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Bhowmik O, Rahman T, Kalyanaraman A. Maptcha: an efficient parallel workflow for hybrid genome scaffolding. BMC Bioinformatics 2024; 25:263. [PMID: 39118013 PMCID: PMC11313021 DOI: 10.1186/s12859-024-05878-4] [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: 03/01/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Genome assembly, which involves reconstructing a target genome, relies on scaffolding methods to organize and link partially assembled fragments. The rapid evolution of long read sequencing technologies toward more accurate long reads, coupled with the continued use of short read technologies, has created a unique need for hybrid assembly workflows. The construction of accurate genomic scaffolds in hybrid workflows is complicated due to scale, sequencing technology diversity (e.g., short vs. long reads, contigs or partial assemblies), and repetitive regions within a target genome. RESULTS In this paper, we present a new parallel workflow for hybrid genome scaffolding that would allow combining pre-constructed partial assemblies with newly sequenced long reads toward an improved assembly. More specifically, the workflow, called Maptcha, is aimed at generating long scaffolds of a target genome, from two sets of input sequences-an already constructed partial assembly of contigs, and a set of newly sequenced long reads. Our scaffolding approach internally uses an alignment-free mapping step to build a ⟨ contig,contig ⟩ graph using long reads as linking information. Subsequently, this graph is used to generate scaffolds. We present and evaluate a graph-theoretic "wiring" heuristic to perform this scaffolding step. To enable efficient workload management in a parallel setting, we use a batching technique that partitions the scaffolding tasks so that the more expensive alignment-based assembly step at the end can be efficiently parallelized. This step also allows the use of any standalone assembler for generating the final scaffolds. CONCLUSIONS Our experiments with Maptcha on a variety of input genomes, and comparison against two state-of-the-art hybrid scaffolders demonstrate that Maptcha is able to generate longer and more accurate scaffolds substantially faster. In almost all cases, the scaffolds produced by Maptcha are at least an order of magnitude longer (in some cases two orders) than the scaffolds produced by state-of-the-art tools. Maptcha runs significantly faster too, reducing time-to-solution from hours to minutes for most input cases. We also performed a coverage experiment by varying the sequencing coverage depth for long reads, which demonstrated the potential of Maptcha to generate significantly longer scaffolds in low coverage settings ( 1 × - 10 × ).
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Affiliation(s)
- Oieswarya Bhowmik
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, 99164, USA.
| | - Tazin Rahman
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, 99164, USA
| | - Ananth Kalyanaraman
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, 99164, USA
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Coombe L, Warren RL, Wong J, Nikolic V, Birol I. ntLink: A Toolkit for De Novo Genome Assembly Scaffolding and Mapping Using Long Reads. Curr Protoc 2023; 3:e733. [PMID: 37039735 PMCID: PMC10091225 DOI: 10.1002/cpz1.733] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
With the increasing affordability and accessibility of genome sequencing data, de novo genome assembly is an important first step to a wide variety of downstream studies and analyses. Therefore, bioinformatics tools that enable the generation of high-quality genome assemblies in a computationally efficient manner are essential. Recent developments in long-read sequencing technologies have greatly benefited genome assembly work, including scaffolding, by providing long-range evidence that can aid in resolving the challenging repetitive regions of complex genomes. ntLink is a flexible and resource-efficient genome scaffolding tool that utilizes long-read sequencing data to improve upon draft genome assemblies built from any sequencing technologies, including the same long reads. Instead of using read alignments to identify candidate joins, ntLink utilizes minimizer-based mappings to infer how input sequences should be ordered and oriented into scaffolds. Recent improvements to ntLink have added important features such as overlap detection, gap-filling, and in-code scaffolding iterations. Here, we present three basic protocols demonstrating how to use each of these new features to yield highly contiguous genome assemblies, while still maintaining ntLink's proven computational efficiency. Further, as we illustrate in the alternate protocols, the lightweight minimizer-based mappings that enable ntLink scaffolding can also be utilized for other downstream applications, such as misassembly detection. With its modularity and multiple modes of execution, ntLink has broad benefit to the genomics community, from genome scaffolding and beyond. ntLink is an open-source project and is freely available from https://github.com/bcgsc/ntLink. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: ntLink scaffolding using overlap detection Basic Protocol 2: ntLink scaffolding with gap-filling Basic Protocol 3: Running in-code iterations of ntLink scaffolding Alternate Protocol 1: Generating long-read to contig mappings with ntLink Alternate Protocol 2: Using ntLink mappings for genome assembly correction with Tigmint-long Support Protocol: Installing ntLink.
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Affiliation(s)
- Lauren Coombe
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, 570 W 7 Ave, Vancouver, BC V5Z 4S6, 604-707-5900
| | - René L. Warren
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, 570 W 7 Ave, Vancouver, BC V5Z 4S6, 604-707-5900
| | - Johnathan Wong
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, 570 W 7 Ave, Vancouver, BC V5Z 4S6, 604-707-5900
| | - Vladimir Nikolic
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, 570 W 7 Ave, Vancouver, BC V5Z 4S6, 604-707-5900
| | - Inanc Birol
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, 570 W 7 Ave, Vancouver, BC V5Z 4S6, 604-707-5900
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Shirasawa K, Moraga R, Ghelfi A, Hirakawa H, Nagasaki H, Ghamkhar K, Barrett BA, Griffiths AG, Isobe SN. An improved reference genome for Trifolium subterraneum L. provides insight into molecular diversity and intra-specific phylogeny. FRONTIERS IN PLANT SCIENCE 2023; 14:1103857. [PMID: 36875612 PMCID: PMC9975737 DOI: 10.3389/fpls.2023.1103857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Subterranean clover (Trifolium subterraneum L., Ts) is a geocarpic, self-fertile annual forage legume with a compact diploid genome (n = x = 8, 544 Mb/1C). Its resilience and climate adaptivity have made it an economically important species in Mediterranean and temperate zones. Using the cultivar Daliak, we generated higher resolution sequence data, created a new genome assembly TSUd_3.0, and conducted molecular diversity analysis for copy number variant (CNV) and single-nucleotide polymorphism (SNP) among 36 cultivars. TSUd_3.0 substantively improves prior genome assemblies with new Hi-C and long-read sequence data, covering 531 Mb, containing 41,979 annotated genes and generating a 94.4% BUSCO score. Comparative genomic analysis among select members of the tribe Trifolieae indicated TSUd 3.0 corrects six assembly-error inversion/duplications and confirmed phylogenetic relationships. Its synteny with T. pratense, T. repens, Medicago truncatula and Lotus japonicus genomes were assessed, with the more distantly related T. repens and M. truncatula showing higher levels of co-linearity with Ts than between Ts and its close relative T. pratense. Resequencing of 36 cultivars discovered 7,789,537 SNPs subsequently used for genomic diversity assessment and sequence-based clustering. Heterozygosity estimates ranged from 1% to 21% within the 36 cultivars and may be influenced by admixture. Phylogenetic analysis supported subspecific genetic structure, although it indicates four or five groups, rather than the three recognized subspecies. Furthermore, there were incidences where cultivars characterized as belonging to a particular subspecies clustered with another subspecies when using genomic data. These outcomes suggest that further investigation of Ts sub-specific classification using molecular and morpho-physiological data is needed to clarify these relationships. This upgraded reference genome, complemented with comprehensive sequence diversity analysis of 36 cultivars, provides a platform for future gene functional analysis of key traits, and genome-based breeding strategies for climate adaptation and agronomic performance. Pangenome analysis, more in-depth intra-specific phylogenomic analysis using the Ts core collection, and functional genetic and genomic studies are needed to further augment knowledge of Trifolium genomes.
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Affiliation(s)
- Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Roger Moraga
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
- Tea Break Bioinformatics Limited, Palmerston North, New Zealand
| | - Andrea Ghelfi
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
| | - Hideki Hirakawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Hideki Nagasaki
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Kioumars Ghamkhar
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Brent A. Barrett
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | | | - Sachiko N. Isobe
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
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Intraintestinal Analysis of the Functional Activity of Microbiomes and Its Application to the Common Marmoset Intestine. mSystems 2022; 7:e0052022. [PMID: 36005400 PMCID: PMC9601136 DOI: 10.1128/msystems.00520-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The intestinal microbiome is closely related to host health, and metatranscriptomic analysis can be used to assess the functional activity of microbiomes by quantifying microbial gene expression levels, helping elucidate the interactions between the microbiome and the environment. However, the functional changes in the microbiome along the host intestinal tract remain unknown, and previous analytical methods have limitations, such as potentially overlooking unknown genes due to dependence on existing databases. The objective of this study is to develop a computational pipeline combined with next-generation sequencing for spatial covariation analysis of the functional activity of microbiomes at multiple intestinal sites (biogeographic locations) within the same individual. This method reconstructs a reference metagenomic sequence across multiple intestinal sites and integrates the metagenome and metatranscriptome, allowing the gene expression levels of the microbiome, including unknown bacterial genes, to be compared among multiple sites. When this method was applied to metatranscriptomic analysis in the intestinal tract of common marmosets, a New World monkey, the reconstructed metagenome covered most of the expressed genes and revealed that the differences in microbial gene expression among the cecum, transverse colon, and feces were more dynamic and sensitive to environmental shifts than the abundances of the genes. In addition, metatranscriptomic profiling at three intestinal sites of the same individual enabled covariation analysis incorporating spatial relevance, accurately predicting the function of a total of 10,856 unknown genes. Our findings demonstrate that our proposed analytical method captures functional changes in microbiomes at the gene resolution level. IMPORTANCE We developed an analysis method that integrates metagenomes and metatranscriptomes from multiple intestinal sites to elucidate how microbial function varies along the intestinal tract. This method enables spatial covariation analysis of the functional activity of microbiomes and accurate identification of gene expression changes among intestinal sites, including changes in the expression of unknown bacterial genes. Moreover, we applied this method to the investigation of the common marmoset intestine, which is anatomically and pharmacologically similar to that of humans. Our findings indicate the expression pattern of the microbiome varies in response to changes in the internal environment along the intestinal tract, and this microbial change may affect the intestinal environment.
