scholarly journals Phenotyping in the era of genomics: MaTrics—a digital character matrix to document mammalian phenotypic traits

2021 ◽  
Author(s):  
Clara Stefen ◽  
Franziska Wagner ◽  
Marika Asztalos ◽  
Peter Giere ◽  
Peter Grobe ◽  
...  
Keyword(s):  
Mammalian Species ◽  
Data Repository ◽  
Phenotypic Traits ◽  
Museum Collections ◽  
Digital Form ◽  
Research Gaps ◽  
Online Resource ◽  
Structure Morphology ◽  
Character Matrix ◽  
Genome Assemblies

AbstractA new and uniquely structured matrix of mammalian phenotypes, MaTrics (Mammalian Traits for Comparative Genomics) in a digital form is presented. By focussing on mammalian species for which genome assemblies are available, MaTrics provides an interface between mammalogy and comparative genomics.MaTrics was developed within a project aimed to find genetic causes of phenotypic traits of mammals using Forward Genomics. This approach requires genomes and comprehensive and recorded information on homologous phenotypes that are coded as discrete categories in a matrix. MaTrics is an evolving online resource providing information on phenotypic traits in numeric code; traits are coded either as absent/present or with several states as multistate. The state record for each species is linked to at least one reference (e.g., literature, photographs, histological sections, CT scans, or museum specimens) and so MaTrics contributes to digitalization of museum collections. Currently, MaTrics covers 147 mammalian species and includes 231 characters related to structure, morphology, physiology, ecology, and ethology and available in a machine actionable NEXUS-format*. Filling MaTrics revealed substantial knowledge gaps, highlighting the need for phenotyping efforts. Studies based on selected data from MaTrics and using Forward Genomics identified associations between genes and certain phenotypes ranging from lifestyles (e.g., aquatic) to dietary specializations (e.g., herbivory, carnivory). These findings motivate the expansion of phenotyping in MaTrics by filling research gaps and by adding taxa and traits. Only databases like MaTrics will provide machine actionable information on phenotypic traits, an important limitation to genomics. MaTrics is available within the data repository Morph·D·Base (www.morphdbase.de).

scholarly journals Phenotyping in the era of genomics: MaTrics – a digital character matrix to document mammalian phenotypic traits coded numerically

2021 ◽  
Author(s):  
Clara Stefen ◽  
Franziska Wagner ◽  
Marika Asztalos ◽  
Peter Giere ◽  
Peter Grobe ◽  
...  
Keyword(s):  
Mammalian Species ◽  
Data Repository ◽  
Phenotypic Traits ◽  
Digital Form ◽  
Research Gaps ◽  
Phenotypic Differences ◽  
Data Links ◽  
Structure Morphology ◽  
Character Matrix ◽  
Genome Assemblies

AbstractA new and uniquely structured matrix of mammalian phenotypes, MaTrics (Mammalian Traits for Comparative Genomics) is presented in a digital form. By focussing on mammalian species for which genome assemblies are available, MaTrics provides an interface between mammalogy and comparative genomics.MaTrics was developed as part of a project to link phenotypic differences between mammals to differences in their genomes using Forward Genomics. Apart from genomes this approach requires information on homologous phenotypes that are numerically encoded (presence-absence; multistate character coding*) in a matrix. MaTrics provides these data, links them to at least one reference (e.g., literature, photographs, histological sections, CT-scans, or museum specimens) and makes them available in a machine actionable NEXUS-format. By making the data computer readable, MatTrics opens a new way for digitizing collections. Currently, MaTrics covers 147 mammalian species and includes 207 characters referring to structure, morphology, physiology, ecology and ethology. Researching these traits revealed substantial knowledge gaps, highlighting the need for substantial phenotyping efforts in the genomic era. Using the trait information documented in MaTrics, previous Forward Genomics screens identified changes in genes that are associated with various phenotypes, ranging from fully-aquatic lifestyle to dietary specializations. These results motivate the continuous expansion of phenotype information, both by filling research gaps or by adding additional taxa and traits. MaTrics is digitally available online within the data repository Morph·D·Base (www.morphdbase.de).

