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Ghavi Hossein-Zadeh N. An overview of recent technological developments in bovine genomics. Vet Anim Sci 2024; 25:100382. [PMID: 39166173 PMCID: PMC11334705 DOI: 10.1016/j.vas.2024.100382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024] Open
Abstract
Cattle are regarded as highly valuable animals because of their milk, beef, dung, fur, and ability to draft. The scientific community has tried a number of strategies to improve the genetic makeup of bovine germplasm. To ensure higher returns for the dairy and beef industries, researchers face their greatest challenge in improving commercially important traits. One of the biggest developments in the last few decades in the creation of instruments for cattle genetic improvement is the discovery of the genome. Breeding livestock is being revolutionized by genomic selection made possible by the availability of medium- and high-density single nucleotide polymorphism (SNP) arrays coupled with sophisticated statistical techniques. It is becoming easier to access high-dimensional genomic data in cattle. Continuously declining genotyping costs and an increase in services that use genomic data to increase return on investment have both made a significant contribution to this. The field of genomics has come a long way thanks to groundbreaking discoveries such as radiation-hybrid mapping, in situ hybridization, synteny analysis, somatic cell genetics, cytogenetic maps, molecular markers, association studies for quantitative trait loci, high-throughput SNP genotyping, whole-genome shotgun sequencing to whole-genome mapping, and genome editing. These advancements have had a significant positive impact on the field of cattle genomics. This manuscript aimed to review recent advances in genomic technologies for cattle breeding and future prospects in this field.
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Affiliation(s)
- Navid Ghavi Hossein-Zadeh
- Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, 41635-1314, Iran
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2
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Huang T, Liu E, Cao B, Li W, Wang G, Gu W, Ma H, Dong F, Wang B, Xu G. A chromosome-level genome assembly and evolutionary analysis of Coregonus ussuriensis Berg. Sci Data 2024; 11:792. [PMID: 39025879 PMCID: PMC11258136 DOI: 10.1038/s41597-024-03642-0] [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: 09/15/2023] [Accepted: 07/12/2024] [Indexed: 07/20/2024] Open
Abstract
Coregonus ussuriensis Berg, distributed widely in cold waters above 45° N latitude, is a savored freshwater whitefish that has been included in the list of endangered animals as a consequence of overfishing. Lack of genomic information seriously hampers evolutionary and genetic research on C. ussuriensis warranting the need to assemble a high-quality reference genome to promote its genetic breeding. We assembled and constructed a reference chromosome-level C. ussuriensis genome (sequence length, 2.51 Gb; contig N50 length, 4.27 Mb) using PacBio sequencing and Hi-C assembly technology, 3,109 contigs were assembled into scaffolds, resulting in a genome assembly with 40 chromosomes and a scaffold N50 length of 62.20 Mb. In addition, 43,320 protein-coding genes were annotated. The peak Ks position in the species comparison reflects the whole-genome replication event of C. ussuriensis. This chromosome-level genome provides reference data for further studies on the molecular breeding of C. ussuriensis.
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Affiliation(s)
- Tianqing Huang
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China
| | - Enhui Liu
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China
| | - Baorui Cao
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China
| | - Wenwen Li
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China
| | - Gaochao Wang
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China
| | - Wei Gu
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China
| | - Haibing Ma
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China
| | - Fulin Dong
- Yantai Jinghai Marine Fishery Co Ltd, Yantai, PR China
| | - Bingqian Wang
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China
| | - Gefeng Xu
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China.
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Schweizer RM, Meidt CG, Benavides LR, Wilson JS, Griswold TL, Sim SB, Geib SM, Branstetter MG. Reference genome for the Mojave poppy bee (Perdita meconis), a specialist pollinator of conservation concern. J Hered 2024; 115:470-479. [PMID: 38088446 PMCID: PMC11235129 DOI: 10.1093/jhered/esad076] [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: 09/15/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 07/11/2024] Open
Abstract
The Mojave poppy bee, Perdita meconis Griswold (Hymenoptera: Anthophila: Andrenidae), is a species of conservation concern that is restricted to the eastern Mojave Desert of North America. It is a specialist pollinator of two poppy genera, Arctomecon and Argemone (Papaveraceae), and is being considered for listing under the US Endangered Species Act along with one of its pollinator hosts, the Las Vegas bearpoppy (Arctomecon californica). Here, we present a near chromosome-level genome of the Mojave poppy bee to provide a genomic resource that will aid conservation efforts and future research. We isolated DNA from a single, small (<7 mm), male specimen collected using non-ideal preservation methods and then performed whole-genome sequencing using PacBio HiFi technology. After quality and contaminant filtering, the final draft genome assembly is 327 Mb, with an N50 length of 17.5 Mb. Annotated repetitive elements compose 37.3% of the genome, although a large proportion (24.87%) of those are unclassified repeats. Additionally, we annotated 18,245 protein-coding genes and 19,433 transcripts. This genome represents one of only a few genomes from the large bee family Andrenidae and one of only a few genomes for pollinator specialists. We highlight both the potential of this genome as a resource for future research, and how high-quality genomes generated from small, non-ideal (in terms of preservation) specimens could facilitate biodiversity genomics.
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Affiliation(s)
- Rena M Schweizer
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT, United States
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Colleen G Meidt
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT, United States
- Department of Biology, Utah State University, Logan, UT, United States
| | - Ligia R Benavides
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT, United States
| | - Joseph S Wilson
- Department of Biology, Utah State University-Tooele, Tooele, UT, United States
| | - Terry L Griswold
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT, United States
| | - Sheina B Sim
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, HI, United States
| | - Scott M Geib
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, HI, United States
| | - Michael G Branstetter
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT, United States
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Wang C, Tang Y, Zhang P, Xiong L, Chen W, Lv X. Detection and phenotype analysis of a novel Ael blood group allele. Vox Sang 2024; 119:74-78. [PMID: 37937512 DOI: 10.1111/vox.13557] [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: 08/03/2023] [Revised: 10/07/2023] [Accepted: 10/15/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND AND OBJECTIVES The presence of blood subtypes may lead to difficulties in blood group identification; however, third-generation sequencing (TGS) can help in accurately identifying difficult blood groups, and study the serological characteristics and molecular mechanism of Ael subtypes. MATERIALS AND METHODS ABO blood group was identified by the standard serological technique, weak blood group antigen was identified by adsorption-elution experiments, ABH substance in the saliva was determined and glycosyltransferase activity of A and B was detected. The ABO gene full-length sequence and promoter region were amplified by specific primers using single-molecule real-time sequencing, with the amplified products being sequenced directly and analysed in real time. RESULTS The patient was serologically identified as Ael subtype, and TGS analysis revealed new intron mutations in Ael patients (c.467C>T; c.29-10T>A). CONCLUSION The discovery of the new allele and the identification of ABO subtypes can be combined with serological characterization and molecular biological methods.
