Genetic characterization based on the D-loop MtDNA and the TSPY genes of the Dwarf Siamang (Hylobates klossii) of Mentawai Island, Indonesia

Hasanah R, Saepuloh U, Perwitasari-Farajallah D, Sinaga W, Hastuti Y, Sajuthi D. 2020. Genetic characterization based on the D-loop MtDNA and the TSPY genes of the Dwarf Siamang (Hylobates klossii) of Mentawai Island, Indonesia. Biodiversitas 21: 2854-2861. Hylobates klossii is an endemic primate on the Mentawai Island, Indonesia that categorized as endangered species due to fragmentation, illegal hunting, and habitat loss. This study aimed to analyze the genetic characterization of H. klossii based on maternal and paternal lineages. The samples were collected from TSI (Bogor, Indonesia) cage consist of two males and two females (blood and fecal of four individuals) and Siberut Island, Mentawai, West Sumatra, Indonesia from one unknown gender (one individual fecal sample). PCR amplification was carried out on DNA and cDNA samples using specific primers for D-loop MtDNA and TSPY genes. The amplicon was analyzed with MEGA-7. The dimensional structure model of the TSPY protein was determined using I-TASSER and visualized with PyMol. The maternal analysis showed five samples consisted of four haplotypes revealed that Nam-nam and April were identic with 0% genetic distance. It’s revealed that Nam-nam and April were mother and son. The paternal analysis of two H. klossii males revealed that April was the closest relative to H. muelleri (99.56% identity) and Gou-gou to H. klossii (100% identity). Characterization of partial TSPY gene (990 bp) of April and Gou-Gou indicated four amino acids mutation, causing the shift in-amino acid structure position. The results assumed that April was a cross-breeding between H. klossii female and H. muelleri male. This genetic characterization is expected to support the conservation efforts through recommendations for good management in H. klossii preservation.

Somatic Mosaicism in Bulls Estimated from Genome-Wide CNV Array and TSPY Gene Copy Numbers

Somatic mosaicism has become a focus in human research due to the implications of individual genetic variability in disease. Here, we assessed somatic copy number variations (CNVs) in Holstein bulls in 2 respects. We estimated genome-wide CNVs and assayed CNVs of the TSPY gene, the most variable bovine gene from the Y chromosome. Somatic tissues (blood, lung, heart, muscle, testis, and brain) of 4 bulls were arrayed on the Illumina Bovine SNP50k chip and qPCR tested for TSPY copy numbers. Our results showed extensive copy number divergence in tissues within the same animal as well as significant copy number alterations of TSPY. We detected a mean of 31 CNVs per animal among which 14 were of germline origin, as they were constantly present in all investigated tissues of the animal, while 18 were specific to 1 tissue. Thus, 57% of the total number of detected CNVs was the result of de novo somatic events. Further, TSPY copy number was found to vary significantly among tissues as well as among the same tissue type from different animals in a wide range from 7 to 224% of the calibrator. Our study shows significant autosomal and Y-chromosomal de novo somatic CNV in bulls.