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Kang JTL, Teo JJY, Bertrand D, Ng A, Ravikrishnan A, Yong M, Ng OT, Marimuthu K, Chen SL, Chng KR, Gan YH, Nagarajan N. Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects. Nat Microbiol 2022; 7:1516-1524. [PMID: 36109646 PMCID: PMC9519440 DOI: 10.1038/s41564-022-01221-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 07/29/2022] [Indexed: 11/09/2022]
Abstract
AbstractLong-term colonization of the gut microbiome by carbapenemase-producing Enterobacteriaceae (CPE) is a growing area of public health concern as it can lead to community transmission and rapid increase in cases of life-threatening CPE infections. Here, leveraging the observation that many subjects are decolonized without interventions within a year, we used longitudinal shotgun metagenomics (up to 12 timepoints) for detailed characterization of ecological and evolutionary dynamics in the gut microbiome of a cohort of CPE-colonized subjects and family members (n = 46; 361 samples). Subjects who underwent decolonization exhibited a distinct ecological shift marked by recovery of microbial diversity, key commensals and anti-inflammatory pathways. In addition, colonization was marked by elevated but unstable Enterobacteriaceae abundances, which exhibited distinct strain-level dynamics for different species (Escherichia coli and Klebsiella pneumoniae). Finally, comparative analysis with whole-genome sequencing data from CPE isolates (n = 159) helped identify substrain variation in key functional genes and the presence of highly similar E. coli and K. pneumoniae strains with variable resistance profiles and plasmid sharing. These results provide an enhanced view into how colonization by multi-drug-resistant bacteria associates with altered gut ecology and can enable transfer of resistance genes, even in the absence of overt infection and antibiotic usage.
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Li M, Li LM. RegScaf: a regression approach to scaffolding. Bioinformatics 2022; 38:2675-2682. [PMID: 35561180 PMCID: PMC9326850 DOI: 10.1093/bioinformatics/btac174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/19/2022] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Crucial to the correctness of a genome assembly is the accuracy of the underlying scaffolds that specify the orders and orientations of contigs together with the gap distances between contigs. The current methods construct scaffolds based on the alignments of 'linking' reads against contigs. We found that some 'optimal' alignments are mistaken due to factors such as the contig boundary effect, particularly in the presence of repeats. Occasionally, the incorrect alignments can even overwhelm the correct ones. The detection of the incorrect linking information is challenging in any existing methods. RESULTS In this study, we present a novel scaffolding method RegScaf. It first examines the distribution of distances between contigs from read alignment by the kernel density. When multiple modes are shown in a density, orientation-supported links are grouped into clusters, each of which defines a linking distance corresponding to a mode. The linear model parameterizes contigs by their positions on the genome; then each linking distance between a pair of contigs is taken as an observation on the difference of their positions. The parameters are estimated by minimizing a global loss function, which is a version of trimmed sum of squares. The least trimmed squares estimate has such a high breakdown value that it can automatically remove the mistaken linking distances. The results on both synthetic and real datasets demonstrate that RegScaf outperforms some popular scaffolders, especially in the accuracy of gap estimates by substantially reducing extremely abnormal errors. Its strength in resolving repeat regions is exemplified by a real case. Its adaptability to large genomes and TGS long reads is validated as well. AVAILABILITY AND IMPLEMENTATION RegScaf is publicly available at https://github.com/lemontealala/RegScaf.git. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mengtian Li
- National Center of Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei M Li
- To whom correspondence should be addressed.
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McCann K, Grant W, Doyle SR. The genome sequence of the Australian filarial nematode, Cercopithifilaria johnstoni. Wellcome Open Res 2021; 6:259. [PMID: 34796277 PMCID: PMC8564745 DOI: 10.12688/wellcomeopenres.17258.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 11/20/2022] Open
Abstract
We present a genome assembly and annotation of an individual female
Cercopithifilaria johnstoni, a parasitic filarial nematode that is transmitted by hard ticks (Ixodidae) to infect a broad range of native Australian murid and marsupial hosts. The genome sequence is 76.9 Mbp in length, and although in draft form (N50 = 99 kbp, N50[n] = 232), is largely complete based on universally conserved orthologs (BUSCOs; genome = 94.9%, protein = 96.5%) and relative to other related filarial species. These data represent the first genomic resources for the genus
Cercopithifilaria, a group of parasites with a broad host range, and form the basis for comparative analysis with the human-infective parasite,
Onchocerca volvulus, both of which are responsible for similar eye and skin pathologies in their respective hosts.
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Affiliation(s)
- Kirsty McCann
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, Australia
| | - Warwick Grant
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, Australia
| | - Stephen R Doyle
- Parasites & Microbes Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
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McCann K, Grant W, Doyle SR. The genome sequence of the Australian filarial nematode, Cercopithifilaria johnstoni. Wellcome Open Res 2021; 6:259. [PMID: 34796277 PMCID: PMC8564745 DOI: 10.12688/wellcomeopenres.17258.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 09/02/2023] Open
Abstract
We present a genome assembly and annotation of an individual female Cercopithifilaria johnstoni, a parasitic filarial nematode that is transmitted by hard ticks (Ixodidae) to infect a broad range of native Australian murid and marsupial hosts. The genome sequence is 76.9 Mbp in length, and although in draft form (N50 = 99 kbp, N50[n] = 232), is largely complete based on universally conserved orthologs (BUSCOs; genome = 94.9%, protein = 96.5%) and relative to other related filarial species. These data represent the first genomic resources for the genus Cercopithifilaria, a group of parasites with a broad host range, and form the basis for comparative analysis with the human-infective parasite, Onchocerca volvulus, both of which are responsible for similar eye and skin pathologies in their respective hosts.
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Affiliation(s)
- Kirsty McCann
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, Australia
| | - Warwick Grant
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, Australia
| | - Stephen R. Doyle
- Parasites & Microbes Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
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Rahman A, Pachter L. SWALO: scaffolding with assembly likelihood optimization. Nucleic Acids Res 2021; 49:e117. [PMID: 34417615 PMCID: PMC8599790 DOI: 10.1093/nar/gkab717] [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: 12/22/2020] [Revised: 06/16/2021] [Accepted: 08/16/2021] [Indexed: 01/01/2023] Open
Abstract
Scaffolding, i.e. ordering and orienting contigs is an important step in genome assembly. We present a method for scaffolding using second generation sequencing reads based on likelihoods of genome assemblies. A generative model for sequencing is used to obtain maximum likelihood estimates of gaps between contigs and to estimate whether linking contigs into scaffolds would lead to an increase in the likelihood of the assembly. We then link contigs if they can be unambiguously joined or if the corresponding increase in likelihood is substantially greater than that of other possible joins of those contigs. The method is implemented in a tool called Swalo with approximations to make it efficient and applicable to large datasets. Analysis on real and simulated datasets reveals that it consistently makes more or similar number of correct joins as other scaffolders while linking very few contigs incorrectly, thus outperforming other scaffolders and demonstrating that substantial improvement in genome assembly may be achieved through the use of statistical models. Swalo is freely available for download at https://atifrahman.github.io/SWALO/.
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Affiliation(s)
- Atif Rahman
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA.,Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka 1205, Bangladesh
| | - Lior Pachter
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA.,Departments of Mathematics and Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA.,Departments of Biology and Computing & Mathematical Sciences, California Institute of Technology, Pasadena, CA 91103, USA
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Coombe L, Li JX, Lo T, Wong J, Nikolic V, Warren RL, Birol I. LongStitch: high-quality genome assembly correction and scaffolding using long reads. BMC Bioinformatics 2021; 22:534. [PMID: 34717540 PMCID: PMC8557608 DOI: 10.1186/s12859-021-04451-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/19/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information. Long reads are better able to span repetitive genomic regions compared to short reads, and thus have tremendous utility for resolving problematic regions and helping generate more complete draft assemblies. Here, we present LongStitch, a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads. RESULTS LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively, previously developed for linked reads, that we adapted for long reads. Here, we describe the LongStitch pipeline and introduce our new long-read scaffolder, ntLink, which utilizes lightweight minimizer mappings to join contigs. LongStitch was tested on short and long-read assemblies of Caenorhabditis elegans, Oryza sativa, and three different human individuals using corresponding nanopore long-read data, and improves the contiguity of each assembly from 1.2-fold up to 304.6-fold (as measured by NGA50 length). Furthermore, LongStitch generates more contiguous and correct assemblies compared to state-of-the-art long-read scaffolder LRScaf in most tests, and consistently improves upon human assemblies in under five hours using less than 23 GB of RAM. CONCLUSIONS Due to its effectiveness and efficiency in improving draft assemblies using long reads, we expect LongStitch to benefit a wide variety of de novo genome assembly projects. The LongStitch pipeline is freely available at https://github.com/bcgsc/longstitch .
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Affiliation(s)
- Lauren Coombe
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research, 100-570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada.
| | - Janet X Li
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research, 100-570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada
| | - Theodora Lo
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research, 100-570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada
| | - Johnathan Wong
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research, 100-570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada
| | - Vladimir Nikolic
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research, 100-570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research, 100-570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research, 100-570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada
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Hirakawa H, Toyoda A, Itoh T, Suzuki Y, Nagano AJ, Sugiyama S, Onodera Y. A spinach genome assembly with remarkable completeness, and its use for rapid identification of candidate genes for agronomic traits. DNA Res 2021; 28:6303609. [PMID: 34142133 PMCID: PMC8231376 DOI: 10.1093/dnares/dsab004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Indexed: 01/23/2023] Open
Abstract
Spinach (Spinacia oleracea) is grown as a nutritious leafy vegetable worldwide. To accelerate spinach breeding efficiency, a high-quality reference genome sequence with great completeness and continuity is needed as a basic infrastructure. Here, we used long-read and linked-read technologies to construct a de novo spinach genome assembly, designated SOL_r1.1, which was comprised of 287 scaffolds (total size: 935.7 Mb; N50 = 11.3 Mb) with a low proportion of undetermined nucleotides (Ns = 0.34%) and with high gene completeness (BUSCO complete 96.9%). A genome-wide survey of resistance gene analogues identified 695 genes encoding nucleotide-binding site domains, receptor-like protein kinases, receptor-like proteins and transmembrane-coiled coil domains. Based on a high-density double-digest restriction-site associated DNA sequencing-based linkage map, the genome assembly was anchored to six pseudomolecules representing ∼73.5% of the whole genome assembly. In addition, we used SOL_r1.1 to identify quantitative trait loci for bolting timing and fruit/seed shape, which harbour biologically plausible candidate genes, such as homologues of the FLOWERING LOCUS T and EPIDERMAL PATTERNING FACTOR-LIKE genes. The new genome assembly, SOL_r1.1, will serve as a useful resource for identifying loci associated with important agronomic traits and for developing molecular markers for spinach breeding/selection programs.