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Affiliation(s)
- Cuibi Wang
- Department of Transfusion, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, Fujian, China
| | - Yichao Tang
- Department of Internal Medicine, Yunxiao County Hospital of Traditional Chinese Medicine, Zhangzhou, Fujian, China
| | - Pingping Zhang
- Department of Transfusion, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, Fujian, China
| | - Leiqun Xiong
- Department of Transfusion, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, Fujian, China
| | - Weiyuan Chen
- Department of Transfusion, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, Fujian, China
| | - Xiaoying Lv
- Department of Transfusion, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, Fujian, China
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Moggioli G, Panossian B, Sun Y, Thiel D, Martín-Zamora FM, Tran M, Clifford AM, Goffredi SK, Rimskaya-Korsakova N, Jékely G, Tresguerres M, Qian PY, Qiu JW, Rouse GW, Henry LM, Martín-Durán JM. Distinct genomic routes underlie transitions to specialised symbiotic lifestyles in deep-sea annelid worms. Nat Commun 2023; 14:2814. [PMID: 37198188 DOI: 10.1038/s41467-023-38521-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 05/03/2023] [Indexed: 05/19/2023] Open
Abstract
Bacterial symbioses allow annelids to colonise extreme ecological niches, such as hydrothermal vents and whale falls. Yet, the genetic principles sustaining these symbioses remain unclear. Here, we show that different genomic adaptations underpin the symbioses of phylogenetically related annelids with distinct nutritional strategies. Genome compaction and extensive gene losses distinguish the heterotrophic symbiosis of the bone-eating worm Osedax frankpressi from the chemoautotrophic symbiosis of deep-sea Vestimentifera. Osedax's endosymbionts complement many of the host's metabolic deficiencies, including the loss of pathways to recycle nitrogen and synthesise some amino acids. Osedax's endosymbionts possess the glyoxylate cycle, which could allow more efficient catabolism of bone-derived nutrients and the production of carbohydrates from fatty acids. Unlike in most Vestimentifera, innate immunity genes are reduced in O. frankpressi, which, however, has an expansion of matrix metalloproteases to digest collagen. Our study supports that distinct nutritional interactions influence host genome evolution differently in highly specialised symbioses.
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Affiliation(s)
- Giacomo Moggioli
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Balig Panossian
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Yanan Sun
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Daniel Thiel
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Martin Tran
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Alexander M Clifford
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Nadezhda Rimskaya-Korsakova
- Friedrich Schiller University Jena, Faculty of Biological Sciences, Institute of Zoology and Evolutionary Research, Erbertstr. 1, 07743, Jena, Germany
| | - Gáspár Jékely
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Martin Tresguerres
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Pei-Yuan Qian
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lee M Henry
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
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Zhang Z, Pei P, Zhang M, Li F, Tang G. Chromosome-level genome assembly of Dastarcus helophoroides provides insights into CYP450 genes expression upon insecticide exposure. PEST MANAGEMENT SCIENCE 2023; 79:1467-1482. [PMID: 36502364 DOI: 10.1002/ps.7319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 10/26/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Dastarcus helophoroides is an important natural enemy of cerambycids, and is wildly used in biological control of pests. Nevertheless, the absence of complete genomic information limits the investigation of the underlying molecular mechanisms. Here, a chromosome-level of Dastarcus helophoroides genome is assembled using a combination strategy of Illumina, PacBio, 10x™ Genomics, and Hi-C. RESULTS The final assembly is 609.09 Mb with contig N50, scaffold N50 and GC content of 5.46 Mb, 42.56 Mb and 31.50%, respectively, and 95.25% of the contigs anchor into 13 chromosomes. In total 14 890 protein-coding genes and 65.37% repeat sequences are predicted in the assembly genome. The phylogenetic analysis of single-copy gene families shared among 20 insect species indicates that Dastarcus helophoroides is placed as the sister species to clade (Nitidulidae+Curculionoidea+Chrysomeloidea) + Tenebrionoidea, and diverges from the related species ~242.9 Mya. In total 36 expanded gene families are identified in Dastarcus helophoroides genome, and are functionally related to drug metabolism and metabolism of xenobiotics by cytochrome P450. Some members of CYP4 Clade and CYP6 Clade are up-regulated in Dastarcus helophoroides adults upon insecticide exposure, of which expressions of DhCYP4Q, DhCYP6A14X1 and DhCYP4C1 are significantly up-regulated. The silencing of the three genes leads to adults more sensitive to insecticide and increased knocked-down rate, which may indicate their critical roles in stress resistance and detoxication. CONCLUSION Our study systematically integrated the chromosome-level genome, transcriptome and gene expression of Dastarcus helophoroides, which will provide valuable resources for understanding mechanisms of pesticide metabolism, growth and development, and utilization of the natural enemy in integrated control. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Zhengqing Zhang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Pei Pei
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Meng Zhang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Feifei Li
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Guanghui Tang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
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Yu M, Wei Q, Song W, Yuan J. Phenotypic and Genetic Analysis of KPC-49, a KPC-2 Variant Conferring Resistance to Ceftazidime-Avibactam and Maintaining Resistance to Imipenem and Meropenem. Infect Drug Resist 2023; 16:2477-2485. [PMID: 37138840 PMCID: PMC10150759 DOI: 10.2147/idr.s406319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
Purpose Klebsiella pneumoniae, a gram-negative bacterium, poses a severe hazard to public health, with many bacterial hosts having developed resistance to most antibiotics in clinical use. The goal of this study was to look into the development of resistance to both ceftazidime-avibactam and carbapenems, including imipenem and meropenem, in a K. pneumonia strain expressing a novel K. pneumoniae carbapenemase-2 (KPC-2) variant, referred to as KPC-49. Methods After 1 day of incubation of K1 on agar containing ceftazidime-avibactam (MIC = 16/4 mg/L), a second KPC-producing K. pneumoniae strain (K2) was recovered. Antimicrobial susceptibility assays, cloning assays, and whole genome sequencing were performed to analyse and evaluate antibiotic resistance phenotypes and genotypes. Results K. pneumoniae strain (K1), that produced KPC-2, was susceptible to ceftazidime-avibactam but resistant to carbapenems. The K2 isolate harboured a novel bla KPC-49 variant, which differs from bla KPC-2 by a single nucleotide (C487A), and results in an arginine-serine substitution at amino acid position 163 (R163S). The mutant K2 strain was resistant to both ceftazidime-avibactam and carbapenems. We demonstrated the ability of KPC-49 to hydrolyse carbapenems, which may be attributed to high KPC-49 expression or presence of an efflux pump and/or absence of membrane pore proteins in K2. Furthermore, blaKPC-like was carried on an IncFII (pHN7A8)/IncR-type plasmid within a TnAs1-orf-orf-orf-orf-orf-orf-ISKpn6-bla KPC-ISKpn27 structure. The bla KPC-like gene was flanked by various insertion sequences and transposon elements, including the Tn3 family transposon, such as TnAs1, TnAs3, IS26, and IS481-ISKpn27. Conclusion New KPC variants are emerging owing to sustained exposure to antimicrobials and modifications in their amino acid sequences. We demonstrated the drug resistance mechanisms of the new mutant strains through experimental whole genome sequencing combined with bioinformatics analysis. Enhanced understanding of laboratory and clinical features of infections due to K. pneumoniae of the new KPC subtype is key to early and accurate anti-infective therapy.
