FGMP: assessing fungal genome completeness and gene content

AbstractBackgroundInexpensive high-throughput DNA sequencing has democratized access to genetic information for most organisms so that research utilizing a genome or transcriptome of an organism is not limited to model systems. However, the quality of the assemblies of sampled genomes can vary greatly which hampers utility for comparisons and meaningful interpretation. The uncertainty of the completeness of a given genome sequence can limit feasibility of asserting patterns of high rates of gene loss reported in many lineages.ResultsWe propose a computational framework and sequence resource for assessing completeness of fungal genomes called FGMP (Fungal Genome Mapping Project). Our approach is based on evolutionary conserved sets of proteins and DNA elements and is applicable to various types of genomic data. We present a comparison of FGMP and state-of-the-art methods for genome completeness assessment utilizing 246 genome assemblies of fungi. We discuss genome assembly improvements/degradations in 57 cases where assemblies have been updated, as recorded by NCBI assembly archive.ConclusionFGMP is an accurate tool for quantifying level of completion from fungal genomic data. It is particularly useful for non-model organisms without reference genomes and can be used directly on unassembled reads, which can help reducing genome sequencing costs.

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From single nuclei to whole genome assemblies

10.1101/625814 ◽

2019 ◽

Cited By ~ 3

Author(s):

Merce Montoliu-Nerin ◽

Marisol Sánchez-García ◽

Claudia Bergin ◽

Manfred Grabherr ◽

Barbara Ellis ◽

...

Keyword(s):

Single Cell ◽

Large Scale ◽

Genomic Data ◽

Life Cycles ◽

Genomic Research ◽

Metagenomic Data ◽

Model Organisms ◽

Genomic Study ◽

And Function ◽

Genome Assemblies

SummaryA large proportion of Earth's biodiversity constitutes organisms that cannot be cultured, have cryptic life-cycles and/or live submerged within their substrates1–4. Genomic data are key to unravel both their identity and function5. The development of metagenomic methods6,7 and the advent of single cell sequencing8–10 have revolutionized the study of life and function of cryptic organisms by upending the need for large and pure biological material, and allowing generation of genomic data from complex or limited environmental samples. Genome assemblies from metagenomic data have so far been restricted to organisms with small genomes, such as bacteria11, archaea12 and certain eukaryotes13. On the other hand, single cell technologies have allowed the targeting of unicellular organisms, attaining a better resolution than metagenomics8,9,14–16, moreover, it has allowed the genomic study of cells from complex organisms one cell at a time17,18. However, single cell genomics are not easily applied to multicellular organisms formed by consortia of diverse taxa, and the generation of specific workflows for sequencing and data analysis is needed to expand genomic research to the entire tree of life, including sponges19, lichens3,20, intracellular parasites21,22, and plant endophytes23,24. Among the most important plant endophytes are the obligate mutualistic symbionts, arbuscular mycorrhizal (AM) fungi, that pose an additional challenge with their multinucleate coenocytic mycelia25. Here, the development of a novel single nuclei sequencing and assembly workflow is reported. This workflow allows, for the first time, the generation of reference genome assemblies from large scale, unbiased sorted, and sequenced AM fungal nuclei circumventing tedious, and often impossible, culturing efforts. This method opens infinite possibilities for studies of evolution and adaptation in these important plant symbionts and demonstrates that reference genomes can be generated from complex non-model organisms by isolating only a handful of their nuclei.

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A Genome for the Environment

10.31219/osf.io/ujrgc ◽

2017 ◽

Author(s):

Dieter Ebert

Keyword(s):

Phenotypic Plasticity ◽

Natural History ◽

Germ Cells ◽

Model System ◽

National Institutes Of Health ◽

Model Systems ◽

Model Organisms ◽

Biological Research ◽

System P ◽

A Genome

Water fleas of the genus Daphnia are among the oldest model systems in biological research. Today, we know more about their natural history and ecology than of any other taxon. The Daphnia model also has left a notable mark on other fields. élie Metchnikoff used Daphnia to test his 1908 Nobel prize–winning idea that macrophages attack invading parasites as part of cellular immunity. August Weismann's studies of water fleas were instrumental in developing his theory that only germ cells transmit heritable information in animals. Richard Woltereck used Daphnia to develop the notion of phenotypic plasticity—that an organism can change its characteristics in response to the environment—an idea that still guides experiments with many organisms that distinguish genetic from environmental effects. With all of these historical achievements, why did the National Institutes of Health (NIH) only recently add Daphnia to its list of model organisms for biomedical research? Moreover, why has Daphnia, at this point in time, become NIH's 13th model system?