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Affiliation(s)
- Hideki Hirakawa
- The Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima 411-8540, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Yutaka Suzuki
- The Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga 520-2194, Japan
| | - Suguru Sugiyama
- School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Yasuyuki Onodera
- The Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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Xiao C, Li J, Xie T, Chen J, Zhang S, Elaksher SH, Jiang F, Jiang Y, Zhang L, Zhang W, Xiang Y, Wu Z, Zhao S, Du X. The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat. Ecol Evol 2021; 11:7779-7795. [PMID: 34188851 PMCID: PMC8216945 DOI: 10.1002/ece3.7611] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 02/05/2023] Open
Abstract
The mammalian Y chromosome offers a unique perspective on the male reproduction and paternal evolutionary histories. However, further understanding of the Y chromosome biology for most mammals is hindered by the lack of a Y chromosome assembly. This study presents an integrated in silico strategy for identifying and assembling the goat Y-linked scaffolds using existing data. A total of 11.5 Mb Y-linked sequences were clustered into 33 scaffolds, and 187 protein-coding genes were annotated. We also identified high abundance of repetitive elements. A 5.84 Mb subset was further ordered into an assembly with the evidence from the goat radiation hybrid map (RH map). The existing whole-genome resequencing data of 96 goats (worldwide distribution) were utilized to exploit the paternal relationships among bezoars and domestic goats. Goat paternal lineages were clearly divided into two clades (Y1 and Y2), predating the goat domestication. Demographic history analyses indicated that maternal lineages experienced a bottleneck effect around 2,000 YBP (years before present), after which goats belonging to the A haplogroup spread worldwide from the Near East. As opposed to this, paternal lineages experienced a population decline around the 10,000 YBP. The evidence from the Y chromosome suggests that male goats were not affected by the A haplogroup worldwide transmission, which implies sexually unbalanced contribution to the goat trade and population expansion in post-Neolithic period.
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Affiliation(s)
- Changyi Xiao
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Jingjin Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Tanghui Xie
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Jianhai Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- Institutes for Systems GeneticsFrontiers Science Center for Disease‐related Molecular NetworkWest China HospitalSichuan UniversityChengduChina
| | - Sijia Zhang
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Salma Hassan Elaksher
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- Genetics and Genetic Engineering DepartmentFaculty of AgricultureBenha UniversityMoshtohorEgypt
| | - Fan Jiang
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Yaoxin Jiang
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Lu Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Wei Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Yue Xiang
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Zhenyang Wu
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- College of Agroforestry Engineering and PlanningTongren UniversityTongrenChina
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Xiaoyong Du
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
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13
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Whole-Genome Sequencing Analysis of Salmonella Isolates from Poultry Farms, a Slaughterhouse, and Retail Stalls in Thailand. Microbiol Resour Announc 2021; 10:10/19/e01063-20. [PMID: 33986103 PMCID: PMC8142589 DOI: 10.1128/mra.01063-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The draft genome sequences of 21 Salmonella isolates obtained from poultry production chains in Hat Yai City, Songkhla Province, Thailand, are reported in this study. Our study revealed that there was Salmonella environmental contamination along poultry production chains and cross-contamination among poultry through inanimate surfaces in the environment.
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14
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Stool metagenome analysis of patients with Klebsiella pneumoniae liver abscess and their domestic partners. Int J Infect Dis 2021; 107:1-4. [PMID: 33862216 DOI: 10.1016/j.ijid.2021.04.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES Hypermucoviscous Klebsiella pneumoniae is an emerging cause of community-acquired liver abscess. The aim of this study was to investigate whether hypermucoviscous strains could be shared among households. METHODS The clinical K. pneumoniae isolates from a cohort of 24 patients with Klebsiella liver abscess were genotyped, and the stool metagenomes of the index patients and their cohabiting domestic partners were analyzed. RESULTS K. pneumoniae was identified in 33% of index patient stools, and one index patient's clinical isolate was identified in their domestic partner's stool. CONCLUSIONS This could represent a transmission event or could represent exposure to a common environmental source.
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15
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Luo J, Wei Y, Lyu M, Wu Z, Liu X, Luo H, Yan C. A comprehensive review of scaffolding methods in genome assembly. Brief Bioinform 2021; 22:6149347. [PMID: 33634311 DOI: 10.1093/bib/bbab033] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/20/2022] Open
Abstract
In the field of genome assembly, scaffolding methods make it possible to obtain a more complete and contiguous reference genome, which is the cornerstone of genomic research. Scaffolding methods typically utilize the alignments between contigs and sequencing data (reads) to determine the orientation and order among contigs and to produce longer scaffolds, which are helpful for genomic downstream analysis. With the rapid development of high-throughput sequencing technologies, diverse types of reads have emerged over the past decade, especially in long-range sequencing, which have greatly enhanced the assembly quality of scaffolding methods. As the number of scaffolding methods increases, biology and bioinformatics researchers need to perform in-depth analyses of state-of-the-art scaffolding methods. In this article, we focus on the difficulties in scaffolding, the differences in characteristics among various kinds of reads, the methods by which current scaffolding methods address these difficulties, and future research opportunities. We hope this work will benefit the design of new scaffolding methods and the selection of appropriate scaffolding methods for specific biological studies.
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Affiliation(s)
- Junwei Luo
- College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, China
| | - Yawei Wei
- College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, China
| | - Mengna Lyu
- College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, China
| | - Zhengjiang Wu
- College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, China
| | - Xiaoyan Liu
- College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, China
| | - Huimin Luo
- School of Computer and Information Engineering, Henan University, Kaifeng, China
| | - Chaokun Yan
- School of Computer and Information Engineering, Henan University, Kaifeng, China
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16
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De-la-Cruz IM, Hallab A, Olivares-Pinto U, Tapia-López R, Velázquez-Márquez S, Piñero D, Oyama K, Usadel B, Núñez-Farfán J. Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae). Sci Rep 2021; 11:882. [PMID: 33441607 PMCID: PMC7806989 DOI: 10.1038/s41598-020-79194-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/03/2020] [Indexed: 01/22/2023] Open
Abstract
Tropane alkaloids and terpenoids are widely used in the medicine and pharmaceutic industry and evolved as chemical defenses against herbivores and pathogens in the annual herb Datura stramonium (Solanaceae). Here, we present the first draft genomes of two plants from contrasting environments of D. stramonium. Using these de novo assemblies, along with other previously published genomes from 11 Solanaceae species, we carried out comparative genomic analyses to provide insights on the genome evolution of D. stramonium within the Solanaceae family, and to elucidate adaptive genomic signatures to biotic and abiotic stresses in this plant. We also studied, in detail, the evolution of four genes of D. stramonium-Putrescine N-methyltransferase, Tropinone reductase I, Tropinone reductase II and Hyoscyamine-6S-dioxygenase-involved in the tropane alkaloid biosynthesis. Our analyses revealed that the genomes of D. stramonium show signatures of expansion, physicochemical divergence and/or positive selection on proteins related to the production of tropane alkaloids, terpenoids, and glycoalkaloids as well as on R defensive genes and other important proteins related with biotic and abiotic pressures such as defense against natural enemies and drought.
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Affiliation(s)
- I M De-la-Cruz
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - A Hallab
- IBG-4 Bioinformatics, CEPLAS, Forschungszentrum Jülich, Julich, Germany
| | - U Olivares-Pinto
- Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de México (UNAM), Campus Juriquilla, Querétaro, Mexico
| | - R Tapia-López
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - S Velázquez-Márquez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - D Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - K Oyama
- Escuela Nacional de Estudios Superiores and Laboratorio Nacional de Análisis y Síntesis Ecológica (LANASE), Universidad Nacional Autónoma de México (UNAM), Campus Morelia, Morelia, Michoacán, Mexico
| | - B Usadel
- IBG-4 Bioinformatics, CEPLAS, Forschungszentrum Jülich, Julich, Germany
- Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - J Núñez-Farfán
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.
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17
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Du H, Diao C, Zhao P, Zhou L, Liu JF. Integrated hybrid de novo assembly technologies to obtain high-quality pig genome using short and long reads. Brief Bioinform 2021; 22:6082823. [PMID: 33429431 DOI: 10.1093/bib/bbaa399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/20/2020] [Accepted: 12/08/2020] [Indexed: 11/12/2022] Open
Abstract
With the rapid progress of sequencing technologies, various types of sequencing reads and assembly algorithms have been designed to construct genome assemblies. Although recent studies have attempted to evaluate the appropriate type of sequencing reads and algorithms for assembling high-quality genomes, it is still a challenge to set the correct combination for constructing animal genomes. Here, we present a comparative performance assessment of 14 assembly combinations-9 software programs with different short and long reads of Duroc pig. Based on the results of the optimization process for genome construction, we designed an integrated hybrid de novo assembly pipeline, HSCG, and constructed a draft genome for Duroc pig. Comparison between the new genome and Sus scrofa 11.1 revealed important breakpoints in two S. scrofa 11.1 genes. Our findings may provide new insights into the pan-genome analysis studies of agricultural animals, and the integrated assembly pipeline may serve as a guide for the assembly of other animal genomes.
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Affiliation(s)
- Heng Du
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Chenguang Diao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Pengju Zhao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lei Zhou
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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18
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Ye CY, Wu D, Mao L, Jia L, Qiu J, Lao S, Chen M, Jiang B, Tang W, Peng Q, Pan L, Wang L, Feng X, Guo L, Zhang C, Kellogg EA, Olsen KM, Bai L, Fan L. The Genomes of the Allohexaploid Echinochloa crus-galli and Its Progenitors Provide Insights into Polyploidization-Driven Adaptation. MOLECULAR PLANT 2020; 13:1298-1310. [PMID: 32622997 DOI: 10.1016/j.molp.2020.07.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/22/2020] [Accepted: 06/30/2020] [Indexed: 05/20/2023]
Abstract
The hexaploid species Echinochloa crus-galli is one of the most detrimental weeds in crop fields, especially in rice paddies. Its evolutionary history is similar to that of bread wheat, arising through polyploidization after hybridization between a tetraploid and a diploid species. In this study, we generated and analyzed high-quality genome sequences of diploid (E. haploclada), tetraploid (E. oryzicola), and hexaploid (E. crus-galli) Echinochloa species. Gene family analysis showed a significant loss of disease-resistance genes such as those encoding NB-ARC domain-containing proteins during Echinochloa polyploidization, contrary to their significant expansionduring wheat polyploidization, suggesting that natural selection might favor reduced investment in resistance in this weed to maximize its growth and reproduction. In contrast to the asymmetric patterns of genome evolution observed in wheat and other crops, no significant differences in selection pressure were detected between the subgenomes in E. oryzicola and E. crus-galli. In addition, distinctive differences in subgenome transcriptome dynamics during hexaploidization were observed between E. crus-galli and bread wheat. Collectively, our study documents genomic mechanisms underlying the adaptation of a major agricultural weed during polyploidization. The genomic and transcriptomic resources of three Echinochloa species and new insights into the polyploidization-driven adaptive evolution would be useful for future breeding cereal crops.
