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Guan D, Sun S, Song L, Zhao P, Nie Y, Huang X, Zhou W, Yan L, Lei Y, Hu Y, Wei F. Taking a color photo: A homozygous 25-bp deletion in Bace2 may cause brown-and-white coat color in giant pandas. Proc Natl Acad Sci U S A 2024; 121:e2317430121. [PMID: 38437540 PMCID: PMC10945837 DOI: 10.1073/pnas.2317430121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/30/2023] [Indexed: 03/06/2024] Open
Abstract
Brown-and-white giant pandas (hereafter brown pandas) are distinct coat color mutants found exclusively in the Qinling Mountains, Shaanxi, China. However, its genetic mechanism has remained unclear since their discovery in 1985. Here, we identified the genetic basis for this coat color variation using a combination of field ecological data, population genomic data, and a CRISPR-Cas9 knockout mouse model. We de novo assembled a long-read-based giant panda genome and resequenced the genomes of 35 giant pandas, including two brown pandas and two family trios associated with a brown panda. We identified a homozygous 25-bp deletion in the first exon of Bace2, a gene encoding amyloid precursor protein cleaving enzyme, as the most likely genetic basis for brown-and-white coat color. This deletion was further validated using PCR and Sanger sequencing of another 192 black giant pandas and CRISPR-Cas9 edited knockout mice. Our investigation revealed that this mutation reduced the number and size of melanosomes of the hairs in knockout mice and possibly in the brown panda, further leading to the hypopigmentation. These findings provide unique insights into the genetic basis of coat color variation in wild animals.
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Affiliation(s)
- Dengfeng Guan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- Jiangxi Provincial Key Laboratory of Conservation Biology, Jiangxi Agricultural University, Nanchang330045, China
| | - Shuyan Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Lingyun Song
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Pengpeng Zhao
- Shaanxi (Louguantai) Rescue and Breeding Center for Rare Wildlife, Xi’an710402, China
| | - Yonggang Nie
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Xin Huang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Wenliang Zhou
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Li Yan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
| | - Yinghu Lei
- Shaanxi (Louguantai) Rescue and Breeding Center for Rare Wildlife, Xi’an710402, China
| | - Yibo Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Fuwen Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- Jiangxi Provincial Key Laboratory of Conservation Biology, Jiangxi Agricultural University, Nanchang330045, China
- University of Chinese Academy of Sciences, Beijing100049, China
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
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Wang Y, Yue Y, Li C, Chen Z, Cai Y, Hu C, Qu Y, Li H, Zhou K, Yan J, Li P. Insights into the adaptive evolution of chromosome and essential traits through chromosome-level genome assembly of Gekko japonicus. iScience 2024; 27:108445. [PMID: 38205241 PMCID: PMC10776941 DOI: 10.1016/j.isci.2023.108445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/05/2023] [Accepted: 11/09/2023] [Indexed: 01/12/2024] Open
Abstract
Gekko japonicus possesses flexible climbing and detoxification abilities under insectivorous habits. Still, the evolutionary mechanisms behind these traits remain unclarified. This study presents a chromosome-level G. japonicus genome, revealing that its evolutionary breakpoint regions were enriched with specific repetitive elements and defense response genes. Gene families unique to G. japonicus and positively selected genes are mainly enriched in immune, sensory, and nervous pathways. Expansion of bitter taste receptor type 2 primarily in insectivorous species could be associated with toxin clearance. Detox cytochrome P450 in G. japonicus has undergone more birth and death processes than biosynthesis-type P450 genes. Proline, cysteine, glycine, and serine in corneous beta proteins of G. japonicus might influence flexibility and setae adhesiveness. Certain thermosensitive transient receptor potential channels under relaxed purifying selection or positive selection in G. japonicus might enhance adaptation to climate change. This genome assembly offers insights into the adaptive evolution of gekkotans.
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Affiliation(s)
- Yinwei Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Youxia Yue
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Chao Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Zhiyi Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Yao Cai
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, Jiangsu 211171, P.R. China
| | - Chaochao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
- Analytical and Testing Center, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Yanfu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Kaiya Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Jie Yan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
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de Menezes Cavalcante Sassi F, Sember A, Deon GA, Liehr T, Padutsch N, Oyakawa OT, Vicari MR, Bertollo LAC, Moreira-Filho O, de Bello Cioffi M. Homeology of sex chromosomes in Amazonian Harttia armored catfishes supports the X-fission hypothesis for the X 1X 2Y sex chromosome system origin. Sci Rep 2023; 13:15756. [PMID: 37735233 PMCID: PMC10514344 DOI: 10.1038/s41598-023-42617-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
The Neotropical monophyletic catfish genus Harttia represents an excellent model to study karyotype and sex chromosome evolution in teleosts. Its species split into three phylogenetic clades distributed along the Brazilian territory and they differ widely in karyotype traits, including the presence of standard or multiple sex chromosome systems in some members. Here, we investigate the chromosomal rearrangements and associated synteny blocks involved in the origin of a multiple X1X2Y sex chromosome system present in three out of six sampled Amazonian-clade species. Using 5S and 18S ribosomal DNA fluorescence in situ hybridization and whole chromosome painting with probes corresponding to X1 and X2 chromosomes of X1X2Y system from H. punctata, we confirm previous assumptions that X1X2Y sex chromosome systems of H. punctata, H. duriventris and H. villasboas represent the same linkage groups which also form the putative XY sex chromosomes of H. rondoni. The shared homeology between X1X2Y sex chromosomes suggests they might have originated once in the common ancestor of these closely related species. A joint arrangement of mapped H. punctata X1 and X2 sex chromosomes in early diverging species of different Harttia clades suggests that the X1X2Y sex chromosome system may have formed through an X chromosome fission rather than previously proposed Y-autosome fusion.