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Sequencing smart: De novo sequencing and assembly approaches for a non-model mammal

GigaScience ◽

10.1093/gigascience/giaa045 ◽

2020 ◽

Vol 9 (5) ◽

Cited By ~ 2

Author(s):

Graham J Etherington ◽

Darren Heavens ◽

David Baker ◽

Ashleigh Lister ◽

Rose McNelly ◽

...

Keyword(s):

De Novo ◽

Cost Effective ◽

Genome Project ◽

Model Organisms ◽

Sequencing Data ◽

Data Types ◽

High Molecular Weight Dna ◽

Assembly Method ◽

A Genome ◽

Genome Assemblies

Abstract Background Whilst much sequencing effort has focused on key mammalian model organisms such as mouse and human, little is known about the relationship between genome sequencing techniques for non-model mammals and genome assembly quality. This is especially relevant to non-model mammals, where the samples to be sequenced are often degraded and of low quality. A key aspect when planning a genome project is the choice of sequencing data to generate. This decision is driven by several factors, including the biological questions being asked, the quality of DNA available, and the availability of funds. Cutting-edge sequencing technologies now make it possible to achieve highly contiguous, chromosome-level genome assemblies, but rely on high-quality high molecular weight DNA. However, funding is often insufficient for many independent research groups to use these techniques. Here we use a range of different genomic technologies generated from a roadkill European polecat (Mustela putorius) to assess various assembly techniques on this low-quality sample. We evaluated different approaches for de novo assemblies and discuss their value in relation to biological analyses. Results Generally, assemblies containing more data types achieved better scores in our ranking system. However, when accounting for misassemblies, this was not always the case for Bionano and low-coverage 10x Genomics (for scaffolding only). We also find that the extra cost associated with combining multiple data types is not necessarily associated with better genome assemblies. Conclusions The high degree of variability between each de novo assembly method (assessed from the 7 key metrics) highlights the importance of carefully devising the sequencing strategy to be able to carry out the desired analysis. Adding more data to genome assemblies does not always result in better assemblies, so it is important to understand the nuances of genomic data integration explained here, in order to obtain cost-effective value for money when sequencing genomes.

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Chemical Responses to the Biotic and Abiotic Environment by Early Diverging Metazoans Revealed in the Post-Genomic Age

Integrative and Comparative Biology ◽

10.1093/icb/icz125 ◽

2019 ◽

Vol 59 (4) ◽

pp. 731-738 ◽

Cited By ~ 1

Author(s):

Beth Okamura ◽

Paul F Long ◽

Laura D Mydlarz

Keyword(s):

Molecular Basis ◽

Genomic Data ◽

Model Systems ◽

Model Organisms ◽

Omics Data ◽

Sensory Biology ◽

Abiotic Environment ◽

Sequencing Platforms ◽

Comparative Evolution ◽

Chemical Mediators

Abstract For many years methodological constraints limited insights on the molecular biology of non-model organisms. However, the development of various sequencing platforms has led to an explosion of transcriptomic and genomic data on non-model systems. As a consequence the molecular drivers of organismal phenotypes are becoming clearer and the chemicals that animals use to detect and respond to their environments are increasingly being revealed—this latter area inspired our symposium theme. The papers in this volume broadly address this theme by their more specific focus in one of the following general areas: 1) sensory biology and the molecular basis of perception, 2) chemicals deployed to deal with the biotic and abiotic environment, and 3) chemical interactions along the parasite–mutualist continuum. Here we outline and synthesize the content of these papers—an exercise which demonstrates that sophisticated gene repertoires enable early diverging metazoans to encode many of the signaling, sensory, defensive, and offensive capacities typically associated with animals that have complex nervous systems. We then consider opportunities and associated challenges that may delay progress in comparative functional biochemistry, a reinvigorated field that can be expected to rapidly expand with new ’omics data. Future knowledge of chemical adaptations should afford new perspectives on the comparative evolution of chemical mediators.

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Sequencing smart: De novo sequencing and assembly approaches for non-model mammals

10.1101/723890 ◽

2019 ◽

Cited By ~ 1

Author(s):

Graham J Etherington ◽

Darren Heavens ◽

David Baker ◽

Ashleigh Lister ◽

Rose McNelly ◽

...

