Current Strategies of Polyploid Plant Genome Sequence Assembly

Frontiers in Plant Science, Journal Year: 2018, Volume and Issue: 9

Published: Nov. 21, 2018

Polyploidy or duplication of an entire genome occurs in the majority angiosperms. The understanding polyploid genomes is important for improvement those crops, which humans rely on sustenance and basic nutrition. As climate change continues to pose a potential threat agricultural production, there will increasingly be demand plant cultivars that can resist biotic abiotic stresses also provide needed improved In past decade, Next Generation Sequencing (NGS) has fundamentally changed genomics landscape by providing tools exploration genomes. Here, we review challenges assembly genomes, present recent advances genomic resources functional molecular genetics breeding. diploid less heterozygous progenitor species are available, discuss lack complexity these currently available reference as they relate crops. Finally, approaches haplotyping phasing impact third generation technologies assembly.

Language: Английский

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Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases

Genes, Journal Year: 2022, Volume and Issue: 13(9), P. 1566 - 1566

Published: Aug. 31, 2022

Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these laboratory: whole genome (WGS), targeted metagenomics and shotgun sequencing. These being utilized initial identification pathogenic organisms, detection antimicrobial resistance mechanisms epidemiologic tracking organisms within outside hospital systems. In this review, we analyze provide a comprehensive summary how currently used public health, basic research, laboratory environments. health arena, WGS is to identify epidemiologically track food borne outbreaks disease surveillance. systems, multi-drug-resistant nosocomial infections transmission organisms. addition, examine approaches (targeted shotgun) circumvent traditional biased culture methods potential pathogens directly from specimens. We also expand on important factors consider when implementing technologies, what possible infectious diagnosis next 5 years.

Language: Английский

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The Carbon Footprint of Bioinformatics

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(3)

Published: Feb. 4, 2022

Bioinformatic research relies on large-scale computational infrastructures which have a nonzero carbon footprint but so far, no study has quantified the environmental costs of bioinformatic tools and commonly run analyses. In this work, we estimate bioinformatics (in kilograms CO2 equivalent units, kgCO2e) using freely available Green Algorithms calculator (www.green-algorithms.org, last accessed 2022). We assessed 1) approaches in genome-wide association studies (GWAS), RNA sequencing, genome assembly, metagenomics, phylogenetics, molecular simulations, as well 2) computation strategies, such parallelization, CPU (central processing unit) versus GPU (graphics unit), cloud local computing infrastructure, geography. particular, found that biobank-scale GWAS emitted substantial kgCO2e simple software upgrades could make it greener, for example, upgrading from BOLT-LMM v1 to v2.3 reduced by 73%. Moreover, switching average data center more efficient one can reduce approximately 34%. Memory over-allocation also be contributor an algorithm's greenhouse gas emissions. The use faster processors or greater parallelization reduces running time lead footprint. Finally, provide guidance how researchers power consumption minimize kgCO2e. Overall, work elucidates common analyses provides solutions empower move toward greener research.

Language: Английский

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Tools and Strategies for Long-Read Sequencing and De Novo Assembly of Plant Genomes

Trends in Plant Science, Journal Year: 2019, Volume and Issue: 24(8), P. 700 - 724

Published: June 14, 2019

Language: Английский

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Reference genome and demographic history of the most endangered marine mammal, the vaquita

Molecular Ecology Resources, Journal Year: 2020, Volume and Issue: 21(4), P. 1008 - 1020

Published: Oct. 22, 2020

Abstract The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in wild. First described 1958, has been rapid decline for more 20 years resulting from inadvertent deaths due to increasing use of large‐mesh gillnets. To understand evolutionary and demographic history vaquita, we used combined long‐read sequencing long‐range scaffolding methods long‐ short‐read RNA generate a near error‐free annotated reference genome assembly cell lines derived female individual. consists 99.92% assembled sequence contained 21 nearly gapless chromosome‐length autosome scaffolds X‐chromosome scaffold, scaffold N50 115 Mb. Genome‐wide heterozygosity lowest (0.01%) any mammalian species analysed date, but evenly distributed across chromosomes, consistent long‐term small population size at genetic equilibrium, rather low diversity recent bottleneck or inbreeding. Historical demography indicates stability less 5,000 ( Ne ) over 200,000 years. Together, these analyses indicate that had ample opportunity purge highly deleterious alleles potentially maintain necessary health.

Language: Английский

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Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Sept. 12, 2023

Heliconius butterflies, a speciose genus of Müllerian mimics, represent classic example an adaptive radiation that includes range derived dietary, life history, physiological and neural traits. However, key lineages within the genus, across broader Heliconiini tribe, lack genomic resources, limiting our understanding how neutral processes shaped genome evolution during their radiation. Here, we generate highly contiguous assemblies for nine Heliconiini, 29 additional reference-assembled genomes, improve 10 existing assemblies. Altogether, provide dataset annotated genomes total 63 species, including 58 species tribe. We use this extensive to robust dated heliconiine phylogeny, describe major patterns introgression, explore architecture, basis innovations in enigmatic group, assessment putative regulatory regions at stem. Our work illustrates increased resolution provided by such dense sampling improves power test gene-phenotype hypotheses, precisely characterize evolve.