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Affiliation(s)
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská, 89, Liběchov, Czech Republic
| | - Geize Aparecida Deon
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, 07747, Jena, Germany.
| | - Niklas Padutsch
- Institut für Humangenetik, Universitätsklinikum Jena, 07747, Jena, Germany
| | | | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - Luiz Antonio Carlos Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Orlando Moreira-Filho
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
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Zhou YL, Wu JJ, Gong GR, Liu M, Li Z, Guo XF, Wei WY, Zhang XJ, Mei J, Zhou L, Wang ZW, Gui JF. Barbel regeneration and function divergence in red-tail catfish (Hemibagrus wyckioides) based on the chromosome-level genomes and comparative transcriptomes. Int J Biol Macromol 2023; 232:123374. [PMID: 36702216 DOI: 10.1016/j.ijbiomac.2023.123374] [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: 09/27/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 01/24/2023]
Abstract
Catfish (Siluriformes) are one of the most diverse vertebrate orders and are characterized by whisker-like barbels, which are important sensory organs in most of teleosts. However, their specific biological functions are still unclear. Red-tail catfish (Hemibagrus wyckioides) is well-known catfish species with four pairs of barbels, of which the maxillary barbels reach two-thirds of the body length. In this study, a 776.58 Mb high-quality chromosome-level genome was assembled into 29 chromosomes. Comparative genome data indicated that the barbeled regeneration gene ccl33 has expanded into 11 tandemly duplicated copies. Transcriptome data revealed the functional differentiation of different barbels and suggested that the maxillary barbel might be necessary for water temperature perception. Taste receptor genes were also characterized in teleosts with different food habits. Selection pressures were revealed to affect the sugar-based solute transport domain of the sweet taste receptor gene t1r2 in carnivorous fishes. In addition, the bitter taste receptor gene t2r200 was found to be lost from the genomes of four catfish species. Therefore, our study provides a genomic foundation for understanding the regeneration and functional differentiation of barbels in red-tail catfish and also reveals novel insights into the feeding evolution of fish species with different feeding habits.
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Affiliation(s)
- Yu-Lin Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Jun-Jie Wu
- Yunnan Institute of Fishery Sciences Research, Kunming 650111, China
| | - Gao-Rui Gong
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Min Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xin-Feng Guo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wen-Yu Wei
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Jie Mei
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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5
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Zhou C, Liu Y, Zhao G, Liu Z, Chen Q, Yue B, Du C, Zhang X. Comparative Analysis of Olfactory Receptor Repertoires Sheds Light on the Diet Adaptation of the Bamboo-Eating Giant Panda Based on the Chromosome-Level Genome. Animals (Basel) 2023; 13:ani13060979. [PMID: 36978520 PMCID: PMC10044402 DOI: 10.3390/ani13060979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/14/2023] [Accepted: 02/28/2023] [Indexed: 03/30/2023] Open
Abstract
The giant panda (Ailuropoda melanoleuca) is the epitome of a flagship species for wildlife conservation and also an ideal model of adaptive evolution. As an obligate bamboo feeder, the giant panda relies on the olfaction for food recognition. The number of olfactory receptor (OR) genes and the rate of pseudogenes are the main factors affecting the olfactory ability of animals. In this study, we used the chromosome-level genome of the giant panda to identify OR genes and compared the genome sequences of OR genes with five other Ursidae species (spectacled bear (Tremarctos ornatus), American black bear (Ursus americanus), brown bear (Ursus arctos), polar bear (Ursus maritimus) and Asian black bear (Ursus thibetanus)). The giant panda had 639 OR genes, including 408 functional genes, 94 partial OR genes and 137 pseudogenes. Among them, 222 OR genes were detected and distributed on 18 chromosomes, and chromosome 8 had the most OR genes. A total of 448, 617, 582, 521 and 792 OR genes were identified in the spectacled bear, American black bear, brown bear, polar bear and Asian black bear, respectively. Clustering analysis based on the OR protein sequences of the six species showed that the OR genes distributed in 69 families and 438 subfamilies based on sequence similarity, and the six mammals shared 72 OR gene subfamilies, while the giant panda had 31 unique OR gene subfamilies (containing 35 genes). Among the 35 genes, there are 10 genes clustered into 8 clusters with 10 known human OR genes (OR8J3, OR51I1, OR10AC1, OR1S2, OR1S1, OR51S1, OR4M1, OR4M2, OR51T1 and OR5W2). However, the kind of odor molecules can be recognized by the 10 known human OR genes separately, which needs further research. The phylogenetic tree showed that 345 (about 84.56%) functional OR genes were clustered as Class-II, while only 63 (about 15.44%) functional OR genes were clustered as Class-I, which required further and more in-depth research. The potential odor specificity of some giant panda OR genes was identified through the similarity to human protein sequences. Sequences similar to OR2B1, OR10G3, OR11H6 and OR11H7P were giant panda-specific lacking, which may be related to the transformation and specialization from carnivore to herbivore of the giant panda. Since our reference to flavoring agents comes from human research, the possible flavoring agents from giant panda-specific OR genes need further investigation. Moreover, the conserved motifs of OR genes were highly conserved in Ursidae species. This systematic study of OR genes in the giant panda will provide a solid foundation for further research on the olfactory function and variation of the giant panda.
