- 著者
- MUHAMMAD SHOAIB AKHTAR RYUICHI ASHINO HIROKI OOTA HAJIME ISHIDA YOSHIHITO NIIMURA KAZUSHIGE TOUHARA AMANDA D. MELIN SHOJI KAWAMURA
- 出版者
- The Anthropological Society of Nippon
- 雑誌
- Anthropological Science (ISSN:09187960)
- 巻号頁・発行日
- pp.211024, (Released:2022-01-20)
- 被引用文献数
- 3
The olfactory receptor (OR) gene family is comprised of hundreds of intact and disrupted genes in humans. The compositions and copy number variation (CNV) of disrupted and intact OR genes among individuals is expected to cause variation in olfactory perception. However, little is known about OR genetic variation in many human populations. In this study, we used targeted capture enrichment and massive parallel short-read sequencing methods to examine genetic variation of OR genes, as well as of neutral genome regions as references, for 69 anonymized unrelated Japanese individuals. The capture probes were designed for 398 intact OR genes in the human reference genome hg38, and 85 neutral references. Probes were also designed for four unannotated and 99 ‘nearly-intact’ (hg38-pseudo) OR genes in hg38 and 53 chimpanzee OR genes in the Pantro3.0 genome database with no orthologs in hg38. All the hg38 OR genes and one Pantro 3.0 OR gene were retrieved. The mean sequencing depth was significantly higher than that of the 1000 Genomes Project. A total of 30 OR genes from hg38-intact and hg38-pseudo categories were newly found to be segregating pseudogenes. One hg38-pseudo OR gene was intact in all individuals. CNV was detected in 63 OR genes. Tajima’s D analysis for OR genes and neutral references was consistent with balancing selection to maintain allelic differences in intact OR genes. These results demonstrate that the targeted capture by probes with diversity-oriented design is far more effective than a whole-genome approach to retrieve OR genes and achieve high-depth sequencing and thus to reveal polymorphisms for the OR multigene family. The composition of OR genes in the human reference genome hg38 does not necessarily represent those in many humans, implying higher perceptual variation than previously thought. The current study inspires further investigation with a similar approach at a global scale.
- 著者
- Min HOU Masahiro HAYASHI Ryuichi ASHINO Amanda D. MELIN Shoji KAWAMURA
- 出版者
- Primate Society of Japan
- 雑誌
- 霊長類研究 Supplement
- 巻号頁・発行日
- pp.32-33, 2020 (Released:2021-04-23)
Taste perception is fundamental in dietary selection for many animals. Bitter taste perception is important not only in dietary selection but also in preventing animals from ingesting potentially toxic compounds. Previous studies have revealed evolutionary divergence of the bitter taste receptor gene (TAS2R) repertoire in mammals, including primates, using publicly available whole genome sequence (WGS) data. Plant tissues contain more toxic compounds than animal tissues do. Herbivores could have less TAS2R genes because they are predicted to be more tolerant and less sensitive to bitter compounds to ingest poisons. On the other hand, herbivores could have more TAS2R genes because they are predicted to be in need of selecting and ingesting bitter plants which other animals avoid. Cercopithecid (African and Asian) monkeys are an excellent subject for studying adaptive evolution of bitter sensation because they have diverged into folivores (colobines) and omnivores (cercopithecines). However, only a few genera have been studied in this context. Dependence on WGS data is also potentially problematic due to its inherent incompleteness especially for multigene families such as TAS2Rs. In this study, we employed the target capture (TC) method specifically probing TAS2Rs followed by massive-parallel sequencing for nine cercopithecid species (seven cercopithecines: two Papio, two Macaca, one each of Cercopithecus, Chlorocebus and Erythrocebus species; two colobines: one each of Semnopithecus and Colobus species). We show that TC is far more effective than WGS in retrieving gene sequence and distinguishing intact and disrupted genes. We also find bitter taste gene composition differs among the species. Further studies are required to investigate whether difference of gene composition result in difference of receptor sensitivity and behavioral reactivity to bitter compounds.