scholarly journals Shared Data Science Infrastructure for Genomics Data

2018 ◽  
Author(s):  
Hamid Bagher ◽  
Usha Muppiral ◽  
Andrew J Severin ◽  
Hridesh Rajan
Keyword(s):  
Data Science ◽  
Gene Annotation ◽  
Large Data ◽  
Biological Data ◽  
Genomic Research ◽  
Data Repository ◽  
Small Data ◽  
Data Repositories ◽  
Shared Data ◽  
Genome Assemblies

AbstractBackgroundCreating a computational infrastructure to analyze the wealth of information contained in data repositories that scales well is difficult due to significant barriers in organizing, extracting and analyzing relevant data. Shared Data Science Infrastructures like Boa can be used to more efficiently process and parse data contained in large data repositories. The main features of Boa are inspired from existing languages for data intensive computing and can easily integrate data from biological data repositories.ResultsHere, we present an implementation of Boa for Genomic research (BoaG) on a relatively small data repository: RefSeq’s 97,716 annotation (GFF) and assembly (FASTA) files and metadata. We used BoaG to query the entire RefSeq dataset and gain insight into the RefSeq genome assemblies and gene model annotations and show that assembly quality using the same assembler varies depending on species.ConclusionsIn order to keep pace with our ability to produce biological data, innovative methods are required. The Shared Data Science Infrastructure, BoaG, can provide greater access to researchers to efficiently explore data in ways previously not possible for anyone but the most well funded research groups. We demonstrate the efficiency of BoaG to explore the RefSeq database of genome assemblies and annotations to identify interesting features of gene annotation as a proof of concept for much larger datasets.

scholarly journals Chromosome-Level Genome Assemblies Expand Capabilities of Genomics for Conservation Biology

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1336
Author(s):  
Azamat Totikov ◽  
Andrey Tomarovsky ◽  
Dmitry Prokopov ◽  
Aliya Yakupova ◽  
Tatiana Bulyonkova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Conservation Biology ◽  
Threatened Species ◽  
Mammalian Species ◽  
Draft Genome ◽  
Chromosome Length ◽  
Chromosome Conformation ◽  
Genome Wide ◽  
Genome Assemblies ◽  
Chromosome Level

Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, genome assemblies of threatened species, when available, tend to be highly fragmented, represented by tens of thousands of scaffolds not assigned to chromosomal locations. The recent advent of high-throughput chromosome conformation capture (Hi-C) enables more contiguous assemblies containing scaffolds spanning the length of entire chromosomes for little additional cost. These inexpensive contiguous assemblies can be generated using Hi-C scaffolding of existing short-read draft assemblies, where N50 of the draft contigs is larger than 0.1% of the estimated genome size and can greatly improve analyses and facilitate visualization of genome-wide features including distribution of genetic diversity in markers along chromosomes or chromosome-length scaffolds. We compared distribution of genetic diversity along chromosomes of eight mammalian species, including six listed as threatened by IUCN, where both draft genome assemblies and newer chromosome-level assemblies were available. The chromosome-level assemblies showed marked improvement in localization and visualization of genetic diversity, especially where the distribution of low heterozygosity across the genomes of threatened species was not uniform.

scholarly journals Comparative analysis of corrected tiger genome provides clues to its neuronal evolution

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Parul Mittal ◽  
Shubham K. Jaiswal ◽  
Nagarjun Vijay ◽  
Rituja Saxena ◽  
Vineet K. Sharma
Keyword(s):  
Neuronal Development ◽  
Mammalian Species ◽  
Draft Genome ◽  
Evolutionary Analysis ◽  
Coding Region ◽  
Genetic Changes ◽  
Gene Sets ◽  
Development Processes ◽  
Neuronal Functions ◽  
Genome Assemblies