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Affiliation(s)
- Chuang Zhou
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Yi Liu
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang Normal University, Neijiang 641000, China
| | - Guangqing Zhao
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Zhengwei Liu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Qian Chen
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Chao Du
- Baotou Teachers College, Baotou 014060, China
| | - Xiuyue Zhang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
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Shukla H, Suryamohan K, Khan A, Mohan K, Perumal RC, Mathew OK, Menon R, Dixon MD, Muraleedharan M, Kuriakose B, Michael S, Krishnankutty SP, Zachariah A, Seshagiri S, Ramakrishnan U. Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation. Gigascience 2022; 12:giac112. [PMID: 36576130 PMCID: PMC9795480 DOI: 10.1093/gigascience/giac112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/17/2022] [Accepted: 10/20/2022] [Indexed: 12/29/2022] Open
Abstract
The tiger, a poster child for conservation, remains an endangered apex predator. Continued survival and recovery will require a comprehensive understanding of genetic diversity and the use of such information for population management. A high-quality tiger genome assembly will be an important tool for conservation genetics, especially for the Indian tiger, the most abundant subspecies in the wild. Here, we present high-quality near-chromosomal genome assemblies of a female and a male wild Indian tiger (Panthera tigris tigris). Our assemblies had a scaffold N50 of >140 Mb, with 19 scaffolds corresponding to the 19 numbered chromosomes, containing 95% of the genome. Our assemblies also enabled detection of longer stretches of runs of homozygosity compared to previous assemblies, which will help improve estimates of genomic inbreeding. Comprehensive genome annotation identified 26,068 protein-coding genes, including several gene families involved in key morphological features such as the teeth, claws, vision, olfaction, taste, and body stripes. We also identified 301 microRNAs, 365 small nucleolar RNAs, 632 transfer RNAs, and other noncoding RNA elements, several of which are predicted to regulate key biological pathways that likely contribute to the tiger's apex predatory traits. We identify signatures of positive selection in the tiger genome that are consistent with the Panthera lineage. Our high-quality genome will enable use of noninvasive samples for comprehensive assessment of genetic diversity, thus supporting effective conservation and management of wild tiger populations.
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Affiliation(s)
- Harsh Shukla
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Kushal Suryamohan
- MedGenome Inc., Department of Research and Development, Foster City, CA 94404, USA
- SciGenom Research Foundation, Narayana Health City, Bangalore, Karnataka 560099, India
| | - Anubhab Khan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Krishna Mohan
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Rajadurai C Perumal
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Oommen K Mathew
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Ramesh Menon
- MedGenome Labs Ltd., Narayana Health City, Bangalore, Karnataka 560099, India
| | - Mandumpala Davis Dixon
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Megha Muraleedharan
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Boney Kuriakose
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Saju Michael
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Sajesh P Krishnankutty
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Arun Zachariah
- SciGenom Research Foundation, Narayana Health City, Bangalore, Karnataka 560099, India
- Wayanad Wildlife Sanctuary, Sultan Bathery, Kerala 673592, India
| | - Somasekar Seshagiri
- SciGenom Research Foundation, Narayana Health City, Bangalore, Karnataka 560099, India
- MedGenome Labs Ltd., Narayana Health City, Bangalore, Karnataka 560099, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
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Willey C, Korstanje R. Sequencing and assembling bear genomes: the bare necessities. Front Zool 2022; 19:30. [PMID: 36451195 PMCID: PMC9710173 DOI: 10.1186/s12983-022-00475-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Unique genetic adaptations are present in bears of every species across the world. From (nearly) shutting down important organs during hibernation to preventing harm from lifestyles that could easily cause metabolic diseases in humans, bears may hold the answer to various human ailments. However, only a few of these unique traits are currently being investigated at the molecular level, partly because of the lack of necessary tools. One of these tools is well-annotated genome assemblies from the different, extant bear species. These reference genomes are needed to allow us to identify differences in genetic variants, isoforms, gene expression, and genomic features such as transposons and identify those that are associated with biomedical-relevant traits. In this review we assess the current state of the genome assemblies of the eight different bear species, discuss current gaps, and the future benefits these reference genomes may have in informing human biomedical applications, while at the same time improving bear conservation efforts.
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Li Y, Xu W, Wang Y, Kou J, Zhang J, Hu S, Zhang L, Wang J, Liu J, Liu H, Luo L, Wang C, Lan J, Hou R, Shen F. An improved, chromosome-level genome of the giant panda (Ailuropoda melanoleuca). Genomics 2022; 114:110501. [PMID: 36270383 DOI: 10.1016/j.ygeno.2022.110501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/21/2022] [Accepted: 10/04/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND The iconic giant panda (Ailuropoda melanoleuca), as both a flagship and umbrella species endemic to China, is a world famous symbol for wildlife conservation. The giant panda has several specific biological traits and holds a relatively small place in evolution. A high-quality genome of the giant panda is key to understanding the biology of this vulnerable species. FINDINGS We generated a 2.48-Gb chromosome-level genome (GPv1) of the giant panda named "Jing Jing" with a contig N50 of 28.56 Mb and scaffold N50 of 134.17 Mb, respectively. The total length of chromosomes (n = 21) was 2.39-Gb, accounting for 96.4% of the whole genome. Compared with the previously published four genomes of the giant panda, our genome is characterized by the highest completeness and the correct sequence orientation. A gap-free and 850 kb length of immunoglobulin heavy-chain gene cluster was manually annotated in close proximity to the telomere of chromosome 14. Additionally, we developed an algorithm to predict the centromere position of each chromosome. We also constructed a complete chromatin structure for "Jing Jing", which includes inter-chromosome interaction pattern, A/B compartment, topologically associated domain (TAD), TAD-clique and promoter-enhancer interaction (PEI). CONCLUSIONS We presented an improved chromosome-level genome and complete chromatin structure for the giant panda. This is a valuable resource for the future genetic and genomic studies on giant panda.
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Affiliation(s)
- Yan Li
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Wei Xu
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Ye Wang
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Jie Kou
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Jiaman Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, China
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, China
| | - Liang Zhang
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Juan Wang
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Jiawen Liu
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Hong Liu
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Li Luo
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Chengdong Wang
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Jingchao Lan
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China.
| | - Fujun Shen
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China.
