A Deep Dive into Genome Assemblies of Non-vertebrate Animals

Non-vertebrate species represent about ~95% of known metazoan (animal) diversity. They remain to this day relatively unexplored genetically, but understanding their genome structure and function is pivotal for expanding our current knowledge of evolution, ecology and biodiversity. Following the continuous improvements and decreasing costs of sequencing technologies, many genome assembly tools have been released, leading to a significant amount of genome projects being completed in recent years. In this review, we examine the current state of genome projects of non-vertebrate animal species. We present an overview of available sequencing technologies, assembly approaches, as well as pre and post-processing steps, genome assembly evaluation methods, and their application to non-vertebrate animal genomes.

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NucMerge: Genome assembly quality improvement assisted by alternative assemblies and paired-end Illumina reads

10.1101/483701 ◽

2018 ◽

Author(s):

Ksenia Khelik ◽

Alexander Johan Nederbragt ◽

Geir Kjetil Sandve ◽

Torbjørn Rognes

Keyword(s):

Genome Assembly ◽

Second Generation ◽

Sequencing Technologies ◽

Assembly Accuracy ◽

Alternative Approach ◽

Second Generation Sequencing ◽

Genome Assemblies ◽

And Inversion ◽

Generation Sequencing ◽

Genome Projects

AbstractBackgroundIn spite of the major breakthroughs in the second-generation sequencing technologies and the developments of a plethora of assemblers over the last ten years, the resulting genome assemblies may still be fragmented and contain errors. It is typical in genome projects with second-generation reads involved to run multiple assemblers with different parameters and choose the best assembly. However, such an approach is always a trade-off between the strengths and weaknesses of the assemblies. To exploit the advantages of different assemblers, an alternative approach that combines the best parts of several assemblies into one may be applied. The existing tools based on such an approach assist in elongation of assembly fragments and/or improvement of assembly accuracy. Though there has been progress with such a strategy, there is still room for improvement of the existing tools.ResultsWe present NucMerge, a tool for improving genome assembly accuracy by incorporating information derived from an alternative assembly and paired-end Illumina reads from the same genome. The tool corrects insertion, deletion, substitution, and inversion errors and locates different inter- and intra-chromosomal rearrangement errors. NucMerge was compared to two existing alternatives, namely Metassembler and GAM-NGS.ConclusionsThe benchmarking results show that NucMerge has generally better performance than the other tools tested, providing accuracy improvement of more assemblies. NucMerge is freely available at https://github.com/uio-bmi/NucMerge under the MPL license.

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The Oxford Handbook of the Auditory Brainstem

10.1093/oxfordhb/9780190849061.001.0001 ◽

2018 ◽

Cited By ~ 1

Keyword(s):

Current Knowledge ◽

Auditory Pathway ◽

Auditory Brainstem ◽

Auditory Midbrain ◽

Current State ◽

Neuronal Mechanisms ◽

Maladaptive Plasticity ◽

And Function ◽

Auditory Field

The Oxford Handbook of the Auditory Brainstem provides an in-depth reference to the organization and function of ascending and descending auditory pathways in the mammalian brainstem. Individual chapters are organized along the auditory pathway, beginning with the cochlea and ending with the auditory midbrain. Each chapter provides an introduction to the respective area and summarizes our current knowledge before discussing the disputes and challenges that the field currently faces.The handbook emphasizes the numerous forms of plasticity that are increasingly observed in many areas of the auditory brainstem. Several chapters focus on neuronal modulation of function and plasticity on the synaptic, neuronal, and circuit level, especially during development, aging, and following peripheral hearing loss. In addition, the book addresses the role of trauma-induced maladaptive plasticity with respect to its contribution in generating central hearing dysfunction, such as hyperacusis and tinnitus.The book is intended for students and postdoctoral fellows starting in the auditory field and for researchers of related fields who wish to get an authoritative and up-to-date summary of the current state of auditory brainstem research. For clinical practitioners in audiology, otolaryngology, and neurology, the book is a valuable resource of information about the neuronal mechanisms that are currently discussed as major candidates for the generation of central hearing dysfunction.

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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise

10.1101/2019.12.19.882399 ◽

2019 ◽

Cited By ~ 5

Author(s):

Valentina Peona ◽

Mozes P.K. Blom ◽

Luohao Xu ◽

Reto Burri ◽

Shawn Sullivan ◽

...

