ABSTRACT. African swine fever virus (ASFV) outbreak has been considered as an emerging and re-emerging disease for almost a century. Diagnostically, simple polymerase chain reaction and sequencing-based molecular detection could be employed for both viral identification and genotyping. This study established a novel phylogenetic analysis and epidemiology comparison based on 205 bp of p72 gene sequences. Based on this partial p72 fragment, an updated list of 44 different genotypes from a total of 516 ASFV sequences compiled from GenBank was generated. Nucleotide diversity was 0.04325 ± 0.00231. The analysis of spatial genetic variation divided the ASFV populations of the African continent into four clades (clade A: central and upper eastern Africa; clade B: eastern Africa; clade C: eastern and southern Africa; and clade D: southern Africa). These results and the developed protocol could serve as useful molecular tools for ASFV diagnosis from degraded DNA or putrefied samples, and also 4567 Phylogeographic analysis of African swine fever virus ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (2): 4566-4574 (2015) provide the phylogeographic perspective to identify the origin of viral outbreaks, facilitating the decision planning to limit their spread.

Asian tapir (Tapirus indicus) is categorized as Endangered on the 2008 IUCN red list. The first full-length mitochondrial DNA (mtDNA) sequence of Asian tapir is 16,717 bp in length. Base composition shows 34.6% A, 27.2% T, 25.8% C and 12.3% G. Highest polymorphic site is on the control region as typical for many species.

Sarcocystis species are heteroxenous cyst-forming coccidian protozoan parasites with a wide host range, including rodents. In this study, Sarcocystis spp. samples were isolated from Bandicota indica, Rattus argentiventer, R. tiomanicus and R. norvegicus across five provinces of Thailand. Two major groups of Sarcocystis cysts were determined in this study: large and small cysts. By sequence comparisons and phylogenetic analyses based on the partial sequences of 28S ribosomal DNA, the large cysts showed the highest identity value (99%) with the S. zamani in GenBank database. While the small cysts could be divided into 2 groups of Sarcocystis: S. singaporensis and presupposed S. zuoi. The further analysis on 18S rDNA supported that the 2 isolates (S2 and B6 no.2) were as identified as S. singaporensis shared a high sequence identity with the S. singaporensis in GenBank database and the unidentified Sarcocystis (4 isolates, i.e., B6 no.10, B6 no.12, B10 no.4 and B10 no.7) showed 96.3–99.5% identity to S. zuoi as well as high distinct identity from others Sarcocystis spp. (≤93%). The result indicated that these four samples should be S. zuoi. In this study, we provided complete sequence of internal transcribed spacer 1 (ITS1), 5.8S rDNA and internal transcribed spacer 2 (ITS2) of these three Sarcocystis species and our new primer set could be useful to study the evolution of Sarcocystis.

Populations of the Endangered Asian tapir Tapirus indicus in Thailand have been severely fragmented and isolated and may be facing a high risk of extinction. Their genetic diversity and population viability remains unknown. The main aim of this study was to assess the genetic diversity of the Asian tapir using the complete mitochondrial cytochrome b gene (1140 bp). We collected 31 blood samples from captive individuals. Two polymorphic sites were found, contributing to 3 maternal lineages: Ti-1 (n = 15), Ti-2 (n = 11), and Ti-3 (n = 5). Comparative analysis with GenBank sequences of other Asian tapirs found another 17 variable sites. These results suggest that there may be up to 7 distinct haplotypes of T. indicus. Furthermore, the pattern of the haplotype distribution corresponded to natural geographic boundaries, including the Isthmus of Kra and the Malacca Strait. One unique haplotype found in Sumatra was genetically distinct from 3 haplotypes found in Thailand and 3 haplotypes from Malaysia. One haplotype shared between Thai and Malaysian populations indicated a possible origin in the tropical rainforest along the Thai-Malay border. In general, the diverged geographic distribution of these haplotypes illustrates the phylogeographic history of the family Tapiridae (T. indicus, T. terrestris, T. pinchaque, and T. bairdii) based on our 963 bp cytochrome b sequences. These baseline genetic data have the potential to enhance effective management of tapirs held in captive breeding programs. However, there is still an urgent need to identify and maintain the genetic diversity of these distinct populations in the wild. KEY WORDS: Cytochrome b gene · Genetic diversity · Malayan tapir · Phylogenetic analysis · ThailandResale or republication not permitted without written consent of the publisher

We presented the powerful techniques for species identification using the short amplicon of mitochondrial cytochrome b gene sequence. Two faecal samples and one single hair sample of the Asian tapir were tested using the new cytochrome b primers. The results showed a high sequence similarity with the mainland Asian tapir group. The comparative sequence analysis of the reserved wild mammals in Thailand and the other endangered mammal species from Southeast Asia comprehensibly verified the potential of our novel primers. The forward and reverse primers were 94.2 and 93.2%, respectively, by the average value of the sequence identity among 77 species sequences, and the overall mean distance was 35.9%. This development technique could provide rapid, simple, and reliable tools for species confirmation. Especially, it could recognize the problematic biological specimens contained less DNA material from illegal products and assist with wildlife crime investigation of threatened species and related forensic casework.