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9
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Comparative analysis of microsatellites in coding regions provides insights into the adaptability of the giant panda, polar bear and brown bear. Genetica 2022; 150:355-366. [DOI: 10.1007/s10709-022-00173-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 09/13/2022] [Indexed: 11/27/2022]
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10
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Chromosome-scale genome assembly of the brown anole (Anolis sagrei), an emerging model species. Commun Biol 2022; 5:1126. [PMID: 36284162 PMCID: PMC9596491 DOI: 10.1038/s42003-022-04074-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 10/06/2022] [Indexed: 12/12/2022] Open
Abstract
Rapid technological improvements are democratizing access to high quality, chromosome-scale genome assemblies. No longer the domain of only the most highly studied model organisms, now non-traditional and emerging model species can be genome-enabled using a combination of sequencing technologies and assembly software. Consequently, old ideas built on sparse sampling across the tree of life have recently been amended in the face of genomic data drawn from a growing number of high-quality reference genomes. Arguably the most valuable are those long-studied species for which much is already known about their biology; what many term emerging model species. Here, we report a highly complete chromosome-scale genome assembly for the brown anole, Anolis sagrei – a lizard species widely studied across a variety of disciplines and for which a high-quality reference genome was long overdue. This assembly exceeds the vast majority of existing reptile and snake genomes in contiguity (N50 = 253.6 Mb) and annotation completeness. Through the analysis of this genome and population resequence data, we examine the history of repetitive element accumulation, identify the X chromosome, and propose a hypothesis for the evolutionary history of fusions between autosomes and the X that led to the sex chromosomes of A. sagrei. A highly-complete chromosome-scale genome assembly of the brown anole, Anolis sagrei, provides insight into the evolution of sex chromosomes and is a crucial resource for this model lizard species.
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11
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Glugoski L, Nogaroto V, Deon GA, Azambuja M, Moreira-Filho O, Vicari MR. Enriched tandemly repeats in chromosomal fusion points of Rineloricaria latirostris (Boulenger, 1900) (Siluriformes: Loricariidae). Genome 2022; 65:479-489. [PMID: 35939838 DOI: 10.1139/gen-2022-0043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cytogenetic data showed the enrichment of repetitive DNAs in chromosomal rearrangement points between closely related species in armored catfishes. Still, few studies integrated cytogenetic and genomic data aiming to identify their prone-to-break DNA sites. Here, we aimed to obtain the repetitive fraction in Rineloricaria latirostris to recognize the microsatellite and homopolymers flanking the regions previously described as chromosomal fusion points. The results indicated that repetitive DNAs in R. latirostris are predominantly DNA transposons, and considering the microsatellite and homopolymers, A/T-rich expansions were the most abundant. The in situ localization demonstrated the A/T-rich repetitive sequences are scattered on the chromosomes, while A/G-rich microsatellites units were accumulated in some regions. The DNA transposon hAT, the 5S rDNA, and 45S rDNA (previously identified in Robertsonian fusion points in R. latirostris) are clusterized with some microsatellites, especially (CA)n, (GA)n, and poly-A, which also are enriched in regions of chromosomal fusions. Our findings demonstrated that repetitive sequences such as rDNAs, hAT transposon, and microsatellite units flank probable evolutionary breakpoint regions in R. latirostris. However, due to the sequence unit homologies in different chromosomal sites, these repeat DNAs only may have facilitated chromosome fusion events in R. latirostris rather than work as a double-strand breakpoint site.
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Affiliation(s)
- Larissa Glugoski
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Sao Carlos, São Paulo, Brazil;
| | - Viviane Nogaroto
- Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, Paraná, Brazil;
| | - Geize Aparecida Deon
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Sao Carlos, São Paulo, Brazil;
| | - Matheus Azambuja
- Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brazil;
| | - Orlando Moreira-Filho
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Sao Carlos, São Paulo, Brazil;
| | - Marcelo Ricardo Vicari
- Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, Paraná, Brazil.,Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brazil;
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12
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Cabrera AA, Rey‐Iglesia A, Louis M, Skovrind M, Westbury MV, Lorenzen ED. How low can you go? Introducing SeXY: sex identification from low-quantity sequencing data despite lacking assembled sex chromosomes. Ecol Evol 2022; 12:e9185. [PMID: 36035270 PMCID: PMC9405501 DOI: 10.1002/ece3.9185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/19/2022] [Indexed: 12/01/2022] Open
Abstract
Accurate sex identification is crucial for elucidating the biology of a species. In the absence of directly observable sexual characteristics, sex identification of wild fauna can be challenging, if not impossible. Molecular sexing offers a powerful alternative to morphological sexing approaches. Here, we present SeXY, a novel sex-identification pipeline, for very low-coverage shotgun sequencing data from a single individual. SeXY was designed to utilize low-effort screening data for sex identification and does not require a conspecific sex-chromosome assembly as reference. We assess the accuracy of our pipeline to data quantity by downsampling sequencing data from 100,000 to 1000 mapped reads and to reference genome selection by mapping to a variety of reference genomes of various qualities and phylogenetic distance. We show that our method is 100% accurate when mapping to a high-quality (highly contiguous N50 > 30 Mb) conspecific genome, even down to 1000 mapped reads. For lower-quality reference assemblies (N50 < 30 Mb), our method is 100% accurate with 50,000 mapped reads, regardless of reference assembly quality or phylogenetic distance. The SeXY pipeline provides several advantages over previously implemented methods; SeXY (i) requires sequencing data from only a single individual, (ii) does not require assembled conspecific sex chromosomes, or even a conspecific reference assembly, (iii) takes into account variation in coverage across the genome, and (iv) is accurate with only 1000 mapped reads in many cases.