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Affiliation(s)
- Chu-Yu Ye
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Dongya Wu
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Lingfeng Mao
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Lei Jia
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200235, China
| | - Sangting Lao
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Meihong Chen
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Bowen Jiang
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Wei Tang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Qiong Peng
- Hunan Weed Science Key Laboratory, Hunan Academy of Agriculture Science, Changsha 410125, China
| | - Lang Pan
- Hunan Weed Science Key Laboratory, Hunan Academy of Agriculture Science, Changsha 410125, China
| | - Lifeng Wang
- Hunan Weed Science Key Laboratory, Hunan Academy of Agriculture Science, Changsha 410125, China
| | - Xiaoxiao Feng
- Agricultural Experiment Station, Zhejiang University, Hangzhou 310058, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Chulong Zhang
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | | | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lianyang Bai
- Hunan Weed Science Key Laboratory, Hunan Academy of Agriculture Science, Changsha 410125, China.
| | - Longjiang Fan
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
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19
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Yurchenko AA, Recknagel H, Elmer KR. Chromosome-Level Assembly of the Common Lizard (Zootoca vivipara) Genome. Genome Biol Evol 2020; 12:1953-1960. [PMID: 32835354 PMCID: PMC7643610 DOI: 10.1093/gbe/evaa161] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 01/01/2023] Open
Abstract
Squamate reptiles exhibit high variation in their phenotypic traits and geographical distributions and are therefore fascinating taxa for evolutionary and ecological research. However, genomic resources are very limited for this group of species, consequently inhibiting research efforts. To address this gap, we assembled a high-quality genome of the common lizard, Zootoca vivipara (Lacertidae), using a combination of high coverage Illumina (shotgun and mate-pair) and PacBio sequencing data, coupled with RNAseq data and genetic linkage map generation. The 1.46-Gb genome assembly has a scaffold N50 of 11.52 Mb with N50 contig size of 220.4 kb and only 2.96% gaps. A BUSCO analysis indicates that 97.7% of the single-copy Tetrapoda orthologs were recovered in the assembly. In total, 19,829 gene models were annotated to the genome using a combination of ab initio and homology-based methods. To improve the chromosome-level assembly, we generated a high-density linkage map from wild-caught families and developed a novel analytical pipeline to accommodate multiple paternity and unknown father genotypes. We successfully anchored and oriented almost 90% of the genome on 19 linkage groups. This annotated and oriented chromosome-level reference genome represents a valuable resource to facilitate evolutionary studies in squamate reptiles.
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Affiliation(s)
- Andrey A Yurchenko
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Hans Recknagel
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
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20
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Kunyavskaya O, Prjibelski AD. SGTK: a toolkit for visualization and assessment of scaffold graphs. Bioinformatics 2020; 35:2303-2305. [PMID: 30475983 DOI: 10.1093/bioinformatics/bty956] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/25/2018] [Accepted: 11/21/2018] [Indexed: 11/12/2022] Open
Abstract
SUMMARY Scaffolding is an important step in every genome assembly pipeline, which allows to order contigs into longer sequences using various types of linkage information, such as mate-pair libraries and long reads. In this work, we operate with a notion of a scaffold graph-a graph, vertices of which correspond to the assembled contigs and edges represent connections between them. We present a software package called Scaffold Graph ToolKit that allows to construct and visualize scaffold graphs using different kinds of sequencing data. We show that the scaffold graph appears to be useful for analyzing and assessing genome assemblies, and demonstrate several use cases that can be helpful for both assembly software developers and their users. AVAILABILITY AND IMPLEMENTATION SGTK is implemented in C++, Python and JavaScript and is freely available at https://github.com/olga24912/SGTK. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Olga Kunyavskaya
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Andrey D Prjibelski
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
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21
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Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. Nat Med 2020; 26:941-951. [PMID: 32514171 PMCID: PMC7303012 DOI: 10.1038/s41591-020-0894-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 04/20/2020] [Indexed: 01/10/2023]
Abstract
Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections. Spatiotemporal characterization of microbial diversity and antibiotic resistance in a tertiary-care hospital reveals broad distribution and persistence of antibiotic-resistant organisms that could cause opportunistic infections in a healthcare setting.
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22
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Olson ND, Treangen TJ, Hill CM, Cepeda-Espinoza V, Ghurye J, Koren S, Pop M. Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. Brief Bioinform 2020; 20:1140-1150. [PMID: 28968737 DOI: 10.1093/bib/bbx098] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/13/2017] [Indexed: 01/09/2023] Open
Abstract
Metagenomic samples are snapshots of complex ecosystems at work. They comprise hundreds of known and unknown species, contain multiple strain variants and vary greatly within and across environments. Many microbes found in microbial communities are not easily grown in culture making their DNA sequence our only clue into their evolutionary history and biological function. Metagenomic assembly is a computational process aimed at reconstructing genes and genomes from metagenomic mixtures. Current methods have made significant strides in reconstructing DNA segments comprising operons, tandem gene arrays and syntenic blocks. Shorter, higher-throughput sequencing technologies have become the de facto standard in the field. Sequencers are now able to generate billions of short reads in only a few days. Multiple metagenomic assembly strategies, pipelines and assemblers have appeared in recent years. Owing to the inherent complexity of metagenome assembly, regardless of the assembly algorithm and sequencing method, metagenome assemblies contain errors. Recent developments in assembly validation tools have played a pivotal role in improving metagenomics assemblers. Here, we survey recent progress in the field of metagenomic assembly, provide an overview of key approaches for genomic and metagenomic assembly validation and demonstrate the insights that can be derived from assemblies through the use of assembly validation strategies. We also discuss the potential for impact of long-read technologies in metagenomics. We conclude with a discussion of future challenges and opportunities in the field of metagenomic assembly and validation.
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23
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Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, Waugh R, Braumann I, Pozniak C, Scholz U, Mayer KFX, Spannagl M, Stein N, Mascher M. TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biol 2019; 20:284. [PMID: 31849336 DOI: 10.1101/631648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/25/2019] [Indexed: 05/29/2023] Open
Abstract
Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.
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Affiliation(s)
- Cécile Monat
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Thomas Lux
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Heidrun Gundlach
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jennifer Ens
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Chengdao Li
- Western Barley Genetics Alliance, School of Veterinary and Life Sciences (VLS), Murdoch University, Murdoch, WA, Australia
- Hubei Collaborative Innovation Center for Grain Industry/School of Agriculture, Yangtze University, Jingzhou, China
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics & Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Alan H Schulman
- Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Robbie Waugh
- The James Hutton Institute, Dundee, UK
- School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Klaus F X Mayer
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Manuel Spannagl
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- Department of Crop Sciences, Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen, Germany.
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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24
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Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, Waugh R, Braumann I, Pozniak C, Scholz U, Mayer KFX, Spannagl M, Stein N, Mascher M. TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biol 2019; 20:284. [PMID: 31849336 PMCID: PMC6918601 DOI: 10.1186/s13059-019-1899-5] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/25/2019] [Indexed: 11/24/2022] Open
Abstract
Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.
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Affiliation(s)
- Cécile Monat
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Thomas Lux
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Heidrun Gundlach
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jennifer Ens
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Chengdao Li
- Western Barley Genetics Alliance, School of Veterinary and Life Sciences (VLS), Murdoch University, Murdoch, WA, Australia
- Hubei Collaborative Innovation Center for Grain Industry/School of Agriculture, Yangtze University, Jingzhou, China
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics & Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Alan H Schulman
- Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Robbie Waugh
- The James Hutton Institute, Dundee, UK
- School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Klaus F X Mayer
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Manuel Spannagl
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- Department of Crop Sciences, Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen, Germany.
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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Qin M, Wu S, Li A, Zhao F, Feng H, Ding L, Ruan J. LRScaf: improving draft genomes using long noisy reads. BMC Genomics 2019; 20:955. [PMID: 31818249 PMCID: PMC6902338 DOI: 10.1186/s12864-019-6337-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 11/26/2019] [Indexed: 12/15/2022] Open
Abstract
Background The advent of third-generation sequencing (TGS) technologies opens the door to improve genome assembly. Long reads are promising for enhancing the quality of fragmented draft assemblies constructed from next-generation sequencing (NGS) technologies. To date, a few algorithms that are capable of improving draft assemblies have released. There are SSPACE-LongRead, OPERA-LG, SMIS, npScarf, DBG2OLC, Unicycler, and LINKS. Hybrid assembly on large genomes remains challenging, however. Results We develop a scalable and computationally efficient scaffolder, Long Reads Scaffolder (LRScaf, https://github.com/shingocat/lrscaf), that is capable of significantly boosting assembly contiguity using long reads. In this study, we summarise a comprehensive performance assessment for state-of-the-art scaffolders and LRScaf on seven organisms, i.e., E. coli, S. cerevisiae, A. thaliana, O. sativa, S. pennellii, Z. mays, and H. sapiens. LRScaf significantly improves the contiguity of draft assemblies, e.g., increasing the NGA50 value of CHM1 from 127.1 kbp to 9.4 Mbp using 20-fold coverage PacBio dataset and the NGA50 value of NA12878 from 115.3 kbp to 12.9 Mbp using 35-fold coverage Nanopore dataset. Besides, LRScaf generates the best contiguous NGA50 on A. thaliana, S. pennellii, Z. mays, and H. sapiens. Moreover, LRScaf has the shortest run time compared with other scaffolders, and the peak RAM of LRScaf remains practical for large genomes (e.g., 20.3 and 62.6 GB on CHM1 and NA12878, respectively). Conclusions The new algorithm, LRScaf, yields the best or, at least, moderate scaffold contiguity and accuracy in the shortest run time compared with other scaffolding algorithms. Furthermore, LRScaf provides a cost-effective way to improve contiguity of draft assemblies on large genomes.