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Affiliation(s)
- Meng Yu
- Clinical Laboratory, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, Shandong, People’s Republic of China
| | - Qingzheng Wei
- Clinical Laboratory, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, Shandong, People’s Republic of China
| | - Weiqing Song
- Clinical Laboratory, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, Shandong, People’s Republic of China
| | - Jiangshui Yuan
- Clinical Laboratory, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, Shandong, People’s Republic of China
- Correspondence: Jiangshui Yuan; Weiqing Song, Clinical Laboratory, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, Shandong, People’s Republic of China, Tel +86-0532-6602-7876, Email ;
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Wang YX, Chen HF, Yin ZY, Chen WL, Lu LT. The genetic adaptations of Toxoptera aurantii facilitated its rapid multiple plant hosts dispersal and invasion. Genomics 2022; 114:110472. [PMID: 36055573 DOI: 10.1016/j.ygeno.2022.110472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/24/2022] [Accepted: 08/27/2022] [Indexed: 01/14/2023]
Abstract
Toxoptera aurantii Boyer de Fonscolombe (Hemiptera: Aphididae) can attack many plant hosts, including tea (Camellia sinensis L.), citrus (Citrus spp.), lychee (Litchi chinensis Sonn.), banana (Musa spp.), and pineapple (Ananas comasus L.) among others. It is a widely distributed hexapod and one of the most destructive pests in tea plantations, causing enormous economic losses in tea production each year. A high-quality reference genome is important to study the phylogenetics and evolution of T. aurantii because its genome is highly heterozygous and repetitive. We obtained a de novo genome assembly of T. aurantii at the chromosome level using a combination of long Nanopore reads from sequencing with high-throughput chromosome conformation capture technology. When finally assembled, the genome was 318.95 Mb on four chromosomes with a 15.19 Mb scaffold N50. A total of 12,162 genes encoded proteins, while there were 22.01% repetitive sequences that totaled 67.73 Mb. Phylogenetic analyses revealed that T. aurantii and Aphis gossypii parted ways approximately 7.6 million years ago (Mya). We used a combination of long-read single-molecule sequencing with Hi-C-based chromatin interaction maps that resulted in a reference chromosomal level reference genome of T. aurantii that was high quality. Our results will enable the exploration of the genetics behind the special biological features of T. aurantii and also provide a source of data that should be useful to compare the compare genome among the Hemiptera.
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Affiliation(s)
- Yan-Xia Wang
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang 550025, China; College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Hu-Fang Chen
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Zheng-Yan Yin
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang 550025, China
| | - Wen-Long Chen
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang 550025, China.
| | - Li-Tang Lu
- College of Tea Science, Guizhou University, Guiyang 550025, China.
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9
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Nouhaud P, Beresford J, Kulmuni J. Assembly of a Hybrid Formica aquilonia × F. polyctena Ant Genome From a Haploid Male. J Hered 2022; 113:353-359. [PMID: 35394540 PMCID: PMC9270870 DOI: 10.1093/jhered/esac019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 04/04/2022] [Indexed: 11/29/2022] Open
Abstract
Formica red wood ants are a keystone species of boreal forest ecosystems and an emerging model system in the study of speciation and hybridization. Here, we performed a standard DNA extraction from a single, field-collected Formica aquilonia × Formica polyctena haploid male and assembled its genome using ~60× of PacBio long reads. After polishing and contaminant removal, the final assembly was 272 Mb (4687 contigs, N50 = 1.16 Mb). Our reference genome contains 98.5% of the core Hymenopteran BUSCOs and was pseudo-scaffolded using the assembly of a related species, F. selysi (28 scaffolds, N50 = 8.49 Mb). Around one-third of the genome consists of repeats, and 17 426 gene models were annotated using both protein and RNAseq data (97.4% BUSCO completeness). This resource is of comparable quality to the few other single individual insect genomes assembled to date and paves the way to genomic studies of admixture in natural populations and comparative genomic approaches in Formica wood ants.
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Affiliation(s)
- Pierre Nouhaud
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Biocenter 3, Viikinkaari 1, 00790 Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, J. A. Palménin tie 260, 10900 Hanko, Finland
| | - Jack Beresford
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Biocenter 3, Viikinkaari 1, 00790 Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, J. A. Palménin tie 260, 10900 Hanko, Finland
| | - Jonna Kulmuni
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Biocenter 3, Viikinkaari 1, 00790 Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, J. A. Palménin tie 260, 10900 Hanko, Finland
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10
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Complete genome analysis of a novel iflavirus from the spotted lanternfly Lycorma delicatula. Arch Virol 2022; 167:2079-2083. [PMID: 35751691 DOI: 10.1007/s00705-022-05503-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/23/2022] [Indexed: 11/02/2022]
Abstract
The spotted lanternfly (Lycorma delicatula) is an invasive pest that causes serious economic losses in fruit and wood production. Here, we identified a novel iflavirus named "Lycorma delicatula iflavirus 1" (LDIV1), in a spotted lanternfly. The full genome sequence of LDIV1 is 10,222 nt in length and encodes a polyprotein containing a picornavirus capsid-protein-domain-like domain, a cricket paralysis virus capsid superfamily domain, an RNA helicase domain, a peptidase C3 superfamily domain, and an RNA-dependent RNA polymerase (RdRp) domain. LDIV1 replicates in the host insect and activates small interfering RNA (siRNA)-based host antiviral immunity. Phylogenetic analysis demonstrated that LDIV1 is most closely related to an unspecified member of the order Picornavirales, with 61.7% sequence identity in the RdRp region and 57.6% sequence identity in the coat protein region, and thus meets the demarcation criteria for new species in the genus Iflavirus. To the best of our knowledge, LDIV1 is the first virus discovered in L. delicatula.
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11
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Filipović I, Rašić G, Hereward J, Gharuka M, Devine GJ, Furlong MJ, Etebari K. A high-quality de novo genome assembly based on nanopore sequencing of a wild-caught coconut rhinoceros beetle (Oryctes rhinoceros). BMC Genomics 2022; 23:426. [PMID: 35672676 PMCID: PMC9172067 DOI: 10.1186/s12864-022-08628-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 05/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND An optimal starting point for relating genome function to organismal biology is a high-quality nuclear genome assembly, and long-read sequencing is revolutionizing the production of this genomic resource in insects. Despite this, nuclear genome assemblies have been under-represented for agricultural insect pests, particularly from the order Coleoptera. Here we present a de novo genome assembly and structural annotation for the coconut rhinoceros beetle, Oryctes rhinoceros (Coleoptera: Scarabaeidae), based on Oxford Nanopore Technologies (ONT) long-read data generated from a wild-caught female, as well as the assembly process that also led to the recovery of the complete circular genome assemblies of the beetle's mitochondrial genome and that of the biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). As an invasive pest of palm trees, O. rhinoceros is undergoing an expansion in its range across the Pacific Islands, requiring new approaches to management that may include strategies facilitated by genome assembly and annotation. RESULTS High-quality DNA isolated from an adult female was used to create four ONT libraries that were sequenced using four MinION flow cells, producing a total of 27.2 Gb of high-quality long-read sequences. We employed an iterative assembly process and polishing with one lane of high-accuracy Illumina reads, obtaining a final size of the assembly of 377.36 Mb that had high contiguity (fragment N50 length = 12 Mb) and accuracy, as evidenced by the exceptionally high completeness of the benchmarked set of conserved single-copy orthologous genes (BUSCO completeness = 99.1%). These quality metrics place our assembly ahead of the published Coleopteran genomes, including that of an insect model, the red flour beetle (Tribolium castaneum). The structural annotation of the nuclear genome assembly contained a highly-accurate set of 16,371 protein-coding genes, with only 2.8% missing BUSCOs, and the expected number of non-coding RNAs. The number and structure of paralogous genes in a gene family like Sigma GST is lower than in another scarab beetle (Onthophagus taurus), but higher than in the red flour beetle (Tribolium castaneum), which suggests expansion of this GST class in Scarabaeidae. The quality of our gene models was also confirmed with the correct placement of O. rhinoceros among other members of the rhinoceros beetles (subfamily Dynastinae) in a phylogeny based on the sequences of 95 protein-coding genes in 373 beetle species from all major lineages of Coleoptera. Finally, we provide a list of 30 candidate dsRNA targets whose orthologs have been experimentally validated as highly effective targets for RNAi-based control of several beetles. CONCLUSIONS The genomic resources produced in this study form a foundation for further functional genetic research and management programs that may inform the control and surveillance of O. rhinoceros populations, and we demonstrate the efficacy of de novo genome assembly using long-read ONT data from a single field-caught insect.