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Affiliation(s)
| | | | - Marie Louis
- Globe InstituteUniversity of CopenhagenCopenhagen KDenmark
- Greenland Institute of Natural ResourcesNuukGreenland
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13
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Zheng Y, Zhou Y, Huang Y, Wang H, Guo H, Yuan B, Zhang J. Transcriptome sequencing of black and white hair follicles in the giant panda. Integr Zool 2022; 18:552-568. [PMID: 35500067 DOI: 10.1111/1749-4877.12652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the completion of the draft assembly of the giant panda genome sequence, RNA sequencing technology has been widely used in genetic research on giant pandas. We used RNA-seq to examine black and white hair follicle samples from adult pandas. By comparison with the giant panda genome, 75 963 SNP loci were labeled, 2 426 differentially expressed genes were identified, and 2 029 new genes were discovered, among which 631 were functionally annotated. A cluster analysis of the differentially expressed genes showed that they were mainly related to the Wnt signaling pathway, ECM-receptor interaction, the p53 signaling pathway and ribosome processing. The enrichment results showed that there were significant differences in the regulatory networks of hair follicles with different colors during the transitional stage of hair follicle resting growth, which may play a regulatory role in melanin synthesis during growth. In conclusion, our results provide new insights and more data support for research on the color formation in giant pandas. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yi Zheng
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
| | - Yingmin Zhou
- Key Laboratory of SFGA on Conservation Biology of Rare Animals in The Giant Panda National Park, China
| | - Yijie Huang
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
| | - Haoqi Wang
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
| | - Haixiang Guo
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
| | - Bao Yuan
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
| | - Jiabao Zhang
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
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14
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Potter S, Bragg JG, Turakulov R, Eldridge MDB, Deakin J, Kirkpatrick M, Edwards RJ, Moritz C. Limited introgression between rock-wallabies with extensive chromosomal rearrangements. Mol Biol Evol 2021; 39:6448774. [PMID: 34865126 PMCID: PMC8788226 DOI: 10.1093/molbev/msab333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chromosome rearrangements can result in the rapid evolution of hybrid incompatibilities. Robertsonian fusions, particularly those with monobrachial homology, can drive reproductive isolation amongst recently diverged taxa. The recent radiation of rock-wallabies (genus Petrogale) is an important model to explore the role of Robertsonian fusions in speciation. Here, we pursue that goal using an extensive sampling of populations and genomes of Petrogale from north-eastern Australia. In contrast to previous assessments using mitochondrial DNA or nuclear microsatellite loci, genomic data are able to separate the most closely related species and to resolve their divergence histories. Both phylogenetic and population genetic analyses indicate introgression between two species that differ by a single Robertsonian fusion. Based on the available data, there is also evidence for introgression between two species which share complex chromosomal rearrangements. However, the remaining results show no consistent signature of introgression amongst species pairs and where evident, indicate generally low introgression overall. X-linked loci have elevated divergence compared with autosomal loci indicating a potential role for genic evolution to produce reproductive isolation in concert with chromosome change. Our results highlight the value of genome scale data in evaluating the role of Robertsonian fusions and structural variation in divergence, speciation, and patterns of molecular evolution.
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Affiliation(s)
- Sally Potter
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia.,Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Jason G Bragg
- National Herbarium of New South Wales, The Royal Botanical Gardens and Domain Trust, Sydney, NSW, Australia
| | - Rustamzhon Turakulov
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Janine Deakin
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX, United States of America
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
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15
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Chung D, Kwon YM, Yang Y. Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii. BMC Genomics 2021; 22:830. [PMID: 34789157 PMCID: PMC8600724 DOI: 10.1186/s12864-021-08162-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/02/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Trichoderma is a genus of fungi in the family Hypocreaceae and includes species known to produce enzymes with commercial use. They are largely found in soil and terrestrial plants. Recently, Trichoderma simmonsii isolated from decaying bark and decorticated wood was newly identified in the Harzianum clade of Trichoderma. Due to a wide range of applications in agriculture and other industries, genomes of at least 12 Trichoderma spp. have been studied. Moreover, antifungal and enzymatic activities have been extensively characterized in Trichoderma spp. However, the genomic information and bioactivities of T. simmonsii from a particular marine-derived isolate remain largely unknown. While we screened for asparaginase-producing fungi, we observed that T. simmonsii GH-Sj1 strain isolated from edible kelp produced asparaginase. In this study, we report a draft genome of T. simmonsii GH-Sj1 using Illumina and Oxford Nanopore technologies. Furthermore, to facilitate biotechnological applications of this species, RNA-sequencing was performed to elucidate the transcriptional profile of T. simmonsii GH-Sj1 in response to asparaginase-rich conditions. RESULTS We generated ~ 14 Gb of sequencing data assembled in a ~ 40 Mb genome. The T. simmonsii GH-Sj1 genome consisted of seven telomere-to-telomere scaffolds with no sequencing gaps, where the N50 length was 6.4 Mb. The total number of protein-coding genes was 13,120, constituting ~ 99% of the genome. The genome harbored 176 tRNAs, which encode a full set of 20 amino acids. In addition, it had an rRNA repeat region consisting of seven repeats of the 18S-ITS1-5.8S-ITS2-26S cluster. The T. simmonsii genome also harbored 7 putative asparaginase-encoding genes with potential medical applications. Using RNA-sequencing analysis, we found that 3 genes among the 7 putative genes were significantly upregulated under asparaginase-rich conditions. CONCLUSIONS The genome and transcriptome of T. simmonsii GH-Sj1 established in the current work represent valuable resources for future comparative studies on fungal genomes and asparaginase production.
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Affiliation(s)
- Dawoon Chung
- National Marine Biodiversity Institute of Korea, Chungchungnam-do, South Korea
| | - Yong Min Kwon
- National Marine Biodiversity Institute of Korea, Chungchungnam-do, South Korea
| | - Youngik Yang
- National Marine Biodiversity Institute of Korea, Chungchungnam-do, South Korea.
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16
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Guang X, Lan T, Wan QH, Huang Y, Li H, Zhang M, Li R, Zhang Z, Lei Y, Zhang L, Zhang H, Li D, Li X, Li H, Xu Y, Qiao M, Wu D, Tang K, Zhao P, Lin JQ, Kumar Sahu S, Liang Q, Jiang W, Zhang D, Xu X, Liu X, Lisby M, Yang H, Kristiansen K, Liu H, Fang SG. Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda. Sci Bull (Beijing) 2021; 66:2002-2013. [PMID: 36654170 DOI: 10.1016/j.scib.2021.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 09/27/2020] [Accepted: 12/25/2020] [Indexed: 02/03/2023]
Abstract
Extant giant pandas are divided into Sichuan and Qinling subspecies. The giant panda has many species-specific characteristics, including comparatively small organs for body size, small genitalia of male individuals, and low reproduction. Here, we report the most contiguous, high-quality chromosome-level genomes of two extant giant panda subspecies to date, with the first genome assembly of the Qinling subspecies. Compared with the previously assembled giant panda genomes based on short reads, our two assembled genomes increased contiguity over 200-fold at the contig level. Additional sequencing of 25 individuals dated the divergence of the Sichuan and Qinling subspecies into two distinct clusters from 10,000 to 12,000 years ago. Comparative genomic analyses identified the loss of regulatory elements in the dachshund family transcription factor 2 (DACH2) gene and specific changes in the synaptotagmin 6 (SYT6) gene, which may be responsible for the reduced fertility of the giant panda. Positive selection analysis between the two subspecies indicated that the reproduction-associated IQ motif containing D (IQCD) gene may at least partly explain the different reproduction rates of the two subspecies. Furthermore, several genes in the Hippo pathway exhibited signs of rapid evolution with giant panda-specific variants and divergent regulatory elements, which may contribute to the reduced inner organ sizes of the giant panda.