Keyword(s):

De Novo ◽

Genome Project ◽

Model Organisms ◽

Value For Money ◽

Sequencing Data ◽

Data Types ◽

High Molecular Weight Dna ◽

Assembly Method ◽

A Genome ◽

Genome Assemblies

AbstractBackgroundWhilst much sequencing effort has focused on key mammalian model organisms such as mouse and human, little is known about the correlation between genome sequencing techniques for non-model mammals and genome assembly quality. This is especially relevant to non-model mammals, where the samples to be sequenced are often degraded and low quality. A key aspect when planning a genome project is the choice of sequencing data to generate. This decision is driven by several factors, including the biological questions being asked, the quality of DNA available, and the availability of funds. Cutting-edge sequencing technologies now make it possible to achieve highly contiguous, chromosome-level genome assemblies, but relies on good quality high-molecular-weight DNA. The funds to generate and combining these data are often only available within large consortiums and sequencing initiatives, and are often not affordable for many independent research groups. For many researchers, value-for-money is a key factor when considering the generation of genomic sequencing data. Here we use a range of different genomic technologies generated from a roadkill European Polecat (Mustela putorius) to assess various assembly techniques on this low-quality sample. We evaluated different approaches for de novo assemblies and discuss their value in relation to biological analyses.ResultsGenerally, assemblies containing more data types achieved better scores in our ranking system. However, when accounting for misassemblies, this was not always the case for Bionano and low-coverage 10x Genomics (for scaffolding only). We also find that the extra cost associated with combining multiple data types is not necessarily associated with better genome assemblies.ConclusionsThe high degree of variability between each de novo assembly method (assessed from the seven key metrics) highlights the importance of carefully devising the sequencing strategy to be able to carry out the desired analysis. Adding more data to genome assemblies not always results in better assemblies so it is important to understand the nuances of genomic data integration explained here, in order to obtain cost-effective value-for-money when sequencing genomes.

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A Genome Scan for Quantitative Trait Loci in a Wild Population of Red Deer (Cervus elaphus)

Genetics ◽

10.1093/genetics/162.4.1863 ◽

2002 ◽

Vol 162 (4) ◽

pp. 1863-1873 ◽

Cited By ~ 3

Author(s):

J Slate ◽

P M Visscher ◽

S MacGregor ◽

D Stevens ◽

M L Tate ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Cervus Elaphus ◽

Quantitative Trait ◽

Red Deer ◽

Wild Population ◽

Additive Genetic Variance ◽

Model Organisms ◽

A Genome ◽

Trait Loci ◽

In The Wild

Abstract Recent empirical evidence indicates that although fitness and fitness components tend to have low heritability in natural populations, they may nonetheless have relatively large components of additive genetic variance. The molecular basis of additive genetic variation has been investigated in model organisms but never in the wild. In this article we describe an attempt to map quantitative trait loci (QTL) for birth weight (a trait positively associated with overall fitness) in an unmanipulated, wild population of red deer (Cervus elaphus). Two approaches were used: interval mapping by linear regression within half-sib families and a variance components analysis of a six-generation pedigree of >350 animals. Evidence for segregating QTL was found on three linkage groups, one of which was significant at the genome-wide suggestive linkage threshold. To our knowledge this is the first time that a QTL for any trait has been mapped in a wild mammal population. It is hoped that this study will stimulate further investigations of the genetic architecture of fitness traits in the wild.

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The genomics of adaptation

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2012.2322 ◽

2012 ◽

Vol 279 (1749) ◽

pp. 5024-5028 ◽

Cited By ~ 35

Author(s):

Jacek Radwan ◽

Wiesław Babik

Keyword(s):

Genetic Variation ◽

Natural Selection ◽

Royal Society ◽

Genetic Basis ◽

Genomic Data ◽

Evolutionary Change ◽

Introductory Article ◽

Technological Advances ◽

A Genome ◽

Genome Level

The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation.

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Bridging the Gap between Vertebrate Cytogenetics and Genomics with Single-Chromosome Sequencing (ChromSeq)

Genes ◽

10.3390/genes12010124 ◽

2021 ◽

Vol 12 (1) ◽

pp. 124

Author(s):

Alessio Iannucci ◽

Alexey I. Makunin ◽

Artem P. Lisachov ◽

Claudio Ciofi ◽

Roscoe Stanyon ◽

...

Keyword(s):

Genome Evolution ◽

Karyotype Evolution ◽

Genomic Data ◽

Anolis Carolinensis ◽

Vertebrate Genome ◽

Single Chromosome ◽

Sequencing Technologies ◽

Novel Approaches ◽

Genome Assemblies ◽

Generation Sequencing

The study of vertebrate genome evolution is currently facing a revolution, brought about by next generation sequencing technologies that allow researchers to produce nearly complete and error-free genome assemblies. Novel approaches however do not always provide a direct link with information on vertebrate genome evolution gained from cytogenetic approaches. It is useful to preserve and link cytogenetic data with novel genomic discoveries. Sequencing of DNA from single isolated chromosomes (ChromSeq) is an elegant approach to determine the chromosome content and assign genome assemblies to chromosomes, thus bridging the gap between cytogenetics and genomics. The aim of this paper is to describe how ChromSeq can support the study of vertebrate genome evolution and how it can help link cytogenetic and genomic data. We show key examples of ChromSeq application in the refinement of vertebrate genome assemblies and in the study of vertebrate chromosome and karyotype evolution. We also provide a general overview of the approach and a concrete example of genome refinement using this method in the species Anolis carolinensis.