Keyword(s):

Dark Matter ◽

Genome Assembly ◽

Sex Chromosome ◽

De Novo ◽

Model Organism ◽

Technology Choice ◽

High Quality ◽

Sequencing Technologies ◽

Downstream Analysis ◽

Genome Assemblies

AbstractGenome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies have opened up a whole new world of genomic biodiversity. Although these technologies generate high-quality genome assemblies, there are still genomic regions difficult to assemble, like repetitive elements and GC-rich regions (genomic “dark matter”). In this study, we compare the efficiency of currently used sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter starting from the same sample. By adopting different de-novo assembly strategies, we were able to compare each individual draft assembly to a curated multiplatform one and identify the nature of the previously missing dark matter with a particular focus on transposable elements, multi-copy MHC genes, and GC-rich regions. Thanks to this multiplatform approach, we demonstrate the feasibility of producing a high-quality chromosome-level assembly for a non-model organism (paradise crow) for which only suboptimal samples are available. Our approach was able to reconstruct complex chromosomes like the repeat-rich W sex chromosome and several GC-rich microchromosomes. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects around the completeness of both the coding and non-coding parts of the genomes.

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Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

10.21203/rs.3.rs-712747/v1 ◽

2021 ◽

Author(s):

Arang Rhie ◽

Ann Mc Cartney ◽

Kishwar Shafin ◽

Michael Alonge ◽

Andrey Bzikadze ◽

...

Keyword(s):

Genome Assembly ◽

Tandem Repeats ◽

Hydatidiform Mole ◽

Segmental Duplications ◽

Sequencing Technologies ◽

Oxford Nanopore ◽

Human Genome Assembly ◽

Long Read ◽

Genome Assemblies ◽

Oxford Nanopore Technologies

Abstract Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first Telomere-to-Telomere (T2T) human genome assembly, which resolves complex segmental duplications and large tandem repeats, including centromeric satellite arrays in a complete hydatidiform mole (CHM13). Though derived from highly accurate sequencing, evaluation revealed that the initial T2T draft assembly had evidence of small errors and structural misassemblies. To correct these errors, we designed a novel repeat-aware polishing strategy that made accurate assembly corrections in large repeats without overcorrection, ultimately fixing 51% of the existing errors and improving the assembly QV to 73.9. By comparing our results to standard automated polishing tools, we outline common polishing errors and offer practical suggestions for genome projects with limited resources. We also show how sequencing biases in both PacBio HiFi and Oxford Nanopore Technologies reads cause signature assembly errors that can be corrected with a diverse panel of sequencing technologies

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An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

10.1101/060921 ◽

2016 ◽

Cited By ~ 5

Author(s):

Ole K. Tørresen ◽

Bastiaan Star ◽

Sissel Jentoft ◽

William B. Reinar ◽

Harald Grove ◽

...

Keyword(s):

Genome Assembly ◽

Gadus Morhua ◽

Tandem Repeats ◽

Atlantic Cod ◽

Genomic Variation ◽

Promoter Regions ◽

Sequencing Technologies ◽

Combining Data ◽

Genome Assemblies ◽

Multiple Assembly

AbstractBackground: The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies.Results: By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21 % of the TRs across the assembly, 19 % in the promoter regions and 12 % in the coding sequences are heterozygous in the sequenced individual.Conclusions: The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.

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Composition and Function of Chicken Gut Microbiota

Animals ◽

10.3390/ani10010103 ◽

2020 ◽

Vol 10 (1) ◽

pp. 103 ◽

Cited By ~ 11

Author(s):

Ivan Rychlik

Keyword(s):

Gut Microbiota ◽

Current Knowledge ◽

Rapid Development ◽

Specific Model ◽

Sequencing Technologies ◽

Chicken Gut Microbiota ◽

And Function ◽

Experimental Group ◽

Intended Use

Studies analyzing the composition of gut microbiota are quite common at present, mainly due to the rapid development of DNA sequencing technologies within the last decade. This is valid also for chickens and their gut microbiota. However, chickens represent a specific model for host–microbiota interactions since contact between parents and offspring has been completely interrupted in domesticated chickens. Nearly all studies describe microbiota of chicks from hatcheries and these chickens are considered as references and controls. In reality, such chickens represent an extreme experimental group since control chicks should be, by nature, hatched in nests in contact with the parent hen. Not properly realising this fact and utilising only 16S rRNA sequencing results means that many conclusions are of questionable biological relevance. The specifics of chicken-related gut microbiota are therefore stressed in this review together with current knowledge of the biological role of selected microbiota members. These microbiota members are then evaluated for their intended use as a form of next-generation probiotics.

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Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution

Nature Communications ◽

10.1038/s41467-021-24573-z ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Yoichiro Nakatani ◽

Prashant Shingate ◽

Vydianathan Ravi ◽

Nisha E. Pillai ◽

Aravind Prasad ◽

...