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Affiliation(s)
- Xuanmin Guang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Qiu-Hong Wan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Hong Li
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Mingchun Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Rengui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Zhizhong Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Yinghu Lei
- Qinling Research Center of Giant Panda Breeding, Shaanxi Academy of Forestry, Xi'an 710082, China
| | - Ling Zhang
- China Wildlife Conservation Association, Beijing 100714, China
| | - Heming Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Desheng Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Xiaoping Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yan Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Maiju Qiao
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Daifu Wu
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Keyi Tang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pengpeng Zhao
- Qinling Research Center of Giant Panda Breeding, Shaanxi Academy of Forestry, Xi'an 710082, China
| | - Jian-Qing Lin
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Danhui Zhang
- Qinling Research Center of Giant Panda Breeding, Shaanxi Academy of Forestry, Xi'an 710082, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Michael Lisby
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518120, China
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; Qingdao-Europe Advanced Institute for Life Sciences, Qingdao 266555, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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17
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Peart CR, Williams C, Pophaly SD, Neely BA, Gulland FMD, Adams DJ, Ng BL, Cheng W, Goebel ME, Fedrigo O, Haase B, Mountcastle J, Fungtammasan A, Formenti G, Collins J, Wood J, Sims Y, Torrance J, Tracey A, Howe K, Rhie A, Hoffman JI, Johnson J, Jarvis ED, Breen M, Wolf JBW. Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution. Mol Ecol Resour 2021; 21:2455-2470. [PMID: 34097816 PMCID: PMC9732816 DOI: 10.1111/1755-0998.13443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/06/2021] [Accepted: 05/26/2021] [Indexed: 12/13/2022]
Abstract
With the advent of chromatin-interaction maps, chromosome-level genome assemblies have become a reality for a wide range of organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome-scale genome assemblies of an emerging wild animal model for carcinogenesis, the California sea lion (Zalophus californianus). Short-read assemblies were scaffolded with two independent chromatin interaction mapping data sets (Hi-C and Chicago), and long-read assemblies with three data types (Hi-C, optical maps and 10X linked reads) following the "Vertebrate Genomes Project (VGP)" pipeline. In both approaches, 18 major scaffolds recovered the karyotype (2n = 36), with scaffold N50s of 138 and 147 Mb, respectively. Synteny relationships at the chromosome level with other pinniped genomes (2n = 32-36), ferret (2n = 34), red panda (2n = 36) and domestic dog (2n = 78) were consistent across approaches and recovered known fissions and fusions. Comparative chromosome painting and multicolour chromosome tiling with a panel of 264 genome-integrated single-locus canine bacterial artificial chromosome probes provided independent evaluation of genome organization. Broad-scale discrepancies between the approaches were observed within chromosomes, most commonly in translocations centred around centromeres and telomeres, which were better resolved in the VGP assembly. Genomic and cytological approaches agreed on near-perfect synteny of the X chromosome, and in combination allowed detailed investigation of autosomal rearrangements between dog and sea lion. This study presents high-quality genomes of an emerging cancer model and highlights that even highly fragmented short-read assemblies scaffolded with Hi-C can yield reliable chromosome-level scaffolds suitable for comparative genomic analyses.
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Affiliation(s)
- Claire R. Peart
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munchen, Germany
| | - Christina Williams
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Saurabh D. Pophaly
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munchen, Germany
- Max Planck institute for Plant Breeding Research, Cologne, Germany
| | - Benjamin A. Neely
- National Institute of Standards and Technology, NIST Charleston, Charleston, South Carolina, USA
| | - Frances M. D. Gulland
- Karen Dryer Wildlife Health Center, University of California Davis, Davis, California, USA
| | - David J. Adams
- Cytometry Core Facility, Wellcome Sanger Institute, Cambridge, UK
| | - Bee Ling Ng
- Cytometry Core Facility, Wellcome Sanger Institute, Cambridge, UK
| | - William Cheng
- Cytometry Core Facility, Wellcome Sanger Institute, Cambridge, UK
| | - Michael E. Goebel
- Institute of Marine Science, University of California Santa Cruz, Santa Cruz, California, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York City, New York, USA
| | - Bettina Haase
- Vertebrate Genome Lab, The Rockefeller University, New York City, New York, USA
| | | | | | - Giulio Formenti
- Vertebrate Genome Lab, The Rockefeller University, New York City, New York, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York City, New York, USA
| | - Joanna Collins
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Jonathan Wood
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Ying Sims
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - James Torrance
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Alan Tracey
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Kerstin Howe
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Joseph I. Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
- British Antarctic Survey, Cambridge, UK
| | - Jeremy Johnson
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
| | - Erich D. Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York City, New York, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
| | - Jochen B. W. Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munchen, Germany
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18
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Tian R, Han K, Geng Y, Yang C, Guo H, Shi C, Xu S, Yang G, Zhou X, Gladyshev VN, Liu X, Chopin LK, Fisher DO, Baker AM, Leiner NO, Fan G, Seim I. A Chromosome-Level Genome of the Agile Gracile Mouse Opossum (Gracilinanus agilis). Genome Biol Evol 2021; 13:evab162. [PMID: 34247236 PMCID: PMC8390783 DOI: 10.1093/gbe/evab162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2021] [Indexed: 12/27/2022] Open
Abstract
There are more than 100 species of American didelphid marsupials (opossums and mouse opossums). Limited genomic resources for didelphids exists, with only two publicly available genome assemblies compared with dozens in the case of their Australasian counterparts. This discrepancy impedes evolutionary and ecological research. To address this gap, we assembled a high-quality chromosome-level genome of the agile gracile mouse opossum (Gracilinanus agilis) using a combination of stLFR sequencing, polishing with mate-pair data, and anchoring onto pseudochromosomes using Hi-C. This species employs a rare life-history strategy, semelparity, and all G. agilis males and most females die at the end of their first breeding season after succumbing to stress and exhaustion. The 3.7-Gb chromosome-level assembly, with 92.6% anchored onto pseudochromosomes, has a scaffold N50 of 683.5 Mb and a contig N50 of 56.9 kb. The genome assembly shows high completeness, with a mammalian BUSCO score of 88.1%. Around 49.7% of the genome contains repetitive elements. Gene annotation yielded 24,425 genes, of which 83.9% were functionally annotated. The G. agilis genome is an important resource for future studies of marsupial biology, evolution, and conservation.