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Affiliation(s)
- Igor Filipović
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia.
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
| | - Gordana Rašić
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - James Hereward
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia
| | - Maria Gharuka
- Research Division, Ministry of Agriculture and Livestock, Honiara, Solomon Islands
| | - Gregor J Devine
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Michael J Furlong
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia
| | - Kayvan Etebari
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia
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12
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Lukyanchikova V, Nuriddinov M, Belokopytova P, Taskina A, Liang J, Reijnders MJMF, Ruzzante L, Feron R, Waterhouse RM, Wu Y, Mao C, Tu Z, Sharakhov IV, Fishman V. Anopheles mosquitoes reveal new principles of 3D genome organization in insects. Nat Commun 2022; 13:1960. [PMID: 35413948 PMCID: PMC9005712 DOI: 10.1038/s41467-022-29599-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 03/24/2022] [Indexed: 11/24/2022] Open
Abstract
Chromosomes are hierarchically folded within cell nuclei into territories, domains and subdomains, but the functional importance and evolutionary dynamics of these hierarchies are poorly defined. Here, we comprehensively profile genome organizations of five Anopheles mosquito species and show how different levels of chromatin architecture influence each other. Patterns observed on Hi-C maps are associated with known cytological structures, epigenetic profiles, and gene expression levels. Evolutionary analysis reveals conservation of chromatin architecture within synteny blocks for tens of millions of years and enrichment of synteny breakpoints in regions with increased genomic insulation. However, in-depth analysis shows a confounding effect of gene density on both insulation and distribution of synteny breakpoints, suggesting limited causal relationship between breakpoints and regions with increased genomic insulation. At the level of individual loci, we identify specific, extremely long-ranged looping interactions, conserved for ~100 million years. We demonstrate that the mechanisms underlying these looping contacts differ from previously described Polycomb-dependent interactions and clustering of active chromatin.
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Affiliation(s)
- Varvara Lukyanchikova
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
- Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Miroslav Nuriddinov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Polina Belokopytova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Alena Taskina
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Jiangtao Liang
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
- Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Maarten J M F Reijnders
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Livio Ruzzante
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Yang Wu
- Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
- Department of Pathogen Biology, School of Public Health, Southern Medical University, 510515, Guangzhou, Guangdong, China
| | - Chunhong Mao
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA, 22911, USA
| | - Zhijian Tu
- Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
- Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
- Department of Genetics and Cell Biology, Tomsk State University, Tomsk, Russia.
| | - Veniamin Fishman
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
- AIRI, Moscow, Russia.
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13
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Athanasopoulou K, Boti MA, Adamopoulos PG, Skourou PC, Scorilas A. Third-Generation Sequencing: The Spearhead towards the Radical Transformation of Modern Genomics. Life (Basel) 2021; 12:life12010030. [PMID: 35054423 PMCID: PMC8780579 DOI: 10.3390/life12010030] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022] Open
Abstract
Although next-generation sequencing (NGS) technology revolutionized sequencing, offering a tremendous sequencing capacity with groundbreaking depth and accuracy, it continues to demonstrate serious limitations. In the early 2010s, the introduction of a novel set of sequencing methodologies, presented by two platforms, Pacific Biosciences (PacBio) and Oxford Nanopore Sequencing (ONT), gave birth to third-generation sequencing (TGS). The innovative long-read technologies turn genome sequencing into an ease-of-handle procedure by greatly reducing the average time of library construction workflows and simplifying the process of de novo genome assembly due to the generation of long reads. Long sequencing reads produced by both TGS methodologies have already facilitated the decipherment of transcriptional profiling since they enable the identification of full-length transcripts without the need for assembly or the use of sophisticated bioinformatics tools. Long-read technologies have also provided new insights into the field of epitranscriptomics, by allowing the direct detection of RNA modifications on native RNA molecules. This review highlights the advantageous features of the newly introduced TGS technologies, discusses their limitations and provides an in-depth comparison regarding their scientific background and available protocols as well as their potential utility in research and clinical applications.
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14
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Van Dam MH, Cabras AA, Henderson JB, Rominger AJ, Pérez Estrada C, Omer AD, Dudchenko O, Lieberman Aiden E, Lam AW. The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution. PLoS Genet 2021; 17:e1009745. [PMID: 34460814 PMCID: PMC8432895 DOI: 10.1371/journal.pgen.1009745] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 09/10/2021] [Accepted: 07/27/2021] [Indexed: 01/01/2023] Open
Abstract
Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders. We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open-source insect genomes. To accomplish this, we add a chromosome level genome to a crucial lineage, Coleoptera. Our assembly of the Pachyrhynchus sulphureomaculatus genome is the first chromosome scale genome for the hyperdiverse Phytophaga lineage and currently the largest insect genome assembled to this scale. The genome is significantly larger than those of other weevils, and this increase in size is caused by repetitive elements. Our results also indicate that, among beetles, there are instances of long-lasting (>200 Ma) localization of genes to a particular chromosome with few translocation events. While some chromosomes have a paucity of translocations, intra-chromosomal synteny was almost absent, with gene order thoroughly shuffled along a chromosome. This large amount of reshuffling within chromosomes with few inter-chromosomal events contrasts with patterns seen in mammals in which the chromosomes tend to exchange larger blocks of material more readily. To place our findings in an evolutionary context, we compared syntenic patterns across Insecta in a phylogenetic framework. For the first time, we find that synteny decays at an exponential rate relative to phylogenetic distance. Additionally, there are significant differences in decay rates between insect orders, this pattern was not driven by Lepidoptera alone which has a substantially different rate.