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Affiliation(s)
- Mao Qin
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No. 7, Pengfei Road, Dapeng District, Shenzhen, 518120, Guangdong, China
| | - Shigang Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No. 7, Pengfei Road, Dapeng District, Shenzhen, 518120, Guangdong, China
| | - Alun Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No. 7, Pengfei Road, Dapeng District, Shenzhen, 518120, Guangdong, China
| | - Fengli Zhao
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No. 7, Pengfei Road, Dapeng District, Shenzhen, 518120, Guangdong, China
| | - Hu Feng
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No. 7, Pengfei Road, Dapeng District, Shenzhen, 518120, Guangdong, China
| | - Lulu Ding
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No. 7, Pengfei Road, Dapeng District, Shenzhen, 518120, Guangdong, China
| | - Jue Ruan
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No. 7, Pengfei Road, Dapeng District, Shenzhen, 518120, Guangdong, China.
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Linking De Novo Assembly Results with Long DNA Reads Using the dnaasm-link Application. BIOMED RESEARCH INTERNATIONAL 2019; 2019:7847064. [PMID: 31111066 PMCID: PMC6487145 DOI: 10.1155/2019/7847064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 12/14/2022]
Abstract
Currently, third-generation sequencing techniques, which make it possible to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities for combining data from next-generation and third-generation sequencing. Herein, we present a new application called dnaasm-link for linking contigs, the result of de novo assembly of second-generation sequencing data, with long DNA reads. Our tool includes an integrated module to fill gaps with a suitable fragment of an appropriate long DNA read, which improves the consistency of the resulting DNA sequences. This feature is very important, in particular for complex DNA regions. Our implementation is found to outperform other state-of-the-art tools in terms of speed and memory requirements, which may enable its usage for organisms with a large genome, something which is not possible in existing applications. The presented application has many advantages: (i) it significantly optimizes memory and reduces computation time; (ii) it fills gaps with an appropriate fragment of a specified long DNA read; (iii) it reduces the number of spanned and unspanned gaps in existing genome drafts. The application is freely available to all users under GNU Library or Lesser General Public License version 3.0 (LGPLv3). The demo application, Docker image, and source code can be downloaded from project homepage.
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Ma W, Zhao X, Yin C, Jiang F, Du X, Chen T, Zhang Q, Qiu L, Xu H, Joe Hull J, Li G, Sung W, Li F, Lin Y. A chromosome‐level genome assembly reveals the genetic basis of cold tolerance in a notorious rice insect pest,
Chilo suppressalis. Mol Ecol Resour 2019; 20:268-282. [DOI: 10.1111/1755-0998.13078] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Weihua Ma
- National Key Laboratory of Crop Genetic Improvement National Centre of Plant Gene ResearchHuazhong Agricultural University Wuhan Hubei China
| | - Xianxin Zhao
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests Institute of Insect Sciences Zhejiang University Hangzhou Zhejiang China
| | - Chuanlin Yin
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests Institute of Insect Sciences Zhejiang University Hangzhou Zhejiang China
| | - Fan Jiang
- College of Informatics Huazhong Agricultural University Wuhan Hubei China
| | - Xiaoyong Du
- College of Informatics Huazhong Agricultural University Wuhan Hubei China
| | - Taiyu Chen
- National Key Laboratory of Crop Genetic Improvement National Centre of Plant Gene ResearchHuazhong Agricultural University Wuhan Hubei China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement National Centre of Plant Gene ResearchHuazhong Agricultural University Wuhan Hubei China
| | - Lin Qiu
- College of Plant Protection Hunan Agricultural University Changsha Hunan China
| | - Hongxing Xu
- Institute of Plant Protection and Microbiology Zhejiang Academy of Agricultural Sciences Hangzhou Zhejiang China
| | - J. Joe Hull
- Department of Agriculture U.S. Agricultural Research Service U.S. Arid Land Agricultural Research Center Maricopa AZ USA
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement National Centre of Plant Gene ResearchHuazhong Agricultural University Wuhan Hubei China
- College of Informatics Huazhong Agricultural University Wuhan Hubei China
| | - Wing‐Kin Sung
- College of Informatics Huazhong Agricultural University Wuhan Hubei China
- Department of Computer Science National University of Singapore Singapore Singapore
- Department of Computational and Systems Biology Genome Institute of Singapore Singapore Singapore
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests Institute of Insect Sciences Zhejiang University Hangzhou Zhejiang China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement National Centre of Plant Gene ResearchHuazhong Agricultural University Wuhan Hubei China
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28
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Chromosome-level genome assembly of golden pompano (Trachinotus ovatus) in the family Carangidae. Sci Data 2019; 6:216. [PMID: 31641137 PMCID: PMC6805935 DOI: 10.1038/s41597-019-0238-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/11/2019] [Indexed: 12/20/2022] Open
Abstract
Golden pompano (Trachinotus ovatus), a marine fish in the Carangidae family, has a wide geographical distribution and adapts to severe environmental rigours. It is also an economically valuable aquaculture fish. To understand the genetic mechanism of adaption to environmental rigours and improve the production in aquaculture, we assembled its genome. By combination of Illumina and Pacbio reads, the obtained genome sequence is 647.5 Mb with the contig N50 of 1.80 Mb and the scaffold N50 of 5.05 Mb. The assembly covers 98.9% of the estimated genome size (655 Mb). Based on Hi-C data, 99.4% of the assembled bases are anchored into 24 pseudo-chromosomes. The annotation includes 21,915 protein-coding genes, in which 95.7% of 2,586 BUSCO vertebrate conserved genes are complete. This genome is expected to contribute to the comparative analysis of the Carangidae family. Measurement(s) | DNA • chromosome conformation capture assay • transcription profiling assay | Technology Type(s) | DNA sequencing • Hi-C • RNA sequencing | Factor Type(s) | organism part | Sample Characteristic - Organism | Trachinotus ovatus | Sample Characteristic - Environment | ocean biome |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9933515
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Zou J, Mao L, Qiu J, Wang M, Jia L, Wu D, He Z, Chen M, Shen Y, Shen E, Huang Y, Li R, Hu D, Shi L, Wang K, Zhu Q, Ye C, Bancroft I, King GJ, Meng J, Fan L. Genome-wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1998-2010. [PMID: 30947395 PMCID: PMC6737024 DOI: 10.1111/pbi.13115] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/16/2019] [Accepted: 03/13/2019] [Indexed: 05/19/2023]
Abstract
Brassica napus (AACC, 2n = 38) is an important oilseed crop grown worldwide. However, little is known about the population evolution of this species, the genomic difference between its major genetic groups, such as European and Asian rapeseed, and the impacts of historical large-scale introgression events on this young tetraploid. In this study, we reported the de novo assembly of the genome sequences of an Asian rapeseed (B. napus), Ningyou 7, and its four progenitors and compared these genomes with other available genomic data from diverse European and Asian cultivars. Our results showed that Asian rapeseed originally derived from European rapeseed but subsequently significantly diverged, with rapid genome differentiation after hybridization and intensive local selective breeding. The first historical introgression of B. rapa dramatically broadened the allelic pool but decreased the deleterious variations of Asian rapeseed. The second historical introgression of the double-low traits of European rapeseed (canola) has reshaped Asian rapeseed into two groups (double-low and double-high), accompanied by an increase in genetic load in the double-low group. This study demonstrates distinctive genomic footprints and deleterious SNP (single nucleotide polymorphism) variants for local adaptation by recent intra- and interspecies introgression events and provides novel insights for understanding the rapid genome evolution of a young allopolyploid crop.
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Affiliation(s)
- Jun Zou
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Lingfeng Mao
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
| | - Jie Qiu
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
| | - Meng Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Lei Jia
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
| | - Dongya Wu
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
| | - Zhesi He
- Department of BiologyYork UniversityHeslingtonUK
| | - Meihong Chen
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
| | - Yifei Shen
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
| | - Enhui Shen
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
| | - Yongji Huang
- Center for Genomics and BiotechnologyHaixia Institute of Science and Technology (HIST)Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Ruiyuan Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Lei Shi
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Kai Wang
- Center for Genomics and BiotechnologyHaixia Institute of Science and Technology (HIST)Fujian Agriculture and Forestry UniversityFuzhouChina
| | | | - Chuyu Ye
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
| | - Ian Bancroft
- Department of BiologyYork UniversityHeslingtonUK
| | - Graham J. King
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreNSWAustralia
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Longjiang Fan
- Institute of Crop Sciences & Institute of BioinformaticsZhejiang UniversityHangzhouChina
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30
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Martin SL, Parent JS, Laforest M, Page E, Kreiner JM, James T. Population Genomic Approaches for Weed Science. PLANTS (BASEL, SWITZERLAND) 2019; 8:E354. [PMID: 31546893 PMCID: PMC6783936 DOI: 10.3390/plants8090354] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/12/2019] [Accepted: 09/14/2019] [Indexed: 12/16/2022]
Abstract
Genomic approaches are opening avenues for understanding all aspects of biological life, especially as they begin to be applied to multiple individuals and populations. However, these approaches typically depend on the availability of a sequenced genome for the species of interest. While the number of genomes being sequenced is exploding, one group that has lagged behind are weeds. Although the power of genomic approaches for weed science has been recognized, what is needed to implement these approaches is unfamiliar to many weed scientists. In this review we attempt to address this problem by providing a primer on genome sequencing and provide examples of how genomics can help answer key questions in weed science such as: (1) Where do agricultural weeds come from; (2) what genes underlie herbicide resistance; and, more speculatively, (3) can we alter weed populations to make them easier to control? This review is intended as an introduction to orient weed scientists who are thinking about initiating genome sequencing projects to better understand weed populations, to highlight recent publications that illustrate the potential for these methods, and to provide direction to key tools and literature that will facilitate the development and execution of weed genomic projects.