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Affiliation(s)
- Ran Tian
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Jiangsu, China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Jiangsu, China
| | - Kai Han
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Yuepan Geng
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Jiangsu, China
| | - Chen Yang
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Jiangsu, China
| | - Han Guo
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Jiangsu, China
| | | | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Jiangsu, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Jiangsu, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Lisa K Chopin
- Ghrelin Research Group, Translational Research Institute, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Diana O Fisher
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Andrew M Baker
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
- Natural Environments Program, Queensland Museum, South Brisbane, Queensland, Australia
| | - Natália O Leiner
- Laboratório de Ecologia de Mamíferos, Instituto de Biologia, Universidade Federal de Uberlândia, MG, Brazil
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Jiangsu, China
- Ghrelin Research Group, Translational Research Institute, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute, Queensland University of Technology, Brisbane, Queensland, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
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19
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Chen M, Ma Y, Wu S, Zheng X, Kang H, Sang J, Xu X, Hao L, Li Z, Gong Z, Xiao J, Zhang Z, Zhao W, Bao Y. Genome Warehouse: A Public Repository Housing Genome-scale Data. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:584-589. [PMID: 34175476 PMCID: PMC9039550 DOI: 10.1016/j.gpb.2021.04.001] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/19/2021] [Accepted: 04/07/2021] [Indexed: 11/09/2022]
Abstract
The Genome Warehouse (GWH) is a public repository housing genome assembly data for a wide range of species and delivering a series of web services for genome data submission, storage, release, and sharing. As one of the core resources in the National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB; https://ngdc.cncb.ac.cn), GWH accepts both full and partial (chloroplast, mitochondrion, and plasmid) genome sequences with different assembly levels, as well as an update of existing genome assemblies. For each assembly, GWH collects detailed genome-related metadata of biological project, biological sample, and genome assembly, in addition to genome sequence and annotation. To archive high-quality genome sequences and annotations, GWH is equipped with a uniform and standardized procedure for quality control. Besides basic browse and search functionalities, all released genome sequences and annotations can be visualized with JBrowse. By May 21, 2021, GWH has received 19,124 direct submissions covering a diversity of 1108 species and has released 8772 of them. Collectively, GWH serves as an important resource for genome-scale data management and provides free and publicly accessible data to support research activities throughout the world. GWH is publicly accessible at https://ngdc.cncb.ac.cn/gwh.
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Affiliation(s)
- Meili Chen
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingke Ma
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Song Wu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinchang Zheng
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongen Kang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Sang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingjian Xu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lili Hao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhaohua Li
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheng Gong
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfa Xiao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhang Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenming Zhao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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20
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Saremi NF, Oppenheimer J, Vollmers C, O'Connell B, Milne SA, Byrne A, Yu L, Ryder OA, Green RE, Shapiro B. An Annotated Draft Genome for the Andean Bear, Tremarctos ornatus. J Hered 2021; 112:377-384. [PMID: 33882130 PMCID: PMC8280923 DOI: 10.1093/jhered/esab021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/20/2021] [Indexed: 12/18/2022] Open
Abstract
The Andean bear is the only extant member of the Tremarctine subfamily and the only extant ursid species to inhabit South America. Here, we present an annotated de novo assembly of a nuclear genome from a captive-born female Andean bear, Mischief, generated using a combination of short and long DNA and RNA reads. Our final assembly has a length of 2.23 Gb, and a scaffold N50 of 21.12 Mb, contig N50 of 23.5 kb, and BUSCO score of 88%. The Andean bear genome will be a useful resource for exploring the complex phylogenetic history of extinct and extant bear species and for future population genetics studies of Andean bears.
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Affiliation(s)
- Nedda F Saremi
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Jonas Oppenheimer
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Christopher Vollmers
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Brendan O'Connell
- Department of Medical and Molecular Genetics, Oregon Health & Science University, Portland, OR
| | - Shard A Milne
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Ashley Byrne
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | | | - Richard E Green
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA
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21
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Huang P, Yu Y, Meng X, Wang T, Yan F, Li E, Shi Z, He H, Yang S, Xia X, Wang J, Feng N. Development of recombinase polymerase amplification assays for rapid and visual detection of canine distemper virus infecting giant panda. BMC Vet Res 2021; 17:172. [PMID: 33892731 PMCID: PMC8063184 DOI: 10.1186/s12917-021-02880-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/14/2021] [Indexed: 12/29/2022] Open
Abstract
Background Canine distemper virus (CDV) is an enveloped negative-strand RNA virus that exhibits a high mutation rate and continuously expands the range of hosts. Notably, CDV has infected giant panda with spill over from viral reservoirs in canines. Giant pandas (Ailuropoda melanoleuca), especially captive pandas, are known to be susceptible to natural infection with CDV. The high fatality rate of CDV poses a serious threat to the safety of the giant panda population. However, vaccines or drugs for canine distemper in giant pandas have not been developed to date. Therefore, a rapid test that can achieve accurate onsite detection of CDV is important to enable the timely implementation of control measures. In this study, we established a nucleic acid visualization assay for targeting the CDV N gene by using combines reverse transcription recombinase polymerase amplification with a closed vertical flow visualization strip (RT-RPA-VF). Results The RT-RPA-VF assay does not require sophisticated equipment, and it was determined to provide rapid detection at 35 °C for 30 min, while the limit of detection was 5 × 101 copies/μl RNA transcripts and 100.5 TCID50 ml− 1 viruses. The results showed that the assay was high specific to CDV and had no cross-reactivity with other viruses infecting the giant panda. Compared with RT-qPCR, RT-RPA-VF assay had a sensitivity of 100% and a specificity of 100% in 29 clinical samples. The coincidence rate between RT-RPA-VF and RT-qPCR was 100% (kappa = 1), indicating that the RT-RPA-VF assay possessed good diagnostic performance on clinical samples. Conclusions The RT-RPA-VF provides a novel alternative for the simple, sensitive, and specific identification of CDV and showed great potential for point of care diagnostics for captive and wild giant panda.