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Affiliation(s)
- Matthew H. Van Dam
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California, United States of America
- Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Science, San Francisco, California, United States of America
| | - Analyn Anzano Cabras
- Coleoptera Research Center, Institute for Biodiversity and Environment, University of Mindanao, Matina, Davao City, Philippines
| | - James B. Henderson
- Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Science, San Francisco, California, United States of America
| | - Andrew J. Rominger
- School of Biology and Ecology, University of Maine, Orono, Maine, United States of America
| | - Cynthia Pérez Estrada
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Arina D. Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Athena W. Lam
- Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Science, San Francisco, California, United States of America
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15
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Targeted Long-Read Sequencing Reveals Comprehensive Architecture, Burden and Transcriptional Signatures from HBV-Associated Integrations and Translocations in HCC Cell Lines. J Virol 2021; 95:e0029921. [PMID: 34287049 DOI: 10.1128/jvi.00299-21] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hepatitis B virus (HBV) can integrate into the chromosomes of infected hepatocytes, creating potentially oncogenic lesions that can lead to hepatocellular carcinoma (HCC). However, our current understanding of integrated HBV DNA architecture, burden and transcriptional activity is incomplete due to technical limitations. A combination of genomics approaches was used to describe HBV integrations and corresponding transcriptional signatures in three HCC cell lines: huH-1, PLC/PRF/5 and Hep3B. To generate high coverage long-read sequencing data, a custom panel of HBV-targeting biotinylated oligonucleotide probes was designed. Targeted long-read DNA sequencing captured entire HBV integration events within individual reads, revealing that integrations may include deletions and inversions of viral sequences. Surprisingly, all three HCC cell lines contain integrations that are associated with host chromosomal translocations. In addition, targeted long-read RNA sequencing allowed for the assignment of transcriptional activity to specific integrations and resolved the contribution of overlapping HBV transcripts. HBV transcripts chimeric with host sequences were resolved in their entirety and often included >1000bp of host sequence. This study provides the first comprehensive description of HBV integrations and associated transcriptional activity in three commonly utilized HCC-derived cell lines. The application of novel methods sheds new light on the complexity of these integrations, including HBV bidirectional transcription, nested transcripts, silent integrations and host genomic rearrangements. The observation of multiple HBV-associated chromosomal translocations gives rise to the hypothesis that HBV may be a driver of genetic instability and provides a potential new mechanism for HCC development. Importance HCC-derived cell lines have served as practical models to study HBV biology for decades. These cell lines harbor multiple HBV integrations and express only HBV surface antigen (HBsAg). To date, an accurate description of the integration burden, architecture and transcriptional profile of these cell lines has been limited due to technical constraints. We have developed a targeted long-read sequencing assay which reveals the entire architecture of integrations in these cell lines. In addition, we identified five chromosomal translocations with integrated HBV DNA at the inter-chromosomal junctions. Incorporation of long-read RNA-Seq data indicated that many integrations and translocations were transcriptionally silent. The observation of multiple HBV-associated translocations has strong implications regarding the potential mechanisms for the development of HBV-associated HCC.
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16
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Sequencing an F1 hybrid of Silurus asotus and S. meridionalis enabled the assembly of high-quality parental genomes. Sci Rep 2021; 11:13797. [PMID: 34226617 PMCID: PMC8257616 DOI: 10.1038/s41598-021-93257-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/16/2021] [Indexed: 01/27/2023] Open
Abstract
Genome complexity such as heterozygosity may heavily influence its de novo assembly. Sequencing somatic cells of the F1 hybrids harboring two sets of genetic materials from both of the paternal and maternal species may avoid alleles discrimination during assembly. However, the feasibility of this strategy needs further assessments. We sequenced and assembled the genome of an F1 hybrid between Silurus asotus and S. meridionalis using the SequelII platform and Hi-C scaffolding technologies. More than 300 Gb raw data were generated, and the final assembly obtained 2344 scaffolds composed of 3017 contigs. The N50 length of scaffolds and contigs was 28.55 Mb and 7.49 Mb, respectively. Based on the mapping results of short reads generated for the paternal and maternal species, each of the 29 chromosomes originating from S. asotus and S. meridionalis was recognized. We recovered nearly 94% and 96% of the total length of S. asotus and S. meridionalis. BUSCO assessments and mapping analyses suggested that both genomes had high completeness and accuracy. Further analyses demonstrated the high collinearity between S. asotus, S. meridionalis, and the related Pelteobagrus fulvidraco. Comparison of the two genomes with that assembled only using the short reads from non-hybrid parental species detected a small portion of sequences that may be incorrectly assigned to the different species. We supposed that at least part of these situations may have resulted from mitotic recombination. The strategy of sequencing the F1 hybrid genome can recover the vast majority of the parental genomes and may improve the assembly of complex genomes.
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17
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Detecting and phasing minor single-nucleotide variants from long-read sequencing data. Nat Commun 2021; 12:3032. [PMID: 34031367 PMCID: PMC8144375 DOI: 10.1038/s41467-021-23289-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 04/15/2021] [Indexed: 02/04/2023] Open
Abstract
Cellular genetic heterogeneity is common in many biological conditions including cancer, microbiome, and co-infection of multiple pathogens. Detecting and phasing minor variants play an instrumental role in deciphering cellular genetic heterogeneity, but they are still difficult tasks because of technological limitations. Recently, long-read sequencing technologies, including those by Pacific Biosciences and Oxford Nanopore, provide an opportunity to tackle these challenges. However, high error rates make it difficult to take full advantage of these technologies. To fill this gap, we introduce iGDA, an open-source tool that can accurately detect and phase minor single-nucleotide variants (SNVs), whose frequencies are as low as 0.2%, from raw long-read sequencing data. We also demonstrate that iGDA can accurately reconstruct haplotypes in closely related strains of the same species (divergence ≥0.011%) from long-read metagenomic data.
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18
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Schneider C, Woehle C, Greve C, D'Haese CA, Wolf M, Hiller M, Janke A, Bálint M, Huettel B. Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola). Gigascience 2021; 10:giab035. [PMID: 34018554 PMCID: PMC8138834 DOI: 10.1093/gigascience/giab035] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/05/2021] [Accepted: 04/27/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Genome sequencing of all known eukaryotes on Earth promises unprecedented advances in biological sciences and in biodiversity-related applied fields such as environmental management and natural product research. Advances in long-read DNA sequencing make it feasible to generate high-quality genomes for many non-genetic model species. However, long-read sequencing today relies on sizable quantities of high-quality, high molecular weight DNA, which is mostly obtained from fresh tissues. This is a challenge for biodiversity genomics of most metazoan species, which are tiny and need to be preserved immediately after collection. Here we present de novo genomes of 2 species of submillimeter Collembola. For each, we prepared the sequencing library from high molecular weight DNA extracted from a single specimen and using a novel ultra-low input protocol from Pacific Biosciences. This protocol requires a DNA input of only 5 ng, permitted by a whole-genome amplification step. RESULTS The 2 assembled genomes have N50 values >5.5 and 8.5 Mb, respectively, and both contain ∼96% of BUSCO genes. Thus, they are highly contiguous and complete. The genomes are supported by an integrative taxonomy approach including placement in a genome-based phylogeny of Collembola and designation of a neotype for 1 of the species. Higher heterozygosity values are recorded in the more mobile species. Both species are devoid of the biosynthetic pathway for β-lactam antibiotics known in several Collembola, confirming the tight correlation of antibiotic synthesis with the species way of life. CONCLUSIONS It is now possible to generate high-quality genomes from single specimens of minute, field-preserved metazoans, exceeding the minimum contig N50 (1 Mb) required by the Earth BioGenome Project.
