The sequence and de novo assembly of hog deer genome

Wang, Wei; Huang, Yan; Chen, Shiyi; Li, Zhenzhen; Yi, Jun; Niu, Lili; Deng, Jia-Po; Chen, Weigang; Pu, Yunfeng; Jia, Xianbo; Qu, Yu; Chen, Ang; Zhong, Yan; Yu, Xiaoxi; Pang, Shuai; Huang, Wanlong; Han, Yue; Liu, Guangjian; Yu, Jianqiu

doi:10.1038/sdata.2018.305

Cited by 11 publications

(7 citation statements)

References 40 publications

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“…Supernova was originally designed for de novo assemblies of human genomes ( Weisenfeld et al 2017 ). Nevertheless, recently it has been successfully used for non-human genome assemblies ( Ozerov et al 2018 ; Wang et al 2019 ; Lu et al 2020 ). For human genomes, a 56× coverage is recommended.…”

Section: Resultsmentioning

confidence: 99%

Genome assembly and annotation of the California harvester antPogonomyrmex californicus

Bohn

Halabian

Schrader

et al. 2020

G3 Genes|Genomes|Genetics

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The harvester ant genus Pogonomyrmex is endemic to arid and semiarid habitats and deserts of North and South America. The California harvester ant Pogonomyrmex californicus is the most widely distributed Pogonomyrmex species in North America. Pogonomyrmex californicus colonies are usually monogynous, i.e. a colony has one queen. However, in a few populations in California, primary polygyny evolved, i.e. several queens cooperate in colony founding after their mating flights and continue to coexist in mature colonies. Here, we present a genome assembly and annotation of P. californicus. The size of the assembly is 241 Mb, which is in agreement with the previously estimated genome size. We were able to annotate 17,889 genes in total, including 15,688 protein-coding ones with BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness at a 95% level. The presented P. californicus genome assembly will pave the way for investigations of the genomic underpinnings of social polymorphism in the number of queens, regulation of aggression, and the evolution of adaptations to dry habitats.

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Section: Resultsmentioning

confidence: 99%

Genome assembly and annotation of the California harvester antPogonomyrmex californicus

Bohn

Halabian

Schrader

et al. 2020

G3 Genes|Genomes|Genetics

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show abstract

“…To assess completeness, we implemented an analysis using expected gene content by searching single-copy orthologs 61 . Short reads only and hybrid approaches achieved the assembly of 100% of core genes, but long reads only had a poor performance.…”

Section: Discussionmentioning

confidence: 99%

High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers

Molina-Mora

Campos-Sánchez

Rodríguez

et al. 2020

Sci Rep

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Genotyping methods and genome sequencing are indispensable to reveal genomic structure of bacterial species displaying high level of genome plasticity. However, reconstruction of genome or assembly is not straightforward due to data complexity, including repeats, mobile and accessory genetic elements of bacterial genomes. Moreover, since the solution to this problem is strongly influenced by sequencing technology, bioinformatics pipelines, and selection criteria to assess assemblers, there is no systematic way to select a priori the optimal assembler and parameter settings. to assembly the genome of Pseudomonas aeruginosa strain AG1 (PaeAG1), short reads (Illumina) and long reads (Oxford Nanopore) sequencing data were used in 13 different non-hybrid and hybrid approaches. PaeAG1 is a multiresistant high-risk sequence type 111 (ST-111) clone that was isolated from a Costa Rican hospital and it was the first report of an isolate of P. aeruginosa carrying both blaVIM-2 and blaIMP-18 genes encoding for metallo-β-lactamases (MBL) enzymes. To assess the assemblies, multiple metrics regard to contiguity, correctness and completeness (3C criterion, as we define here) were used for benchmarking the 13 approaches and select a definitive assembly. In addition, annotation was done to identify genes (coding and RNA regions) and to describe the genomic content of PaeAG1. Whereas long reads and hybrid approaches showed better performances in terms of contiguity, higher correctness and completeness metrics were obtained for short read only and hybrid approaches. A manually curated and polished hybrid assembly gave rise to a single circular sequence with 100% of core genes and known regions identified, >98% of reads mapped back, no gaps, and uniform coverage. The strategy followed to obtain this high-quality 3C assembly is detailed in the manuscript and we provide readers with an all-in-one script to replicate our results or to apply it to other troublesome cases. The final 3C assembly revealed that the PaeAG1 genome has 7,190,208 bp, a 65.7% GC content and 6,709 genes (6,620 coding sequences), many of which are included in multiple mobile genomic elements, such as 57 genomic islands, six prophages, and two complete integrons with blaVIM-2 and blaIMP-18 MBL genes. Up to 250 and 60 of the predicted genes are anticipated to play a role in virulence (adherence, quorum sensing and secretion) or antibiotic resistance (β-lactamases, efflux pumps, etc). Altogether, the assembly and annotation of the PaeAG1 genome provide new perspectives to continue studying the genomic diversity and gene content of this important human pathogen. Genotyping methods and genome sequencing are indispensable to reveal genomic structure and evolution of bacterial clones with high resolution 1. In this sense, production of large amounts of short sequencing data from genomes (reads) has been facilitated by continuous advances in Next Generation Sequencing (NGS) technologies.

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“…Supernova was originally designed for de novo assemblies of human genomes (Weisenfeld et al 2017). However, recently it has been successfully used for non-human genome assemblies (Ozerov et al 2018;Wang et al 2019;Lu et al 2020). For human genomes, a 56x coverage is recommended, however, since there is not much information on the optimal coverage for non-model genomes, we performed a series of assemblies.…”

Section: Genome Assembly and Evaluationmentioning

confidence: 99%

High-Quality Genome Assembly and Annotation of the California Harvester AntPogonomyrmex californicus(Buckley, 1867)

Bohn

Halabian

Schrader

et al. 2020

Preprint

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The harvester ant genus Pogonomyrmex is endemic to arid and semiarid habitats and deserts of North and South America and California harvester ant Pogonomyrmex californicus is the most widely distributed Pogonomyrmex species in the North America. P. californicus colonies are usually monogynous, i.e. a colony has one queen. However, in a few populations in California, primary polygyny evolved, i.e. several queens cooperate in colony founding after their mating flights and continue to coexist in mature colonies. Here, we present high quality genome assembly and annotation of P. californicus. The size of the assembly is 241 Mb, which is in good agreement with previously estimated genome size and we were able to annotate 17,889 genes in total, including 15,688 protein-coding ones with BUSCO completeness at the 95% level. This high quality genome will pave the way for investigations of the genomic underpinnings of social polymorphism in queen number, regulation of aggression, and the evolution of adaptations to dry habitats in P. californicus.

show abstract

The sequence and de novo assembly of hog deer genome

Cited by 11 publications

References 40 publications

Genome assembly and annotation of the California harvester antPogonomyrmex californicus

Genome assembly and annotation of the California harvester antPogonomyrmex californicus

High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers

High-Quality Genome Assembly and Annotation of the California Harvester AntPogonomyrmex californicus(Buckley, 1867)

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