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Affiliation(s)
- Pei Huang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China.,Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Yue Yu
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
| | - Xianyong Meng
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China.,Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Tiecheng Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,College of Life Sciences, Shandong Normal University, Jinan, China
| | - Feihu Yan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Entao Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Zhikang Shi
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China.,Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Hongbin He
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Songtao Yang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China.,Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Xianzhu Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Jianzhong Wang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China.
| | - Na Feng
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China. .,College of Life Sciences, Shandong Normal University, Jinan, China.
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22
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Zhao Z, Zhou Y, Wang S, Zhang X, Wang C, Li S. LDscaff: LD-based scaffolding of de novo genome assemblies. BMC Bioinformatics 2020; 21:570. [PMID: 33371875 PMCID: PMC7768660 DOI: 10.1186/s12859-020-03895-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022] Open
Abstract
Background Genome assembly is fundamental for de novo genome analysis. Hybrid assembly, utilizing various sequencing technologies increases both contiguity and accuracy. While such approaches require extra costly sequencing efforts, the information provided millions of existed whole-genome sequencing data have not been fully utilized to resolve the task of scaffolding. Genetic recombination patterns in population data indicate non-random association among alleles at different loci, can provide physical distance signals to guide scaffolding. Results In this paper, we propose LDscaff for draft genome assembly incorporating linkage disequilibrium information in population data. We evaluated the performance of our method with both simulated data and real data. We simulated scaffolds by splitting the pig reference genome and reassembled them. Gaps between scaffolds were introduced ranging from 0 to 100 KB. The genome misassembly rate is 2.43% when there is no gap. Then we implemented our method to refine the Giant Panda genome and the donkey genome, which are purely assembled by NGS data. After LDscaff treatment, the resulting Panda assembly has scaffold N50 of 3.6 MB, 2.5 times larger than the original N50 (1.3 MB). The re-assembled donkey assembly has an improved N50 length of 32.1 MB from 23.8 MB. Conclusions Our method effectively improves the assemblies with existed re-sequencing data, and is an potential alternative to the existing assemblers required for the collection of new data.
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Affiliation(s)
- Zicheng Zhao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.,Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
| | - Yingxiao Zhou
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.,BGI-Shenzhen, Shenzhen, 518083, China
| | - Shuai Wang
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
| | - Xiuqing Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng City, 252059, Shandong, China.
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China.
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23
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Abstract
Attraction to feces in wild mammalian species is extremely rare. Here we introduce the horse manure rolling (HMR) behavior of wild giant pandas (Ailuropoda melanoleuca). Pandas not only frequently sniffed and wallowed in fresh horse manure, but also actively rubbed the fecal matter all over their bodies. The frequency of HMR events was highly correlated with an ambient temperature lower than 15 °C. BCP/BCPO (beta-caryophyllene/caryophyllene oxide) in fresh horse manure was found to drive HMR behavior and attenuated the cold sensitivity of mice by directly targeting and inhibiting transient receptor potential melastatin 8 (TRPM8), an archetypical cold-activated ion channel of mammals. Therefore, horse manure containing BCP/BCPO likely bestows the wild giant pandas with cold tolerance at low ambient temperatures. Together, our study described an unusual behavior, identified BCP/BCPO as chemical inhibitors of TRPM8 ion channel, and provided a plausible chemistry-auxiliary mechanism, in which animals might actively seek and utilize potential chemical resources from their habitat for temperature acclimatization.
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24
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Fan H, Wu Q, Wei F, Yang F, Ng BL, Hu Y. Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution. Genome Biol 2019; 20:267. [PMID: 31810476 PMCID: PMC6898958 DOI: 10.1186/s13059-019-1889-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/15/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromosome evolution is an important driver of speciation and species evolution. Previous studies have detected chromosome rearrangement events among different Carnivora species using chromosome painting strategies. However, few of these studies have focused on chromosome evolution at a nucleotide resolution due to the limited availability of chromosome-level Carnivora genomes. Although the de novo genome assembly of the giant panda is available, current short read-based assemblies are limited to moderately sized scaffolds, making the study of chromosome evolution difficult. RESULTS Here, we present a chromosome-level giant panda draft genome with a total size of 2.29 Gb. Based on the giant panda genome and published chromosome-level dog and cat genomes, we conduct six large-scale pairwise synteny alignments and identify evolutionary breakpoint regions. Interestingly, gene functional enrichment analysis shows that for all of the three Carnivora genomes, some genes located in evolutionary breakpoint regions are significantly enriched in pathways or terms related to sensory perception of smell. In addition, we find that the sweet receptor gene TAS1R2, which has been proven to be a pseudogene in the cat genome, is located in an evolutionary breakpoint region of the giant panda, suggesting that interchromosomal rearrangement may play a role in the cat TAS1R2 pseudogenization. CONCLUSIONS We show that the combined strategies employed in this study can be used to generate efficient chromosome-level genome assemblies. Moreover, our comparative genomics analyses provide novel insights into Carnivora chromosome evolution, linking chromosome evolution to functional gene evolution.
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Affiliation(s)
- Huizhong Fan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Bee Ling Ng
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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