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Affiliation(s)
- Clément Schneider
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Abteilung Bodenzoologie, Am Museum 1, 02826 Görlitz, Germany
| | - Christian Woehle
- Max Planck Institute for Plant Breeding Research, Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Cyrille A D'Haese
- Unité Mécanismes adaptatifs & Evolution (MECADEV), CNRS, Muséum national d'Histoire naturelle, 45 rue Buffon 75005 Paris, France
| | - Magnus Wolf
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany
| | - Axel Janke
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding Research, Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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Du Z, Wu Y, Chen Z, Cao L, Ishikawa T, Kamitani S, Sota T, Song F, Tian L, Cai W, Li H. Global phylogeography and invasion history of the spotted lanternfly revealed by mitochondrial phylogenomics. Evol Appl 2021; 14:915-930. [PMID: 33897812 PMCID: PMC8061274 DOI: 10.1111/eva.13170] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022] Open
Abstract
Biological invasion has been a serious global threat due to increasing international trade and population movements. Tracking the source and route of invasive species and evaluating the genetic differences in their native regions have great significance for the effective monitoring and management, and further resolving the invasive mechanism. The spotted lanternfly Lycorma delicatula is native to China and invaded South Korea, Japan, and the United States during the last decade, causing severe damages to the fruits and timber industries. However, its global phylogeographic pattern and invasion history are not clearly understood. We applied high-throughput sequencing to obtain 392 whole mitochondrial genome sequences from four countries to ascertain the origin, dispersal, and invasion history of the spotted lanternfly. Phylogenomic analyses revealed that the spotted lanternfly originated from southwestern China, diverged into six phylogeographic lineages, and experienced northward expansion across the Yangtze River in the late Pleistocene. South Korea populations were derived from multiple invasions from eastern China and Japan with two different genetic sources of northwestern (Loess Plateau) and eastern (East Plain) lineages in China, whereas the each of Japan and the United States had only one. The United States populations originated through single invasive event from South Korea, which served as a bridgehead of invasion. The environmental conditions, especially the distribution of host Ailanthus trees, and adaptability possibly account for the rapid spread of the spotted lanternfly in the native and introduced regions.
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Affiliation(s)
- Zhenyong Du
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Yunfei Wu
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Zhuo Chen
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Liangming Cao
- The Key Laboratory of Forest ProtectionNational Forestry and Grassland AdministrationResearch Institute of Forest Ecology, Environment and ProtectionChinese Academy of ForestryBeijingChina
| | - Tadashi Ishikawa
- Laboratory of EntomologyFaculty of AgricultureTokyo University of AgricultureAtsugiJapan
| | - Satoshi Kamitani
- Entomological LaboratoryGraduate School of Bioresource and Bioenvironmental SciencesKyushu UniversityFukuokaJapan
| | - Teiji Sota
- Department of ZoologyGraduate School of ScienceKyoto UniversitySakyoJapan
| | - Fan Song
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Li Tian
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Wanzhi Cai
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Hu Li
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
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20
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Padgitt-Cobb LK, Kingan SB, Wells J, Elser J, Kronmiller B, Moore D, Concepcion G, Peluso P, Rank D, Jaiswal P, Henning J, Hendrix DA. A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome. THE PLANT GENOME 2021; 14:e20072. [PMID: 33605092 DOI: 10.1002/tpg2.20072] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/03/2020] [Indexed: 05/25/2023]
Abstract
Hop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing and contain compounds of therapeutic interest including xanthohumol. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large (2.8 Gb), repetitive, and heterozygous genome of hop. We present a draft haplotype-phased assembly of the Cascade cultivar genome. Our draft assembly and annotation of the Cascade genome is the most extensive representation of the hop genome to date. PacBio long-read sequences from hop were assembled with FALCON and partially phased with FALCON-Unzip. Comparative analysis of haplotype sequences provides insight into selective pressures that have driven evolution in hop. We discovered genes with greater sequence divergence enriched for stress-response, growth, and flowering functions in the draft phased assembly. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is over 70% repetitive. We identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze the draft phased assembly serve to deepen our understanding of the genomic landscape of hop and may have broader applicability to the study of other large, complex genomes.
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Affiliation(s)
- Lillian K Padgitt-Cobb
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Sarah B Kingan
- Pacific Biosciences of California, Menlo Park, CA, 94025, USA
| | - Jackson Wells
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Brent Kronmiller
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | | | | | - Paul Peluso
- Pacific Biosciences of California, Menlo Park, CA, 94025, USA
| | - David Rank
- Pacific Biosciences of California, Menlo Park, CA, 94025, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | | | - David A Hendrix
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA
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21
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Liu H. Seasonal Development, Cumulative Growing Degree-Days, and Population Density of Spotted Lanternfly (Hemiptera: Fulgoridae) on Selected Hosts and Substrates. ENVIRONMENTAL ENTOMOLOGY 2020; 49:1171-1184. [PMID: 32737483 DOI: 10.1093/ee/nvaa074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Indexed: 06/11/2023]
Abstract
Seasonal development, cumulative growing degree-days (CUMDD10), and population density of Lycorma delicatula (White) were studied through weekly sampling of 30 plants (5 plants/species, 3 common plus 3 site-specific species per site) at six sites in Pennsylvania in 2019. In total, 24,159 L. delicatula (1,987 egg masses, 1,068 first instars, 239 second instars, 153 third instars, 410 fourth instars, and 20,302 adults) were recorded in 28 wk. Seasonal development followed similar pattern at all sites despite differences in starting, peaking, and ending time for specific life stages. The average CUMDD10 requirement for the onset of the first instars, second instars, third instars, fourth instars, adults, and eggs was 270, 465, 645, 825, 1,112, and 1,825, respectively. Population density ranged from 0 to 207.4, 0-298.9, and 0-9.6/m2 for nymphs, adults, and egg masses, respectively. Significant difference in population density was found between sites, hosts/substrates, and sampling weeks. Favored oviposition substrates included tree-of-heaven and black birch despite egg masses being laid on many other surfaces. Nymphs fed on different hosts in early stages but preferred American beech, tree-of-heaven, black birch, and multiflora rose. Adults were predominately found on tree-of-heaven with preoviposition surge on black birch and red maple. Sizable nymph and adult populations persisted on summer grape throughout the season. Tree-of-heaven played an irreplaceable role in the seasonal development and life history of L. delicatula in the field. Survey and detection activities should focus on tree-of-heaven with management efforts directed to aggregating adults for maximum efficacy.