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Affiliation(s)
- Sara L Martin
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Jean-Sebastien Parent
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Martin Laforest
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada.
| | - Eric Page
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, Harrow, ON N0R 1G0, Canada.
| | - Julia M Kreiner
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
| | - Tracey James
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
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Mandric I, Knyazev S, Zelikovsky A. Repeat-aware evaluation of scaffolding tools. Bioinformatics 2019; 34:2530-2537. [PMID: 29547882 DOI: 10.1093/bioinformatics/bty131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 03/09/2018] [Indexed: 01/08/2023] Open
Abstract
Summary Genomic sequences are assembled into a variable, but large number of contigs that should be scaffolded (ordered and oriented) for facilitating comparative or functional analysis. Finding scaffolding is computationally challenging due to misassemblies, inconsistent coverage across the genome and long repeats. An accurate assessment of scaffolding tools should take into account multiple locations of the same contig on the reference scaffolding rather than matching a repeat to a single best location. This makes mapping of inferred scaffoldings onto the reference a computationally challenging problem. This paper formulates the repeat-aware scaffolding evaluation problem, which is to find a mapping of the inferred scaffolding onto the reference maximizing number of correct links and proposes a scalable algorithm capable of handling large whole-genome datasets. Our novel scaffolding validation framework has been applied to assess the most of state-of-the-art scaffolding tools on the representative subset of Genome Assembly Golden-Standard Evaluations (GAGE) datasets and some novel simulated datasets. Availability and implementation The source code of this evaluation framework is available at https://github.com/mandricigor/repeat-aware. The documentation is hosted at https://mandricigor.github.io/repeat-aware. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Igor Mandric
- Department of Computer Science, Georgia State University, Atlanta, GA, USA
| | - Sergey Knyazev
- Department of Computer Science, Georgia State University, Atlanta, GA, USA
| | - Alex Zelikovsky
- Department of Computer Science, Georgia State University, Atlanta, GA, USA.,The laboratory of bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
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Dittberner H, Becker C, Jiao WB, Schneeberger K, Hölzel N, Tellier A, de Meaux J. Strengths and potential pitfalls of hay transfer for ecological restoration revealed by RAD-seq analysis in floodplain Arabis species. Mol Ecol 2019; 28:3887-3901. [PMID: 31338892 DOI: 10.1111/mec.15194] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 06/21/2019] [Accepted: 07/03/2019] [Indexed: 12/24/2022]
Abstract
Achieving high intraspecific genetic diversity is a critical goal in ecological restoration as it increases the adaptive potential and long-term resilience of populations. Thus, we investigated genetic diversity within and between pristine sites in a fossil floodplain and compared it to sites restored by hay transfer between 1997 and 2014. RAD-seq genotyping revealed that the stenoecious floodplain species Arabis nemorensis is co-occurring with individuals that, based on ploidy, ITS-sequencing and morphology, probably belong to the close relative Arabis sagittata, which has a documented preference for dry calcareous grasslands but has not been reported in floodplain meadows. We show that hay transfer maintains genetic diversity for both species. Additionally, in A. sagittata, transfer from multiple genetically isolated pristine sites resulted in restored sites with increased diversity and admixed local genotypes. In A. nemorensis, transfer did not create novel admixture dynamics because genetic diversity between pristine sites was less differentiated. Thus, the effects of hay transfer on genetic diversity also depend on the genetic make-up of the donor communities of each species, especially when local material is mixed. Our results demonstrate the efficiency of hay transfer for habitat restoration and emphasize the importance of prerestoration characterization of microgeographic patterns of intraspecific diversity of the community to guarantee that restoration practices reach their goal, that is maximize the adaptive potential of the entire restored plant community. Overlooking these patterns may alter the balance between species in the community. Additionally, our comparison of summary statistics obtained from de novo- and reference-based RAD-seq pipelines shows that the genomic impact of restoration can be reliably monitored in species lacking prior genomic knowledge.
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Affiliation(s)
| | - Christian Becker
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Wen-Biao Jiao
- Max-Planck-Institute for Plant Breeding Research, Cologne, Germany
| | | | - Norbert Hölzel
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Aurélien Tellier
- Center of Life and Food Sciences Weihenstephan, Technical University of Munich, Freising, Germany
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Ghurye J, Treangen T, Fedarko M, Hervey WJ, Pop M. MetaCarvel: linking assembly graph motifs to biological variants. Genome Biol 2019; 20:174. [PMID: 31451112 PMCID: PMC6710874 DOI: 10.1186/s13059-019-1791-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 08/13/2019] [Indexed: 01/01/2023] Open
Abstract
Reconstructing genomic segments from metagenomics data is a highly complex task. In addition to general challenges, such as repeats and sequencing errors, metagenomic assembly needs to tolerate the uneven depth of coverage among organisms in a community and differences between nearly identical strains. Previous methods have addressed these issues by smoothing genomic variants. We present a variant-aware metagenomic scaffolder called MetaCarvel, which combines new strategies for repeat detection with graph analytics for the discovery of variants. We show that MetaCarvel can accurately reconstruct genomic segments from complex microbial mixtures and correctly identify and characterize several classes of common genomic variants.
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Affiliation(s)
- Jay Ghurye
- Department of Computer Science, University of Maryland, College Park, MD, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
| | - Todd Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Marcus Fedarko
- Department of Computer Science, University of Maryland, College Park, MD, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
| | - W Judson Hervey
- Center for Bio/Molecular Science & Engineering, United States Naval Research Laboratory, Washington, DC, USA
| | - Mihai Pop
- Department of Computer Science, University of Maryland, College Park, MD, USA.
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.
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Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes. Nat Biotechnol 2019; 37:937-944. [PMID: 31359005 DOI: 10.1038/s41587-019-0191-2] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 06/11/2019] [Indexed: 12/15/2022]
Abstract
Characterization of microbiomes has been enabled by high-throughput metagenomic sequencing. However, existing methods are not designed to combine reads from short- and long-read technologies. We present a hybrid metagenomic assembler named OPERA-MS that integrates assembly-based metagenome clustering with repeat-aware, exact scaffolding to accurately assemble complex communities. Evaluation using defined in vitro and virtual gut microbiomes revealed that OPERA-MS assembles metagenomes with greater base pair accuracy than long-read (>5×; Canu), higher contiguity than short-read (~10× NGA50; MEGAHIT, IDBA-UD, metaSPAdes) and fewer assembly errors than non-metagenomic hybrid assemblers (2×; hybridSPAdes). OPERA-MS provides strain-resolved assembly in the presence of multiple genomes of the same species, high-quality reference genomes for rare species (<1%) with ~9× long-read coverage and near-complete genomes with higher coverage. We used OPERA-MS to assemble 28 gut metagenomes of antibiotic-treated patients, and showed that the inclusion of long nanopore reads produces more contiguous assemblies (200× improvement over short-read assemblies), including more than 80 closed plasmid or phage sequences and a new 263 kbp jumbo phage. High-quality hybrid assemblies enable an exquisitely detailed view of the gut resistome in human patients.
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Andonov R, Djidjev H, François S, Lavenier D. Complete assembly of circular and chloroplast genomes based on global optimization. J Bioinform Comput Biol 2019; 17:1950014. [PMID: 31288643 DOI: 10.1142/s0219720019500148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
This paper focuses on the last two stages of genome assembly, namely, scaffolding and gap-filling, and shows that they can be solved as part of a single optimization problem. Our approach is based on modeling genome assembly as a problem of finding a simple path in a specific graph that satisfies as many distance constraints as possible encoding the insert-size information. We formulate it as a mixed-integer linear programming (MILP) problem and apply an optimization solver to find the exact solutions on a benchmark of chloroplasts. We show that the presence of repetitions in the set of unitigs is the main reason for the existence of multiple equivalent solutions that are associated to alternative subpaths. We also describe two sufficient conditions and we design efficient algorithms for identifying these subpaths. Comparisons of the results achieved by our tool with the ones obtained with recent assemblers are presented.
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Affiliation(s)
- Rumen Andonov
- * Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France
| | - Hristo Djidjev
- † Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Mammalian Systems Biotechnology Reveals Global Cellular Adaptations in a Recombinant CHO Cell Line. Cell Syst 2019; 4:530-542.e6. [PMID: 28544881 DOI: 10.1016/j.cels.2017.04.009] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/14/2017] [Accepted: 04/26/2017] [Indexed: 01/16/2023]
Abstract
Effective development of host cells for therapeutic protein production is hampered by the poor characterization of cellular transfection. Here, we employed a multi-omics-based systems biotechnology approach to elucidate the genotypic and phenotypic differences between a wild-type and recombinant antibody-producing Chinese hamster ovary (CHO) cell line. At the genomic level, we observed extensive rearrangements in specific targeted loci linked to transgene integration sites. Transcriptional re-wiring of DNA damage repair and cellular metabolism in the antibody producer, via changes in gene copy numbers, was also detected. Subsequent integration of transcriptomic data with a genome-scale metabolic model showed a substantial increase in energy metabolism in the antibody producer. Metabolomics, lipidomics, and glycomics analyses revealed an elevation in long-chain lipid species, potentially associated with protein transport and secretion requirements, and a surprising stability of N-glycosylation profiles between both cell lines. Overall, the proposed knowledge-based systems biotechnology framework can further accelerate mammalian cell-line engineering in a targeted manner.
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Stankowski S, Chase MA, Fuiten AM, Rodrigues MF, Ralph PL, Streisfeld MA. Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers. PLoS Biol 2019; 17:e3000391. [PMID: 31339877 PMCID: PMC6660095 DOI: 10.1371/journal.pbio.3000391] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/26/2019] [Accepted: 07/03/2019] [Indexed: 12/12/2022] Open
Abstract
Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic "landscape" of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use whole-genome sequencing and simulations to shed light on the processes that have shaped the genomic landscape during a radiation of monkeyflowers. After inferring the phylogenetic relationships among the 9 taxa in this radiation, we show that highly similar diversity (π) and differentiation (FST) landscapes have emerged across the group. Variation in these landscapes was strongly predicted by the local density of functional elements and the recombination rate, suggesting that the landscapes have been shaped by widespread natural selection. Using the varying divergence times between pairs of taxa, we show that the correlations between FST and genome features arose almost immediately after a population split and have become stronger over time. Simulations of genomic landscape evolution suggest that background selection (BGS; i.e., selection against deleterious mutations) alone is too subtle to generate the observed patterns, but scenarios that involve positive selection and genetic incompatibilities are plausible alternative explanations. Finally, tests for introgression among these taxa reveal widespread evidence of heterogeneous selection against gene flow during this radiation. Combined with previous evidence for adaptation in this system, we conclude that the correlation in FST among these taxa informs us about the processes contributing to adaptation and speciation during a rapid radiation.
