Dataset: Blood parasites of South African cranes
The study investigated the occurrence, systematics, phylogenetic relationships and ecology (geographical distribution and host-parasite relationships) of haemosporidian parasites from selected populations of cranes (order: Gruiformes) in South African in order to document their prevalence and diversity. It contributes to (1) our understanding of the diversity of avian Haemosporidia of priority avian species (2) the expansion of host range and geographical distribution of these parasites (3) additional information on the barcodes of priority avian taxa for which there is paucity of information. Blood samples were collected from three South African cranes species from selected conservation facilities. DNA was extracted from the samples and analysed by PCR. The cytochrome b gene was sequenced from positive samples. The prevalence of the parasites was determined. Genetic distances, haplotype networks and nucleotide diversity (π) were calculated to estimate genetic diversity. Evolutionary relationships of the new sequences were determined by phylogenetic analysis. Parasite DNA was detected in cranes from 10 facilities, with an overall prevalence of 37.41%. Overall haplotype diversity was high (Hd=0.927) with low nucleotide diversity (π=0.099). A total of 15 lineages (cyt b haplotypes) were identified from South African cranes, with 11 being unique South African haplotypes, composed of three Leucocytozoon haplotypes (Hd=0.600; π=0.038), seven for Haemoproteus (Hd=0.81; π=0.046) and five for Plasmodium species (Hd=0.895; π=0.050). Haemoproteus antigonis was the most common and diverse species and is reported for the first time in South African birds by this study. Metadata (locality, date of collection, species, sex, age, Biobank reference number), PCR results, sequence alignment and sequence data (MalAvi lineages, GenBank Accession numbers, genetic distances) are presented. These data contribute valuable information that can be used in subsequent studies. Highlights: haemosporidian infections (Plasmodium, Haemoproteus and Leucocytozoon spp.) in cranes in South Africa are common and genetically diverse; 15 unique lineages and six distinct species are described, two of these are novel species of captive bred cranes in South African; this is the first report on the occurrence of Haemoproteus antigonis in South Africa and confirmation of cranes as the only hosts of H. antigonis.
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Genomic DNA was extracted from approximately 40 μl of avian blood using the Quick-gDNA™ Mini Prep Extraction kit (Zymo Research, Inqaba Biotec, South Africa) according to the manufacturer's protocol. The primary PCR was performed primers HaemNF1 and HaemNR3. Primers HaemFL and HaemR2L (Leucocytozoon spp.) or HaemF and HaemR2 (Plasmodium /or Haemoproteus spp.) were used for the secondary PCRs. Synthetic DNA of Plasmodium relictum and Leucocytozoon fringillinarun (gBlocks® - Integrated DNA Technologies (IDT), Whitehead Scientific) were used as positive controls, and molecular grade water as a negative control. PCR cycling conditions were as follows: initial denaturation at 95 ᵒC for 5 min, 20 cycles (primary PCR) and 35 cycles (nested PCRs) of denaturation at 94 ᵒC for 30 s, annealing at 50 ᵒC for 30 s, extension at 72 ᵒC for 45 s, followed by a final extension at 72 ᵒC for 10 min. The resulting amplicons were visualised on a 2% agarose gel stained with the SYBR Safe DNA Gel Stain (Thermo Fisher Scientific). 20 μl of amplicons were purified using 1 μl Exonuclease I and 2 μl FastAp Thermosensitive Alkaline Phosphatase (Thermo Fisher Scientific) and sequenced in both directions using nested PCR primers indicated above. The sequences were assembled, edited and aligned using the CLC Main Workbench programme (CLC Bio, Boston, MA, USA). Genetic distances (p-distance), haplotype diversity (h) and nucleotide diversity (π) were calculated to estimate the levels of genetic variation in each haemosporidian parasite group. Inter- and intraspecific p-distances between lineages of were calculated using DNASP. Haplotype networks were constructed to visualise patterns of parasite geographical substructure among the cranes using PopART v. 1.7. Phylogenetic trees were constructed in Geneious using Bayesian phylogenetic inference (BI) and MEGAX under maximum likelihood (ML) parameters using Toxoplasma gondii (MN077084) as the outgroup. Statistical analysis was performed using SPSS Statistics 28 software (https://www.ibm.com/products/spss-statistics). The prevalence (proportion of infection individuals) of avian haemosporidian infections was estimated at a significance level of 5% (p < 0.05) and 95% confidence internal (CI).