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Affiliation(s)
- Houping Liu
- Pennsylvania Department of Conservation and Natural Resources, Harrisburg, PA
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22
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Svrzikapa N, Longo KA, Prasad N, Boyanapalli R, Brown JM, Dorset D, Yourstone S, Powers J, Levy SE, Morris AJ, Vargeese C, Goyal J. Investigational Assay for Haplotype Phasing of the Huntingtin Gene. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 19:162-173. [PMID: 33209959 PMCID: PMC7648085 DOI: 10.1016/j.omtm.2020.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/04/2020] [Indexed: 01/20/2023]
Abstract
Novel treatments for Huntington's disease (HD), a progressive neurodegenerative disorder, include selective targeting of the mutant allele of the huntingtin gene (mHTT) carrying the abnormally expanded disease-causing cytosine-adenine-guanine (CAG) repeat. WVE-120101 and WVE-120102 are investigational stereopure antisense oligonucleotides that enable selective suppression of mHTT by targeting single-nucleotide polymorphisms (SNPs) that are in haplotype phase with the CAG repeat expansion. Recently developed long-read sequencing technologies can capture CAG expansions and distant SNPs of interest and potentially facilitate haplotype-based identification of patients for clinical trials of oligonucleotide therapies. However, improved methods are needed to phase SNPs with CAG repeat expansions directly and reliably without need for familial genotype/haplotype data. Our haplotype phasing method uses single-molecule real-time sequencing and a custom algorithm to determine with confidence bases at SNPs on mutant alleles, even without familial data. Herein, we summarize this methodology and validate the approach using patient-derived samples with known phasing results. Comparison of experimentally measured CAG repeat lengths, heterozygosity, and phasing with previously determined results showed improved performance. Our methodology enables the haplotype phasing of SNPs of interest and the disease-causing, expanded CAG repeat of the huntingtin gene, enabling accurate identification of patients with HD eligible for allele-selective clinical studies.
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Affiliation(s)
- Nenad Svrzikapa
- Wave Life Sciences Ltd., Cambridge, MA 02138, USA.,Department of Paediatrics, Medical Sciences Division, University of Oxford, Oxford OX3 9DU, UK
| | | | - Nripesh Prasad
- HudsonAlpha Discovery, Discovery Life Sciences, Huntsville, AL 35806, USA.,Genomic Services Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | | | - Daniel Dorset
- HudsonAlpha Discovery, Discovery Life Sciences, Huntsville, AL 35806, USA.,Genomic Services Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Jason Powers
- Q Solutions
- EA Genomics, LLC, Morrisville, NC 27560, USA
| | - Shawn E Levy
- HudsonAlpha Discovery, Discovery Life Sciences, Huntsville, AL 35806, USA.,Genomic Services Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | | | - Jaya Goyal
- Wave Life Sciences Ltd., Cambridge, MA 02138, USA
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23
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Yuan Y, Chung CYL, Chan TF. Advances in optical mapping for genomic research. Comput Struct Biotechnol J 2020; 18:2051-2062. [PMID: 32802277 PMCID: PMC7419273 DOI: 10.1016/j.csbj.2020.07.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/08/2020] [Accepted: 07/24/2020] [Indexed: 12/28/2022] Open
Abstract
Recent advances in optical mapping have allowed the construction of improved genome assemblies with greater contiguity. Optical mapping also enables genome comparison and identification of large-scale structural variations. Association of these large-scale genomic features with biological functions is an important goal in plant and animal breeding and in medical research. Optical mapping has also been used in microbiology and still plays an important role in strain typing and epidemiological studies. Here, we review the development of optical mapping in recent decades to illustrate its importance in genomic research. We detail its applications and algorithms to show its specific advantages. Finally, we discuss the challenges required to facilitate the optimization of optical mapping and improve its future development and application.
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Key Words
- 3D, three-dimensional
- DBG, de Bruijn graph
- DLS, direct label and strain
- DNA, deoxyribonucleic acid
- Genome assembly
- Hi-C, high-throughput chromosome conformation capture
- Mb, million base pair
- Next generation sequencing
- OLC, overlap-layout-consensus
- Optical mapping
- PCR, polymerase chain reaction
- PacBio, Pacific Biosciences
- SRS, short-read sequencing
- SV, structural variation
- Structural variation
- bp, base pair
- kb, kilobase pair
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Affiliation(s)
- Yuxuan Yuan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
- AoE Centre for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Claire Yik-Lok Chung
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
- AoE Centre for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security, The Chinese University of Hong Kong, Hong Kong SAR, China
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24
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Adams M, McBroome J, Maurer N, Pepper-Tunick E, Saremi N, Green RE, Vollmers C, Corbett-Detig R. One fly-one genome: chromosome-scale genome assembly of a single outbred Drosophila melanogaster. Nucleic Acids Res 2020; 48:e75. [PMID: 32491177 PMCID: PMC7367183 DOI: 10.1093/nar/gkaa450] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/16/2020] [Accepted: 05/18/2020] [Indexed: 02/02/2023] Open
Abstract
A high quality genome assembly is a vital first step for the study of an organism. Recent advances in technology have made the creation of high quality chromosome scale assemblies feasible and low cost. However, the amount of input DNA needed for an assembly project can be a limiting factor for small organisms or precious samples. Here we demonstrate the feasibility of creating a chromosome scale assembly using a hybrid method for a low input sample, a single outbred Drosophila melanogaster. Our approach combines an Illumina shotgun library, Oxford nanopore long reads, and chromosome conformation capture for long range scaffolding. This single fly genome assembly has a N50 of 26 Mb, a length that encompasses entire chromosome arms, contains 95% of expected single copy orthologs, and a nearly complete assembly of this individual's Wolbachia endosymbiont. The methods described here enable the accurate and complete assembly of genomes from small, field collected organisms as well as precious clinical samples.
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Affiliation(s)
- Matthew Adams
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jakob McBroome
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nicholas Maurer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Evan Pepper-Tunick
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nedda F Saremi
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Dovetail Genomics, Scotts Valley, CA 95066, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Russell B Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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25
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Wu S, Gao S, Wang S, Meng J, Wickham J, Luo S, Tan X, Yu H, Xiang Y, Hu S, Zhao L, Sun J. A Reference Genome of Bursaphelenchus mucronatus Provides New Resources for Revealing Its Displacement by Pinewood Nematode. Genes (Basel) 2020; 11:genes11050570. [PMID: 32438771 PMCID: PMC7288286 DOI: 10.3390/genes11050570] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/20/2020] [Accepted: 05/08/2020] [Indexed: 12/19/2022] Open
Abstract
The Bursaphelenchus mucronatus, which was highly similar with Bursaphelenchus xylophilus in terms of morphological characteristics and biological properties—but had weaker pathogenicity to forests—was a native species often displaced by B. xylophilus when occupying the same niche. Since the draft genome of the invasive B. xylophilus has been published, the absence of a reference genome of B. mucronatus still prevents us from understanding the molecular evidences behind competitive displacement. In this study, we employed Single Molecule, Real-Time (SMRT) sequencing and a Hi-C scaffolding approach to yield a near chromosome-level assembly of B. mucronatus, including six pseudo-chromosomes. The assembly size is 73 Mb, with scaffold N50 of 11.50 Mb and contig N50 of 1.48 Mb. Comparative genomics results showed high similarity between B. xylophilus and B. mucronatus. However, the losing of orphan genes and species-specific orthologous genes in B. mucronatus may indicate weaker adaptability to the environment. The gene family contractions of GPCRs (G Protein-Coupled Receptors) and cellulases in B. mucronatus may jointly contribute to its displacement by B. xylophilus. Overall, we introduced a valuable genomic resource for molecular and evolutionary studies of B. mucronatus, especially for studying the competitive displacement by the pinewood nematode, which could help us control the pathogenicity of pine wilt diseases.