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Affiliation(s)
- Sean Stankowski
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Madeline A. Chase
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Allison M. Fuiten
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Murillo F. Rodrigues
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Peter L. Ralph
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Matthew A. Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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Richardson MF, Munyard K, Croft LJ, Allnutt TR, Jackling F, Alshanbari F, Jevit M, Wright GA, Cransberg R, Tibary A, Perelman P, Appleton B, Raudsepp T. Chromosome-Level Alpaca Reference Genome VicPac3.1 Improves Genomic Insight Into the Biology of New World Camelids. Front Genet 2019; 10:586. [PMID: 31293619 PMCID: PMC6598621 DOI: 10.3389/fgene.2019.00586] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/04/2019] [Indexed: 12/11/2022] Open
Abstract
The development of high-quality chromosomally assigned reference genomes constitutes a key feature for understanding genome architecture of a species and is critical for the discovery of the genetic blueprints of traits of biological significance. South American camelids serve people in extreme environments and are important fiber and companion animals worldwide. Despite this, the alpaca reference genome lags far behind those available for other domestic species. Here we produced a chromosome-level improved reference assembly for the alpaca genome using the DNA of the same female Huacaya alpaca as in previous assemblies. We generated 190X Illumina short-read, 8X Pacific Biosciences long-read and 60X Dovetail Chicago® chromatin interaction scaffolding data for the assembly, used testis and skin RNAseq data for annotation, and cytogenetic map data for chromosomal assignments. The new assembly VicPac3.1 contains 90% of the alpaca genome in just 103 scaffolds and 76% of all scaffolds are mapped to the 36 pairs of the alpaca autosomes and the X chromosome. Preliminary annotation of the assembly predicted 22,462 coding genes and 29,337 isoforms. Comparative analysis of selected regions of the alpaca genome, such as the major histocompatibility complex (MHC), the region involved in the Minute Chromosome Syndrome (MCS) and candidate genes for high-altitude adaptations, reveal unique features of the alpaca genome. The alpaca reference genome VicPac3.1 presents a significant improvement in completeness, contiguity and accuracy over VicPac2 and is an important tool for the advancement of genomics research in all New World camelids.
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Affiliation(s)
- Mark F Richardson
- Genomics Centre, Deakin University, Geelong, VIC, Australia.,Centre for Integrative Ecology, Deakin University, Geelong, VIC, Australia
| | - Kylie Munyard
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Larry J Croft
- Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Theodore R Allnutt
- Bioinformatics Core Research Group, Deakin University, Geelong, VIC, Australia
| | - Felicity Jackling
- Department of Genetics, The University of Melbourne, Melbourne, VIC, Australia
| | - Fahad Alshanbari
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - Matthew Jevit
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - Gus A Wright
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - Rhys Cransberg
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Ahmed Tibary
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States
| | - Polina Perelman
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Belinda Appleton
- Centre for Integrative Ecology, Deakin University, Geelong, VIC, Australia
| | - Terje Raudsepp
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
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Abstract
The computational reconstruction of genome sequences from shotgun sequencing data has been greatly simplified by the advent of sequencing technologies that generate long reads. In the case of relatively small genomes (e.g., bacterial or viral), complete genome sequences can frequently be reconstructed computationally without the need for further experiments. However, large and complex genomes, such as those of most animals and plants, continue to pose significant challenges. In such genomes, assembly software produces incomplete and fragmented reconstructions that require additional experimentally derived information and manual intervention in order to reconstruct individual chromosome arms. Recent technologies originally designed to capture chromatin structure have been shown to effectively complement sequencing data, leading to much more contiguous reconstructions of genomes than previously possible. Here, we survey these technologies and the algorithms used to assemble and analyze large eukaryotic genomes, placed within the historical context of genome scaffolding technologies that have been in existence since the dawn of the genomic era.
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Affiliation(s)
- Jay Ghurye
- Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Mihai Pop
- Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
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41
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Malli RPN, Adal AM, Sarker LS, Liang P, Mahmoud SS. De novo sequencing of the Lavandula angustifolia genome reveals highly duplicated and optimized features for essential oil production. PLANTA 2019; 249:251-256. [PMID: 30269192 DOI: 10.1007/s00425-018-3012-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/15/2018] [Indexed: 05/11/2023]
Abstract
The first draft genome for a member of the genus Lavandula is described. This 870 Mbp genome assembly is composed of over 688 Mbp of non-gap sequences comprising 62,141 protein-coding genes. Lavenders (Lavandula: Lamiaceae) are economically important plants widely grown around the world for their essential oils (EOs), which contribute to the cosmetic, personal hygiene, and pharmaceutical industries. To better understand the genetic mechanisms involved in EO production, identify genes involved in important biological processes, and find genetic markers for plant breeding, we generated the first de novo draft genome assembly for L. angustifolia (Maillette). This high-quality draft reveals a moderately repeated (> 48% repeated elements) 870 Mbp genome, composed of over 688 Mbp of non-gap sequences in 84,291 scaffolds with an N50 value of 96,735 bp. The genome contains 62,141 protein-coding genes and 2003 RNA-coding genes, with a large proportion of genes showing duplications, possibly reflecting past genome polyploidization. The draft genome contains full-length coding sequences for all genes involved in both cytosolic and plastidial pathways of isoprenoid metabolism, and all terpene synthase genes previously described from lavenders. Of particular interest is the observation that the genome contains a high copy number (14 and 7, respectively) of DXS (1-deoxyxylulose-5-phosphate synthase) and HDR (4-hydroxy-3-methylbut-2-enyl diphosphate reductase) genes, encoding the two known regulatory steps in the plastidial isoprenoid biosynthetic pathway. The latter generates precursors for the production of monoterpenes, the most abundant essential oil constituents in lavender. Furthermore, the draft genome contains a variety of monoterpene synthase genes, underlining the production of several monoterpene essential oil constituents in lavender. Taken together, these findings indicate that the genome of L. angustifolia is highly duplicated and optimized for essential oil production.
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Affiliation(s)
- Radesh P N Malli
- Department of Biological Sciences, Brock University, St. Catharines, ON, Canada
| | - Ayelign M Adal
- Department of Biology, University of British Columbia, Kelowna, BC, Canada
| | - Lukman S Sarker
- Department of Biology, University of British Columbia, Kelowna, BC, Canada
| | - Ping Liang
- Department of Biological Sciences, Brock University, St. Catharines, ON, Canada.
| | - Soheil S Mahmoud
- Department of Biology, University of British Columbia, Kelowna, BC, Canada.
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Wee Y, Bhyan SB, Liu Y, Lu J, Li X, Zhao M. The bioinformatics tools for the genome assembly and analysis based on third-generation sequencing. Brief Funct Genomics 2018; 18:1-12. [DOI: 10.1093/bfgp/ely037] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/03/2018] [Accepted: 10/19/2018] [Indexed: 02/06/2023] Open
Affiliation(s)
- YongKiat Wee
- School of Science and Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland, Australia
| | - Salma Begum Bhyan
- School of Science and Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland, Australia
| | - Yining Liu
- The School of Public Health, Institute for Chemical Carcinogenesis,Guangzhou Medical University, Dongfengxi Road, Guangzhou, China
| | - Jiachun Lu
- The School of Public Health, Institute for Chemical Carcinogenesis,Guangzhou Medical University, Dongfengxi Road, Guangzhou, China
- The School of Public Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiaoyan Li
- Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung & Blood Vessel Disease, Beijing, China
| | - Min Zhao
- School of Science and Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland, Australia
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43
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Sohn JI, Nam JW. The present and future of de novo whole-genome assembly. Brief Bioinform 2018; 19:23-40. [PMID: 27742661 DOI: 10.1093/bib/bbw096] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Indexed: 12/15/2022] Open
Abstract
As the advent of next-generation sequencing (NGS) technology, various de novo assembly algorithms based on the de Bruijn graph have been developed to construct chromosome-level sequences. However, numerous technical or computational challenges in de novo assembly still remain, although many bright ideas and heuristics have been suggested to tackle the challenges in both experimental and computational settings. In this review, we categorize de novo assemblers on the basis of the type of de Bruijn graphs (Hamiltonian and Eulerian) and discuss the challenges of de novo assembly for short NGS reads regarding computational complexity and assembly ambiguity. Then, we discuss how the limitations of the short reads can be overcome by using a single-molecule sequencing platform that generates long reads of up to several kilobases. In fact, the long read assembly has caused a paradigm shift in whole-genome assembly in terms of algorithms and supporting steps. We also summarize (i) hybrid assemblies using both short and long reads and (ii) overlap-based assemblies for long reads and discuss their challenges and future prospects. This review provides guidelines to determine the optimal approach for a given input data type, computational budget or genome.
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44
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Kobayashi Y, Maeda T, Yamaguchi K, Kameoka H, Tanaka S, Ezawa T, Shigenobu S, Kawaguchi M. The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi. BMC Genomics 2018; 19:465. [PMID: 29914365 PMCID: PMC6007072 DOI: 10.1186/s12864-018-4853-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/04/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Mycorrhizal symbiosis is one of the most fundamental types of mutualistic plant-microbe interaction. Among the many classes of mycorrhizae, the arbuscular mycorrhizae have the most general symbiotic style and the longest history. However, the genomes of arbuscular mycorrhizal (AM) fungi are not well characterized due to difficulties in cultivation and genetic analysis. In this study, we sequenced the genome of the AM fungus Rhizophagus clarus HR1, compared the sequence with the genome sequence of the model species R. irregularis, and checked for missing genes that encode enzymes in metabolic pathways related to their obligate biotrophy. RESULTS In the genome of R. clarus, we confirmed the absence of cytosolic fatty acid synthase (FAS), whereas all mitochondrial FAS components were present. A KEGG pathway map identified the absence of genes encoding enzymes for several other metabolic pathways in the two AM fungi, including thiamine biosynthesis and the conversion of vitamin B6 derivatives. We also found that a large proportion of the genes encoding glucose-producing polysaccharide hydrolases, that are present even in ectomycorrhizal fungi, also appear to be absent in AM fungi. CONCLUSIONS In this study, we found several new genes that are absent from the genomes of AM fungi in addition to the genes previously identified as missing. Missing genes for enzymes in primary metabolic pathways imply that AM fungi may have a higher dependency on host plants than other biotrophic fungi. These missing metabolic pathways provide a genetic basis to explore the physiological characteristics and auxotrophy of AM fungi.
