Blood samples were collected from broiler chickens originated from endemic area in Indonesia, i.e., Pasuruan, Lamongan, Blitar, Lumajang, Boyolali, Purwokerto, and Banjarmasin in 2017. Collected blood was used for microscopic examination, sequencing using BLAST method to identify the nucleotide structure of cytochrome b (cyt b) gene that determines the species, and the phylogenetics analysis of L. caulleryi that infected broiler chickens in endemic areas in Indonesia, using Mega 5 software.

Results

The results showed that Plasmodium sp. and L. caulleryi were infected broiler chickens in endemic areas in Indonesia. L. caulleryi in one area had very close phylogenetic relations with those in other areas. The genetic distance between L. caulleryi taxa from various endemic areas is very close (<5%).

Conclusion

There is a very close phylogenetics among strains of L. caulleryi that infected broiler chickens in various endemic areas in Indonesia.

Genetic differentiation in blue shark, Prionace glauca, from the central Pacific Ocean, as inferred by mitochondrial cytochrome b region

Six hundred and ninety-seven base pairs of cytochrome b gene of mtDNA was sequenced and analyzed for 78 blue shark Prionace glauca individuals from three sampled locations in the central Pacific Ocean (CPO). In total, three polymorphic sites were detected which defined four haplotypes. The haplotype diversity (h) ranged from 0.517 to 0.768, and nucleotide diversity (π) was between 0.0007 and 0.0011. Analysis of molecular variance indicated a non-significant differentiation among subpopulations. Furthermore, pairwise F_ST score analysis revealed a non-significant differentiation among three sampled regions. Generally, low genetic differences were found between different geographic locations in the CPO. This study suggests a single panmictic population of P. glauca in the CPO.

Study of Genetic Marker of Cuscuses (Marsupialia: Phalangeridae) from Maluku and Papua Based on Cytochrome b Gene Sequences

Cuscuses is marsupials animal (Phalangeridae) which has limited spread in eastern Indonesia (Sulawesi, Maluku, Papua and Timor islands), Australia and Papua New Guinea. The ex-situ and in-situ conservation of cuscuses under captivating condition is an alternative solution to protect from extinction. This study aimed to determine nucleotide sequences and genetic marker on cyt b gene with sequencing method of each species on two provinces. Whole genome DNA was extracted from 22 samples of cuscuses obtained from different habitats, Maluku (13 individuals) and Papua (8 individuals) according to the protocol of Qiamp DNA Blood Mini Kit (Qiagen) and then it was used as template for amplification of cyt b gene by using PCR method. The PCR product were then purified using column chromatography and were used as template for sequencing reaction. Results sequencing of cyt b gene were analyzed using MEGA program versions 6.0. The PCR product gives results nucleotides of 982 bp according to database GeneBank and sequencing product gives results nucleotides of 771 bp. Nucleotides alignment of Phalanger members was found 24 nucleotides distinguishing and Spilocuscus members was found 11 nucleotides distinguishing, which can be used as genetic marker between Phalanger and Spilocuscus members from Papua and Maluku.

Genetic characterization of Bagarius species using cytochrome c oxidase I and cytochrome b genes

In this study, we first inferred the genetic variability of two Bagarius bagarius populations collected from Ganges and Brahmaputra rivers of India using two mtDNA markers. Sequence analysis of COI gene did not show significant differences between two populations whereas cytochrome b gene showed significant differences between two populations. Followed by, genetic relationship of B. bagarius and B. yarrielli was analyzed using COI and cytochrome b gene and the results showed a higher level genetic variation between two species. The present study provides support for the suitability of COI and cytochrome b genes for the identification of B. bagarius and B. yarrielli.

[Phylogeny of genus Spermophilus and position of Alashan ground squirrel (Spermophilus alashanicus, Buchner, 1888) on phylogenetic tree of Paleartic short-tailed ground squirrels]

Phylogenetic relationships within a group of Paleartic short tailed ground squirrels (Spermophilus), recently defined as genus, are not sufficiently clear and need a critical revision. Interspecies hybridization, found in Eurasian Spermophilus, can affect the results of reconstruction of molecular phylogeny. Alashan ground squirrel position on the phylogenetic tree needs clarification. We analyzed eight nucleotide sequences of cytb gene of S. alashanicus and 127 sequences of other Spermophilus species form GenBank. S.alashanicus and S. dauricus close phylogenetic relationship, and their affinity to ancestral forms of the group are revealed. Monophyly of Colobotis subgenus was confirmed. Paraphyly of eastern and western forms of S. relictus was shown.

Population structure of Squatina guggenheim (Squatiniformes, Squatinidae) from the south-western Atlantic Ocean

Population genetic analyses based on both mitochondrial cytochrome b and the internal transcribed spacer 2 of recombinant (r)DNA genes were implemented to examine hypotheses of population differentiation in the angular angel shark Squatina guggenheim, one of the four most-widespread endemic species inhabiting coastal ecosystems in the south-western Atlantic Ocean. A total of 82 individuals of S. guggenheim from 10 sampling sites throughout the Río de la Plata mouth, its maritime front, the outer shelf at the subtropical confluence and the coastal areas of the south-west Atlantic Ocean, were included. The analysis of molecular variance (AMOVA) based on the second internal transcribed spacer (its-2) region supports that the samples from the outer shelf represent an isolated group from other sites. Historical gene flow in a coalescent-based approach revealed significant immigration and emigration asymmetry between sampling sites. Based on the low level of genetic diversity, the existence of a long-term population decline or a past recent population expansion following a population bottleneck could be proposed in S. guggenheim. This demographic differentiation suggests a degree of vulnerability to overexploitation in this endemic and endangered south-west Atlantic Ocean shark, given its longevity and low reproductive potential.

