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Babarinde IA, Adeola AC, Djagoun CAMS, Nneji LM, Okeyoyin AO, Niba G, Wanzie NK, Oladipo OC, Adebambo AO, Bello SF, Ng’ang’a SI, Olaniyi WA, Okoro VMO, Adedeji BE, Olatunde O, Ayoola AO, Matouke MM, Wang YY, Sanke OJ, Oseni SO, Nwani CD, Murphy RW. Population structure and evolutionary history of the greater cane rat ( Thryonomys swinderianus) from the Guinean Forests of West Africa. Front Genet 2023; 14:1041103. [PMID: 36923796 PMCID: PMC10010571 DOI: 10.3389/fgene.2023.1041103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 02/07/2023] [Indexed: 03/02/2023] Open
Abstract
Grasscutter (Thryonomys swinderianus) is a large-body old world rodent found in sub-Saharan Africa. The body size and the unique taste of the meat of this major crop pest have made it a target of intense hunting and a potential consideration as a micro-livestock. However, there is insufficient knowledge on the genetic diversity of its populations across African Guinean forests. Herein, we investigated the genetic diversity, population structures and evolutionary history of seven Nigerian wild grasscutter populations together with individuals from Cameroon, Republic of Benin, and Ghana, using five mitochondrial fragments, including D-loop and cytochrome b (CYTB). D-loop haplotype diversity ranged from 0.571 (± 0.149) in Republic of Benin to 0.921 (± 0.013) in Ghana. Within Nigeria, the haplotype diversity ranged from 0.659 (± 0.059) in Cross River to 0.837 (± 0.075) in Ondo subpopulation. The fixation index (FST), haplotype frequency distribution and analysis of molecular variance revealed varying levels of population structures across populations. No significant signature of population contraction was detected in the grasscutter populations. Evolutionary analyses of CYTB suggests that South African population might have diverged from other populations about 6.1 (2.6-10.18, 95% CI) MYA. Taken together, this study reveals the population status and evolutionary history of grasscutter populations in the region.
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Affiliation(s)
- Isaac A. Babarinde
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Adeniyi C. Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Kunming, China
- Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Chabi A. M. S. Djagoun
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, Cotonou, Benin
| | - Lotanna M. Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States
| | - Agboola O. Okeyoyin
- National Park Service Headquarters, Federal Capital Territory, Abuja, Nigeria
| | - George Niba
- National Centre for Animal Husbandry and Veterinary Training, Jakiri, North West Region, Cameroon
| | - Ndifor K. Wanzie
- Department of Zoology, University of Douala, Douala, Cameroon
- Department of Zoology, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | | | - Ayotunde O. Adebambo
- Animal Genetics & Biotechnology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Semiu F. Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Said I. Ng’ang’a
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wasiu A. Olaniyi
- Department of Animal Science, Faculty of Agriculture, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | - Victor M. O. Okoro
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | | | - Omotoso Olatunde
- Department of Zoology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Adeola O. Ayoola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Kunming, China
| | - Moise M. Matouke
- Department of Fisheries and Aquatic Resources Management, University of Buea, Buea, Cameroon
| | | | - Oscar J. Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Saidu O. Oseni
- Department of Animal Sciences, Faculty of Agriculture, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Christopher D. Nwani
- Department of Zoology and Environmental Biology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Nigeria
| | - Robert W. Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
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The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome. BMC Genomics 2022; 23:487. [PMID: 35787153 PMCID: PMC9251931 DOI: 10.1186/s12864-022-08717-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/16/2022] [Indexed: 12/30/2022] Open
Abstract
Investigating the functions and activities of genes requires proper annotation of the transcribed units. However, transcript assembly efforts have produced a surprisingly large variation in the number of transcripts, and especially so for noncoding transcripts. This heterogeneity in assembled transcript sets might be partially explained by sequencing depth. Here, we used real and simulated short-read sequencing data as well as long-read data to systematically investigate the impact of sequencing depths on the accuracy of assembled transcripts. We assembled and analyzed transcripts from 671 human short-read data sets and four long-read data sets. At the first level, there is a positive correlation between the number of reads and the number of recovered transcripts. However, the effect of the sequencing depth varied based on cell or tissue type, the type of read and the nature and expression levels of the transcripts. The detection of coding transcripts saturated rapidly with both short and long-reads, however, there was no sign of early saturation for noncoding transcripts at any sequencing depth. Increasing long-read sequencing depth specifically benefited transcripts containing transposable elements. Finally, we show how single-cell RNA-seq can be guided by transcripts assembled from bulk long-read samples, and demonstrate that noncoding transcripts are expressed at similar levels to coding transcripts but are expressed in fewer cells. This study highlights the impact of sequencing depth on transcript assembly.
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Glaberman S, Bulls SE, Vazquez JM, Chiari Y, Lynch VJ. Concurrent evolution of anti-aging gene duplications and cellular phenotypes in long-lived turtles. Genome Biol Evol 2021; 13:6430984. [PMID: 34792580 PMCID: PMC8688777 DOI: 10.1093/gbe/evab244] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 11/23/2022] Open
Abstract
There are many costs associated with increased body size and longevity in animals, including the accumulation of genotoxic and cytotoxic damage that comes with having more cells and living longer. Yet, some species have overcome these barriers and have evolved remarkably large body sizes and long lifespans, sometimes within a narrow window of evolutionary time. Here, we demonstrate through phylogenetic comparative analysis that multiple turtle lineages, including Galapagos giant tortoises, concurrently evolved large bodies, long lifespans, and reduced cancer risk. We also show through comparative genomic analysis that Galapagos giant tortoises have gene duplications related to longevity and tumor suppression. To examine the molecular basis underlying increased body size and lifespan in turtles, we treated cell lines from multiple species, including Galapagos giant tortoises, with drugs that induce different types of cytotoxic stress. Our results indicate that turtle cells, in general, are resistant to oxidative stress related to aging, whereas Galapagos giant tortoise cells, specifically, are sensitive to endoplasmic reticulum stress, which may give this species an ability to mitigate the effects of cellular stress associated with increased body size and longevity.
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Affiliation(s)
- Scott Glaberman
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA.,Department of Biology, University of South Alabama, Mobile, AL, USA
| | | | - Juan Manuel Vazquez
- Department of Integrative Biology, University of California - Berkeley, Berkeley, CA, USA
| | - Ylenia Chiari
- Department of Biology, George Mason University, Fairfax, VA, USA
| | - Vincent J Lynch
- Department of Biological Sciences, University at Buffalo, SUNY, Buffalo, NY, USA
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