Keyword(s):

Evolutionary History ◽

Gene Loss ◽

De Novo ◽

Genome Structure ◽

Origin And Evolution ◽

Long Read ◽

History Of ◽

And Function ◽

Genome Assemblies ◽

Key Questions

AbstractAncient polyploidization events have had a lasting impact on vertebrate genome structure, organization and function. Some key questions regarding the number of ancient polyploidization events and their timing in relation to the cyclostome-gnathostome divergence have remained contentious. Here we generate de novo long-read-based chromosome-scale genome assemblies for the Japanese lamprey and elephant shark. Using these and other representative genomes and developing algorithms for the probabilistic macrosynteny model, we reconstruct high-resolution proto-vertebrate, proto-cyclostome and proto-gnathostome genomes. Our reconstructions resolve key questions regarding the early evolutionary history of vertebrates. First, cyclostomes diverged from the lineage leading to gnathostomes after a shared tetraploidization (1R) but before a gnathostome-specific tetraploidization (2R). Second, the cyclostome lineage experienced an additional hexaploidization. Third, 2R in the gnathostome lineage was an allotetraploidization event, and biased gene loss from one of the subgenomes shaped the gnathostome genome by giving rise to remarkably conserved microchromosomes. Thus, our reconstructions reveal the major evolutionary events and offer new insights into the origin and evolution of vertebrate genomes.

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A Chromosome-Scale Assembly of the En ormous (32 Gb) Axolotl Genome

10.1101/373548 ◽

2018 ◽

Cited By ~ 3

Author(s):

Jeramiah J. Smith ◽

Nataliya Timoshevskaya ◽

Vladimir A. Timoshevskiy ◽

Melissa C. Keinath ◽

Drew Hardy ◽

...

Keyword(s):

Large Scale ◽

Genome Structure ◽

Large Deletion ◽

Ambystoma Mexicanum ◽

Biological Research ◽

Genome Wide ◽

Genetic Stocks ◽

Gene Structures ◽

And Function ◽

Genome Assemblies

ABSTRACTThe axolotl (Ambystoma mexicanum) provides critical models for studying regeneration, evolution and development. However, its large genome (~32 gigabases) presents a formidable barrier to genetic analyses. Recent efforts have yielded genome assemblies consisting of thousands of unordered scaffolds that resolve gene structures, but do not yet permit large scale analyses of genome structure and function. We adapted an established mapping approach to leverage dense SNP typing information and for the first time assemble the axolotl genome into 14 chromosomes. Moreover, we used fluorescence in situ hybridization to verify the structure of these 14 scaffolds and assign each to its corresponding physical chromosome. This new assembly covers 27.3 gigabases and encompasses 94% of annotated gene models on chromosomal scaffolds. We show the assembly’s utility by resolving genome-wide orthologies between the axolotl and other vertebrates, identifying the footprints of historical introgression events that occurred during the development of axolotl genetic stocks, and precisely mapping several phenotypes including a large deletion underlying the cardiac mutant. This chromosome-scale assembly will greatly facilitate studies of the axolotl in biological research.

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Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny

10.1101/2020.02.04.934711 ◽

2020 ◽

Cited By ~ 2

Author(s):

Julian Catchen ◽

Angel Amores ◽

Susan Bassham

Keyword(s):

Genetic Map ◽

Reference Genome ◽

Genome Structure ◽

Orthologous Gene ◽

Genetic Maps ◽

Conserved Synteny ◽

Sequencing Technologies ◽

Sequencing Library ◽

Tool Set ◽

And Function

AbstractThe pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead such research. Fortunately, integration of additional, independent streams of information, such as a genetic map – particularly a marker-dense map from RADseq, for example – and conserved orthologous gene order from related taxa can be used to scaffold together unlinked, disordered fragments and to restructure a reference genome where it is incorrectly joined. We present a tool set for automating these processes, one that additionally tracks any changes to the assembly and to the genetic map, and which allows the user to scrutinize these changes with the help of web-based, graphical visualizations. Chromonomer takes a user-defined reference genome, a map of genetic markers, and, optionally, conserved synteny information to construct an improved reference genome of chromosome models: a “chromonome”. We demonstrate Chromonomer’s performance on genome assemblies and genetic maps that have disparate characteristics and levels of quality.

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Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401485 ◽

2020 ◽

Vol 10 (11) ◽

pp. 4115-4128 ◽

Cited By ~ 1

Author(s):

Julian Catchen ◽

Angel Amores ◽

Susan Bassham

Keyword(s):

Genetic Map ◽

Reference Genome ◽

Genome Structure ◽

Orthologous Gene ◽

Genetic Maps ◽

Conserved Synteny ◽

Sequencing Technologies ◽

Sequencing Library ◽

Tool Set ◽

And Function

The pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead this research. Fortunately, integration of additional, independent streams of information, such as a marker-dense genetic map and conserved orthologous gene order from related taxa, can be used to scaffold together unlinked, disordered fragments and to restructure a reference genome where it is incorrectly joined. We present a tool set for automating these processes, one that additionally tracks any changes to the assembly and to the genetic map, and which allows the user to scrutinize these changes with the help of web-based, graphical visualizations. Chromonomer takes a user-defined reference genome, a map of genetic markers, and, optionally, conserved synteny information to construct an improved reference genome of chromosome models: a “chromonome”. We demonstrate Chromonomer’s performance on genome assemblies and genetic maps that have disparate characteristics and levels of quality.

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