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Affiliation(s)
- Shuangyang Wu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (S.W.); (J.M.); (J.W.); (Y.X.); (L.Z.)
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (S.G.); (S.W.); (S.L.); (X.T.); (H.Y.); (S.H.)
| | - Sen Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (S.G.); (S.W.); (S.L.); (X.T.); (H.Y.); (S.H.)
| | - Jie Meng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (S.W.); (J.M.); (J.W.); (Y.X.); (L.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jacob Wickham
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (S.W.); (J.M.); (J.W.); (Y.X.); (L.Z.)
| | - Sainan Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (S.G.); (S.W.); (S.L.); (X.T.); (H.Y.); (S.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyu Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (S.G.); (S.W.); (S.L.); (X.T.); (H.Y.); (S.H.)
| | - Haiying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (S.G.); (S.W.); (S.L.); (X.T.); (H.Y.); (S.H.)
| | - Yujia Xiang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (S.W.); (J.M.); (J.W.); (Y.X.); (L.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (S.G.); (S.W.); (S.L.); (X.T.); (H.Y.); (S.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lilin Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (S.W.); (J.M.); (J.W.); (Y.X.); (L.Z.)
| | - Jianghua Sun
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (S.W.); (J.M.); (J.W.); (Y.X.); (L.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel.: +86-10-64807121
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26
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Urban JM. Perspective: shedding light on spotted lanternfly impacts in the USA. PEST MANAGEMENT SCIENCE 2020; 76:10-17. [PMID: 31525270 DOI: 10.1002/ps.5619] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/08/2019] [Accepted: 09/09/2019] [Indexed: 06/10/2023]
Abstract
Spotted lanternfly (SLF), Lycorma delicatula (Hemiptera: Fulgoridae) is an invasive phloem-feeding planthopper currently being quarantined in a 24 000 km2 area in eastern Pennsylvania, New Jersey, Maryland, and Delaware, with a second population under quarantine in a 46 km2 area in Virginia. Because this insect feeds on over 70 species of plants, it has the potential to impact a wide range of sectors, and as a result, there has been great public speculation that the economic impact of SLF could be severe. SLF is a large-bodied voracious feeder that reduces plant resources directly by feeding, and indirectly, from sooty mold that grows on its excrement and blocks photosynthesis. SLF is causing severe damage to vineyards from feeding, and is a significant nuisance pest. It has high potential for spread via human-mediated transport, particularly of egg cases, and may therefore significantly impact commerce in the near future. The ultimate impacts of this insect are not yet known, and will depend upon its longer term impacts on plant and tree health, and the extent to which its range expands. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Julie M Urban
- Department of Entomology, 501 Agricultural Sciences and Industries, Pennsylvania State University, University Park, PA, USA
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27
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Fu Z, Li Y, Elling AA, Snyder WE. A draft genome of a field-collected Steinernema feltiae strain NW. J Nematol 2020; 52:1-7. [PMID: 32180379 PMCID: PMC7265891 DOI: 10.21307/jofnem-2020-003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Indexed: 11/26/2022] Open
Abstract
Advances in sequencing technologies have accelerated our understanding of the complex genetic network of organisms and genomic divergences that are linked to evolutionary processes. While many model organisms and laboratory strains have been sequenced, wild populations are underrepresented in the growing list of sequenced genomes. Here, we present a de novo assembly of Steinernema feltiae, strain NW, collected from a working agricultural field in south central Washington, USA. Leveraging Pacific Biosciences (PacBio) long reads, we sequenced strain NW to a high depth (99×). The resulting de novo assembly is significantly larger than the previous assembly generated from the laboratory strain SN, with a noticeable improvement in continuity and completeness. Comparative analysis of two assemblies revealed numerous single nucleotide polymorphisms (SNPs), breakpoints, and indels present between the two genomes. This alternative genome resource and annotation could benefit the research community to examine the genetic foundation of evolutionary processes as well as genomic variation among conspecific populations.
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Affiliation(s)
- Zhen Fu
- Department of Entomology, Washington State University , Pullman, WA ; Current: Department of Entomology, Texas A&M University , College Station, TX
| | - Yuxiang Li
- Department of Plant Pathology, Washington State University , Pullman, WA
| | - Axel A Elling
- Department of Plant Pathology, Washington State University , Pullman, WA ; Current: Bayer Crop Science, Cary, NC
| | - William E Snyder
- Department of Entomology, Washington State University , Pullman, WA ; Current: Department of Entomology, University of Georgia , Athens, GA
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28
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Kingan SB, Urban J, Lambert CC, Baybayan P, Childers AK, Coates B, Scheffler B, Hackett K, Korlach J, Geib SM. A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system. Gigascience 2019; 8:giz122. [PMID: 31609423 PMCID: PMC6791401 DOI: 10.1093/gigascience/giz122] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/08/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies; however, long-read methods have historically had greater input DNA requirements and higher costs than next-generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female spotted lanternfly (Lycorma delicatula) using a single Pacific Biosciences SMRT Cell. The spotted lanternfly is an invasive species recently discovered in the northeastern United States that threatens to damage economically important crop plants in the region. RESULTS The DNA from 1 individual was used to make 1 standard, size-selected library with an average DNA fragment size of ∼20 kb. The library was run on 1 Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from unique library molecules, representing ∼36× coverage of the genome. The assembly had high contiguity (contig N50 length = 1.5 Mb), completeness, and sequence level accuracy as estimated by conserved gene set analysis (96.8% of conserved genes both complete and without frame shift errors). Furthermore, it was possible to segregate more than half of the diploid genome into the 2 separate haplotypes. The assembly also recovered 2 microbial symbiont genomes known to be associated with L. delicatula, each microbial genome being assembled into a single contig. CONCLUSIONS We demonstrate that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species.
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Affiliation(s)
- Sarah B Kingan
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Julie Urban
- Department of Entomology, 501 ASI Building, The Pennsylvania State University, University Park, PA 16802, USA
| | | | - Primo Baybayan
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Anna K Childers
- USDA-ARS, Bee Research Laboratory, 10300 Baltimore Avenue, Building 306, Room 315, BARC-East, Beltsville, MD 20705, USA
| | - Brad Coates
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, 2333 Genetics Laboratory, 819 Wallace Road, Ames, IA 50011, USA
| | - Brian Scheffler
- USDA-ARS, Genomics and Bioinformatics Research, 141 Experiment Station Road, Stoneville, MS 38776, USA
| | - Kevin Hackett
- USDA-ARS, Office of National Programs, George Washington Carver Center, 5601 Sunnyside Avenue, Beltsville, MD 20705, USA
| | - Jonas Korlach
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Scott M Geib
- USDA-ARS, Daniel K Inouye U.S. Pacific Basin Agricultural Research Center, 64 Nowelo St., Hilo, HI 96720, USA
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