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Affiliation(s)
- Yuuki Kobayashi
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Japan
| | - Taro Maeda
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Japan
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Hiromu Kameoka
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Japan
| | - Sachiko Tanaka
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Japan
| | - Tatsuhiro Ezawa
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Japan
- The Graduate University for Advanced Studies (SOKENDAI), Hayama, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Japan
- The Graduate University for Advanced Studies (SOKENDAI), Hayama, Japan
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45
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Austin CM, Tan MH, Harrisson KA, Lee YP, Croft LJ, Sunnucks P, Pavlova A, Gan HM. De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read. Gigascience 2018; 6:1-6. [PMID: 28873963 PMCID: PMC5597895 DOI: 10.1093/gigascience/gix063] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/11/2017] [Indexed: 12/02/2022] Open
Abstract
One of the most iconic Australian fish is the Murray cod, Maccullochella peelii (Mitchell 1838), a freshwater species that can grow to ∼1.8 metres in length and live to age ≥48 years. The Murray cod is of a conservation concern as a result of strong population contractions, but it is also popular for recreational fishing and is of growing aquaculture interest. In this study, we report the whole genome sequence of the Murray cod to support ongoing population genetics, conservation, and management research, as well as to better understand the evolutionary ecology and history of the species. A draft Murray cod genome of 633 Mbp (N50 = 109 974bp; BUSCO and CEGMA completeness of 94.2% and 91.9%, respectively) with an estimated 148 Mbp of putative repetitive sequences was assembled from the combined sequencing data of 2 fish individuals with an identical maternal lineage; 47.2 Gb of Illumina HiSeq data and 804 Mb of Nanopore data were generated from the first individual while 23.2 Gb of Illumina MiSeq data were generated from the second individual. The inclusion of Nanopore reads for scaffolding followed by subsequent gap-closing using Illumina data led to a 29% reduction in the number of scaffolds and a 55% and 54% increase in the scaffold and contig N50, respectively. We also report the first transcriptome of Murray cod that was subsequently used to annotate the Murray cod genome, leading to the identification of 26 539 protein-coding genes. We present the whole genome of the Murray cod and anticipate this will be a catalyst for a range of genetic, genomic, and phylogenetic studies of the Murray cod and more generally other fish species of the Percichthydae family.
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Affiliation(s)
- Christopher M Austin
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia.,Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia.,School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
| | - Mun Hua Tan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia.,Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia.,School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
| | - Katherine A Harrisson
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, Victoria, Australia
| | - Yin Peng Lee
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia.,School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
| | - Laurence J Croft
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia.,Malaysian Genomics Resource Centre Berhad, Boulevard Signature Office, Kuala Lumpur, Malaysia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, Victoria, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, Victoria, Australia
| | - Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia.,Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia.,School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
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Di Genova A, Ruz GA, Sagot MF, Maass A. Fast-SG: an alignment-free algorithm for hybrid assembly. Gigascience 2018; 7:4993155. [PMID: 29741627 PMCID: PMC6007556 DOI: 10.1093/gigascience/giy048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 03/01/2018] [Accepted: 04/19/2018] [Indexed: 12/01/2022] Open
Abstract
Background Long-read sequencing technologies are the ultimate solution for genome repeats, allowing near reference-level reconstructions of large genomes. However, long-read de novo assembly pipelines are computationally intense and require a considerable amount of coverage, thereby hindering their broad application to the assembly of large genomes. Alternatively, hybrid assembly methods that combine short- and long-read sequencing technologies can reduce the time and cost required to produce de novo assemblies of large genomes. Results Here, we propose a new method, called Fast-SG, that uses a new ultrafast alignment-free algorithm specifically designed for constructing a scaffolding graph using light-weight data structures. Fast-SG can construct the graph from either short or long reads. This allows the reuse of efficient algorithms designed for short-read data and permits the definition of novel modular hybrid assembly pipelines. Using comprehensive standard datasets and benchmarks, we show how Fast-SG outperforms the state-of-the-art short-read aligners when building the scaffoldinggraph and can be used to extract linking information from either raw or error-corrected long reads. We also show how a hybrid assembly approach using Fast-SG with shallow long-read coverage (5X) and moderate computational resources can produce long-range and accurate reconstructions of the genomes of Arabidopsis thaliana (Ler-0) and human (NA12878). Conclusions Fast-SG opens a door to achieve accurate hybrid long-range reconstructions of large genomes with low effort, high portability, and low cost.
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Affiliation(s)
- Alex Di Genova
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
- Mathomics Bioinformatics Laboratory, Center for Mathematical Modeling, University of Chile, Av. Beauchef 851., 7th floor, Santiago, Chile
- Inria Grenoble Rhon̂e-Alpes, 655, Avenue de l’Europe, 38334 Montbonnot, France
- CNRS, UMR5558, Université Claude Bernard Lyon 1, 43, Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France
- Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
| | - Gonzalo A Ruz
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Marie-France Sagot
- Inria Grenoble Rhon̂e-Alpes, 655, Avenue de l’Europe, 38334 Montbonnot, France
- CNRS, UMR5558, Université Claude Bernard Lyon 1, 43, Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France
| | - Alejandro Maass
- Mathomics Bioinformatics Laboratory, Center for Mathematical Modeling, University of Chile, Av. Beauchef 851., 7th floor, Santiago, Chile
- Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
- Department of Mathematical Engineering, University of Chile, Av. Beauchef 851., 5th floor, Santiago, Chile
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Nunez JCB, Elyanow RG, Ferranti DA, Rand DM. Population Genomics and Biogeography of the Northern Acorn Barnacle (Semibalanus balanoides) Using Pooled Sequencing Approaches. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_58] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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48
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Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed. Nat Commun 2017; 8:1031. [PMID: 29044108 PMCID: PMC5647321 DOI: 10.1038/s41467-017-01067-5] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 08/16/2017] [Indexed: 01/06/2023] Open
Abstract
Barnyardgrass (Echinochloa crus-galli) is a pernicious weed in agricultural fields worldwide. The molecular mechanisms underlying its success in the absence of human intervention are presently unknown. Here we report a draft genome sequence of the hexaploid species E. crus-galli, i.e., a 1.27 Gb assembly representing 90.7% of the predicted genome size. An extremely large repertoire of genes encoding cytochrome P450 monooxygenases and glutathione S-transferases associated with detoxification are found. Two gene clusters involved in the biosynthesis of an allelochemical 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) and a phytoalexin momilactone A are found in the E. crus-galli genome, respectively. The allelochemical DIMBOA gene cluster is activated in response to co-cultivation with rice, while the phytoalexin momilactone A gene cluster specifically to infection by pathogenic Pyricularia oryzae. Our results provide a new understanding of the molecular mechanisms underlying the extreme adaptation of the weed.
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49
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Neu E, Featherston J, Rees J, Debener T. A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication. PLoS One 2017; 12:e0185310. [PMID: 28981525 PMCID: PMC5628827 DOI: 10.1371/journal.pone.0185310] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/11/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Black spot is one of the most severe and damaging diseases of garden roses. We present the draft genome sequence of its causative agent Diplocarpon rosae as a working tool to generate molecular markers and to analyze functional and structural characteristics of this fungus. RESULTS The isolate DortE4 was sequenced with 191x coverage of different read types which were assembled into 2457 scaffolds. By evidence supported genome annotation with the MAKER pipeline 14,004 gene models were predicted and transcriptomic data indicated that 88.5% of them are expressed during the early stages of infection. Analyses of k-mer distributions resulted in unexpectedly large genome size estimations between 72.5 and 91.4 Mb, which cannot be attributed to its repeat structure and content of transposable elements alone, factors explaining such differences in other fungal genomes. In contrast, different lines of evidences demonstrate that a huge proportion (approximately 80%) of genes are duplicated, which might indicate a whole genome duplication event. By PCR-RFLP analysis of six paralogous gene pairs of BUSCO orthologs, which are expected to be single copy genes, we could show experimentally that the duplication is not due to technical error and that not all isolates tested possess all of the paralogs. CONCLUSIONS The presented genome sequence is still a fragmented draft but contains almost the complete gene space. Therefore, it provides a useful working tool to study the interaction of D. rosae with the host and the influence of a genome duplication outside of the model yeast in the background of a phytopathogen.
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Affiliation(s)
- Enzo Neu
- Institute for Plant Genetics, Leibniz University Hannover, Hannover, Germany
| | - Jonathan Featherston
- Agricultural Research Council, Biotechnology Platform, Onderstepoort, Pretoria, South Africa
| | - Jasper Rees
- Agricultural Research Council, Biotechnology Platform, Onderstepoort, Pretoria, South Africa
| | - Thomas Debener
- Institute for Plant Genetics, Leibniz University Hannover, Hannover, Germany
- * E-mail:
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Madoui MA, Dossat C, d'Agata L, van Oeveren J, van der Vossen E, Aury JM. MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data. BMC Bioinformatics 2016; 17:115. [PMID: 26936254 PMCID: PMC4776351 DOI: 10.1186/s12859-016-0969-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/23/2016] [Indexed: 12/20/2022] Open
Abstract
Background Scaffolding is an essential step in the genome assembly process. Current methods based on large fragment paired-end reads or long reads allow an increase in contiguity but often lack consistency in repetitive regions, resulting in fragmented assemblies. Here, we describe a novel tool to link assemblies to a genome map to aid complex genome reconstruction by detecting assembly errors and allowing scaffold ordering and anchoring. Results We present MaGuS (map-guided scaffolding), a modular tool that uses a draft genome assembly, a Whole Genome Profiling™ (WGP) map, and high-throughput paired-end sequencing data to estimate the quality and to enhance the contiguity of an assembly. We generated several assemblies of the Arabidopsis genome using different scaffolding programs and applied MaGuS to select the best assembly using quality metrics. Then, we used MaGuS to perform map-guided scaffolding to increase contiguity by creating new scaffold links in low-covered and highly repetitive regions where other commonly used scaffolding methods lack consistency. Conclusions MaGuS is a powerful reference-free evaluator of assembly quality and a WGP map-guided scaffolder that is freely available at https://github.com/institut-de-genomique/MaGuS. Its use can be extended to other high-throughput sequencing data (e.g., long-read data) and also to other map data (e.g., genetic maps) to improve the quality and the contiguity of large and complex genome assemblies. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0969-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mohammed-Amin Madoui
- CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057, Evry, France.
| | - Carole Dossat
- CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057, Evry, France.
| | - Léo d'Agata
- CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057, Evry, France.
| | - Jan van Oeveren
- Keygene NV, Agro Business Park 90, 6708 PW, Wageningen, The Netherlands.
| | | | - Jean-Marc Aury
- CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057, Evry, France.
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