Language: Английский

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Reference Genomes from Distantly Related Species Can Be Used for Discovery of Single Nucleotide Polymorphisms to Inform Conservation Management

Genes, Journal Year: 2018, Volume and Issue: 10(1), P. 9 - 9

Published: Dec. 22, 2018

Threatened species recovery programmes benefit from incorporating genomic data into conservation management strategies to enhance recovery. However, a lack of readily available resources, including conspecific reference genomes, often limits the inclusion data. Here, we investigate utility closely related high-quality genomes for single nucleotide polymorphism (SNP) discovery using critically endangered kakī/black stilt (Himantopus novaezelandiae) and four Charadriiform as proof concept. We compare diversity estimates (i.e., diversity, individual heterozygosity, relatedness) based on kakī SNPs discovered genotyping-by-sequencing whole genome resequencing reads mapped conordinal (killdeer, Charadrius vociferus), confamilial (pied avocet, Recurvirostra avosetta), congeneric stilt, Himantopus himantopus) genomes. Results indicate that calculated correlate significantly with genome. Congeneric references provide higher correlations more similar measures relatedness. While may be necessary address other questions in conservation, SNP is cost-effective approach estimating threatened species.

Language: Английский

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Twelve quick steps for genome assembly and annotation in the classroom

PLoS Computational Biology, Journal Year: 2020, Volume and Issue: 16(11), P. e1008325 - e1008325

Published: Nov. 12, 2020

Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting budgets individual research groups. Third-generation long-read DNA technologies are used, providing extensive genomic toolkits that were reserved for a few select model organisms. Generating high-quality assemblies annotations many aquatic species still presents significant challenges due to their large sizes, complexity, high chromosome numbers. Indeed, selecting most appropriate software platforms annotation pipelines new project can be daunting because tools often only work in limited contexts. In genomics, generating assembly/annotation has an indispensable tool better understanding biology any species. Herein, we state 12 steps help researchers get started projects by presenting guidelines broadly applicable (to species), sustainable over time, cover all aspects assembly from start finish. We review some commonly used approaches, including practical methods extract choices best library preparations. addition, discuss range potential bioinformatics pipelines, structural functional (e.g., transposable elements repetitive sequences). This paper also includes information on how build wide community project, importance data management, make results Findable, Accessible, Interoperable, Reusable (FAIR) submitting them public repository sharing with community.

Language: Английский

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Haplotype-specific assembly of shattered chromosomes in esophageal adenocarcinomas

Cell Genomics, Journal Year: 2024, Volume and Issue: 4(2), P. 100484 - 100484

Published: Jan. 16, 2024

The epigenetic landscape of cancer is regulated by many factors, but primarily it derives from the underlying genome sequence. Chromothripsis a catastrophic localized shattering event that drives, and often initiates, evolution. We characterized five esophageal adenocarcinoma organoids with chromothripsis using long-read sequencing transcriptome epigenome profiling. Complex structural variation subclonal variants meant haplotype-aware de novo methods were required to generate contiguous assemblies. Chromosomes assembled separately scaffolded haplotype-resolved Hi-C reads, producing accurate assemblies even up 900 rearrangements. There widespread differences between chromothriptic wild-type copies chromosomes in topologically associated domains, chromatin accessibility, histone modifications, gene expression. Differential peaks most enriched within 10 kb variants. Alterations higher-order chromosome organization frequently occurred near differential marks. Overall, reshapes regulation, causing coordinated changes landscape, transcription, conformation.

Language: Английский

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Insights into the Genomics of Clownfish Adaptive Radiation: Genetic Basis of the Mutualism with Sea Anemones

Genome Biology and Evolution, Journal Year: 2019, Volume and Issue: 11(3), P. 869 - 882

Published: Feb. 28, 2019

Clownfishes are an iconic group of coral reef fishes, especially known for their mutualism with sea anemones.This is particularly interesting as it likely acted the key innovation that triggered clownfish adaptive radiation.Indeed, after acquisition mutualism, clownfishes diversified into multiple ecological niches linked host and habitat use.However, despite importance this genetic mechanisms allowing to interact anemones still unclear.Here, we used a comparative genomics molecular evolutionary analyses investigate basis anemones.We assembled annotated genome nine species one closely related outgroup.Orthologous genes inferred between these additional publicly available teleost genomes resulted in almost 16,000 were tested positively selected substitutions potentially involved adaptation live identified 17 signal positive selection at origin radiation.Two them (Versican core protein Protein O-GlcNAse) show functions associated N-acetylated sugars, which be anemone discharge toxins.This study provides first insights anemones.Indeed, candidate protection form anemones, thus evolution mutualism.Additionally, genomic resources acquired represent valuable resource further investigation radiation.

Language: Английский

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