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Abstract 426: Laminin Downregulation Facilitates Cardiomyocyte Coupling in situ to Increase Contractile Function

Circulation Research ◽

10.1161/res.119.suppl_1.426 ◽

2016 ◽

Vol 119 (suppl_1) ◽

Author(s):

Ayla Sessions ◽

Gaurav Kaushik ◽

Adam Engler

Keyword(s):

Basement Membrane ◽

Contractile Function ◽

Current Model ◽

Model Systems ◽

Model Organisms ◽

Muscle Physiology ◽

Heart Tube ◽

Age Related ◽

New Evidence

Aging is associated with extensive remodeling of the heart, including basement membrane extracellular matrix (ECM) components that surround cardiomyocytes. Remodeling is thought to contribute to impaired cardiac mechanotransduction, but the contribution of specific basement membrane ECM components to age-related cardiac remodeling is unclear, owing to current model systems being complex and slow to age. To investigate the effect of basement membrane remodeling on mechanical function in genetically tractable, rapidly aging, and simple model organisms, we employed Drosophila melanogaster, which has a simple trilayered heart tube composed of only basement membrane ECM. We observed differential regulation of collagens between laboratory Drosophila strains , i.e. yellow-white ( yw ) and white-1118 ( w 1118 ), leading to changes in muscle physiology, which were linked to severity of dysfunction with age. Therefore, we sought to understand the extent to which basement membrane ECM modulates lateral cardiomyocyte coupling and contractile function during aging. Cardiac-restricted knockdown of ECM genes Pericardin , Laminin A , and Viking in Drosophila prevented age-associated heart tube restriction and increased contractility, even under viscous load. Most notably, reduction of Laminin A expression decreased levels of other genes that co-assemble in ECM, leading to overall preservation of contractile velocity and extension of median organismal lifespan by 3 weeks or 39%. These data provide new evidence of a direct link between basement membrane ECM homeostasis, contractility, and maintenance of lifespan.

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Abstract 371: Down Regulation of ECM Genes Laminin and Collagen IV Lead to Preserved Cardiac Function With Age and Increased Lifespan in Drosophila

Circulation Research ◽

10.1161/res.117.suppl_1.371 ◽

2015 ◽

Vol 117 (suppl_1) ◽

Author(s):

Ayla O Sessions

Keyword(s):

Diastolic Dysfunction ◽

High Speed ◽

Current Model ◽

Collagen Iv ◽

Model Systems ◽

Model Organisms ◽

Heart Tube ◽

Ecm Remodeling ◽

Intercalated Discs ◽

And Performance

Increased deposition of extracellular matrix (ECM) is observed in all advanced age heart failure patients, but current model systems are complex and slow to age. To investigate the effect of extracellular remodeling on mechanical function in genetically tractable, rapidly aging, and simple model organisms, we employed Drosophila melanogaster, which has a simple trilayered heart tube. We found that two common wildtype strains of Drosophila, i.e. yellow-white (yw) and white-1118 (w1118), exhibit different cytoskeletal and ECM remodeling with age. Using a recently developed nanoindentation method to measure cardiomyocyte stiffness and high speed optical imaging to assess contractility of intact Drosophila hearts, we found that yw flies had stiffer intercalated discs (ICD) and exhibited diastolic dysfunction with age. On the other hand, w1118 flies had a shorter lifespan compared to yw, did not exhibit ICD stiffening, had a less severe diastolic dysfunction, and showed an increase in ECM layer thickness between ventral muscle (VM) and cardiomyocyte (CM) layers of the heart tube. To modulate ECM and assess its effect in the aged w1118 flies, we knocked-down ECM genes LamininA and Viking (homologous to Collagen IV). Both ECM KD genotypes exhibited diastolic dilation with increased fractional shortening at adult (1wk) and aged (5wk) time points. The LamininA KD resulted in decreased cardiomyocyte stiffness correlating with increased relaxation velocities in adult flies and preservation of shortening and relaxation velocities in aged flies over controls. However, both the LamininA and Collagen IV KD flies experienced a basal increase in the decoupling of their cardiomyocytes as determined by heart period variance and % fibrillar heart-beats. These conductance issues were not enough to counteract the increased cardiac output and performance with age, and the Collagen IV KD outlived controls by 1.5 weeks median survival and the LamininA KD by 3 weeks. This suggests that the cell-ECM contacts in the basement membrane are intimately tied not only to the coupling of the cardiomyocytes of the Drosophila heart tube but also to cytoskeletal remodeling, but perhaps different ECM proteins have different mechanisms for interacting with the cardiomyocyte cytoskeleton.

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