Genetic diversity and population structure of black Dahe pig based on DNA sequences analyses of mitochondrial and nuclear genes

To investigate the genetic diversity and population structure of black Dahe pigs, we collected 175 samples from 5 local populations and sequenced them using a combination of two selected molecular markers for mitochondrial cytochrome b and Major Histocompatibility Complex (MHC) DRB. Overall, the results of AMOVA and phylogenetic tree and gene flow analyses detected high levels of gene flow among the five populations, particularly individual pigs from Dahe town (Pop1) or Yingshang town (Pop2) to other populations (Pop3, Pop4, and Pop5). The genetic diversity analyses showed that the diversity indices of the five populations did not vary significantly, but they were much lower than those of other Chinese pig species. These results suggest that distinct gene flow, unstable population pattern, and lower genetic diversity have been influenced mainly by human introductions for economic ends. These findings provide genetic information that could be used for the preservation and further genetic improvement of the black Dahe pig, as well as an important reference for the evaluation, conservation, and utilization of the genetic resources of this breed.

Using cytochrome b gene of mtDNA as a DNA barcoding marker in chicken strains

This was the second study to apply using of a cytochrome b gene as barcoding tool in distinguishing among chicken strains. We performed polymerase chain reaction (PCR) amplification using universal primer to amplify around 415 bp fragment of cytochrome b gene of mtDNA. The tree reported that both Saudi chicken strains (black and dark brown) are closely related and it might be separated from same origin rather than bronze ones. The phylogenetic tree also, exploited that native chicken strains were closely related to cluster of Ceylon jungle fowl, black Minorca egg chicken and Fayoumi egg chicken. The genetic divergence between these populations or types of chickens in Saudi Arabia was low (0.02) and it was very low (0.011), when compared to other species of Gallus. We confirmed that short fragment of cyt-b gene as a universal DNA barcode region. It was much more accurate and efficient tool to discriminate inter-species than intra-species. Applying cyt-b of mtDNA was successfully distinguished among native strains and other species of Gallus as in a previous study. However, applying this thought on different species of farm animal species is recommended.

Plasmodium falciparum mitochondrial genetic diversity exhibits isolation-by-distance patterns supporting a sub-Saharan African origin

The geographical distribution of single nucleotide polymorphism (SNP) in the mitochondrial genome of the human malaria parasite Plasmodium falciparum was investigated. We identified 88 SNPs in 516 isolates from seven parasite populations in Africa, Southeast Asia and Oceania. Analysis of the SNPs postulated a sub-Saharan African origin and recovered a strong negative correlation between within-population SNP diversity and geographic distance from the putative African origin over Southeast Asia and Oceania. These results are consistent with those previously obtained for nuclear genome-encoded housekeeping genes, indicating that the pattern of inheritance does not substantially affect the geographical distribution of SNPs.

Complete mitochondrial genomes of the Japanese pink coral (Corallium elatius) and the Mediterranean red coral (Corallium rubrum): a reevaluation of the phylogeny of the family Coralliidae based on molecular data

Precious corals are soft corals belonging to the family Coralliidae (Anthozoa: Octocorallia: Alcyonacea) and class Anthozoa, whose skeletal axes are used for jewelry. The family Coralliidae includes ca. 40 species and was originally thought to comprise of the single genus Corallium. In 2003, Corallium was split into two genera, Corallium and Paracorallium, and seven species were moved to this newly identified genus on the bases of morphological features. Previously, we determined the complete mitochondrial genome sequence of two precious corals Paracorallium japonicum and Corallium konojoi, in order to clarify their systematic positions. The two genomes showed high nucleotide sequence identity, but their gene order arrangements were not identical. Here, we determined three complete mitochondrial genome sequences from the one specimen of Mediterranean Corallium rubrum and two specimens of Corallium elatius coming from Kagoshima (South Japan). The circular mitochondrial genomes of C. rubrum and C. elatius are 18,915bp and 18,969-18,970bp in length, respectively, and encode 14 typical octocorallian protein-coding genes (nad1-6, nad4L, cox1-3, cob, atp6, atp8, and mtMutS, which is an octocoral-specific mismatch repair gene homologue), two ribosomal RNA genes (rns and rnl), and one transfer RNA (trnM). The overall nucleotide differences between C. konojoi and each C. elatius haplotype (T2007 and I2011) are only 10 and 11 nucleotides, respectively; this degree of similarity indicates that C. elatius and C. konojoi are very closely related species. Notably, the C. rubrum mitochondrial genome shows more nucleotide sequence identity to P. japonicum (99.5%) than to its congeneric species C. konojoi (95.3%) and C. elatius (95.3%). Moreover, the gene order arrangement of C. rubrum was the same as that of P. japonicum, while that of C. elatius was the same as C. konojoi. Phylogenetic analysis based on three mitochondrial genes from 24 scleraxonian species shows that the family Coralliidae is separated into two distinct groups, recovering Corallium as a paraphyletic genus. Our results indicate that the currently accepted generic classification of Coralliidae should be reconsidered.