AbstractThe availability of completed and draft genome assemblies of tiger, leopard, and other felids provides an opportunity to gain comparative insights on their unique evolutionary adaptations. However, genome-wide comparative analyses are susceptible to errors in genome sequences and thus require accurate genome assemblies for reliable evolutionary insights. In this study, while analyzing the tiger genome, we found almost one million erroneous substitutions in the coding and non-coding region of the genome affecting 4,472 genes, hence, biasing the current understanding of tiger evolution. Moreover, these errors produced several misleading observations in previous studies. Thus, to gain insights into the tiger evolution, we corrected the erroneous bases in the genome assembly and gene set of tiger using ‘SeqBug’ approach developed in this study. We sequenced the first Bengal tiger genome and transcriptome from India to validate these corrections. A comprehensive evolutionary analysis was performed using 10,920 orthologs from nine mammalian species including the corrected gene sets of tiger and leopard and using five different methods at three hierarchical levels, i.e. felids, Panthera, and tiger. The unique genetic changes in tiger revealed that the genes showing signatures of adaptation in tiger were enriched in development and neuronal functioning. Specifically, the genes belonging to the Notch signalling pathway, which is among the most conserved pathways involved in embryonic and neuronal development, were found to have significantly diverged in tiger in comparison to the other mammals. Our findings suggest the role of adaptive evolution in neuronal functions and development processes, which correlates well with the presence of exceptional traits such as sensory perception, strong neuro-muscular coordination, and hypercarnivorous behaviour in tiger.

scholarly journals Mapping material culture: exploring the interface between museum artefacts and their geographical context

2010 ◽  
Vol 32 (1) ◽  
pp. 73-93 ◽  
Author(s):  
Trevor Cowie ◽  
Peter McKeague
Keyword(s):  
Material Culture ◽  
Royal Commission ◽  
Museum Collections ◽  
Online Resource ◽  
Historical Monuments ◽  
National Museums ◽  
Geographical Context

This paper describes the results of an exploratory project undertaken by National Museums Scotland and the Royal Commission on the Ancient and Historical Monuments of Scotland to enhance their respective databases through sharing information relating to their respective areas of expertise. The resulting MAGI (Museum Artefact Geographical Interface) project highlighted the huge potential for creating an online resource to re-connect objects in museum collections with the locations of their discovery.

scholarly journals Digital levendegørelse - 1700-tals faktionsleg på Facebook

1970 ◽  
pp. 60
Author(s):  
Mette Boritz ◽  
Mia Ramsing Jensen ◽  
Charlotte S.H. Jensen ◽  
Ida Lund-Andersen
Keyword(s):  
Cultural History ◽  
Young Women ◽  
Young Girl ◽  
Living History ◽  
National Museum ◽  
Museum Collections ◽  
Digital Form ◽  
Target Groups ◽  
Women And Girls ◽  
Day By Day

Living history is becoming increasingly popular within the museum world, and is found in many different forms. In this article, we wish to introduce the term ”digital living history” and consider what happens when a decision is made to generate living history in digital form in conjunction with cultural history and museum collections, and what kinds of potential and which challenges are involved in such a process. At the same time, the article will consider to what extent ”digital living history” can be used to engage in a dialogue with target groups not often encountered in museum contexts. The article is based on a project about a fictive young girl named Ida Charlotte, who posted an account of her thoughts and experiences on Facebook, as these unfolded day by day over a six- month period in 1772. This project, which was targeted at young women and girls, was run by the National Museum of Denmark in 2010, and was followed by a series of surveys that are examined in this article. 

scholarly journals Comparative analysis of corrected tiger genome provides clues to their neuronal evolution

2019 ◽  
Author(s):  
Parul Mittal ◽  
Shubham Jaiswal ◽  
Nagarjun Vijay ◽  
Rituja Saxena ◽  
Vineet K. Sharma
Keyword(s):  
Neuronal Development ◽  
Mammalian Species ◽  
Draft Genome ◽  
Evolutionary Analysis ◽  
Coding Region ◽  
Genetic Changes ◽  
Gene Sets ◽  
Development Processes ◽  
Neuronal Functions ◽  
Genome Assemblies

AbstractThe availability of completed and draft genome assemblies of tiger, leopard, and other felids provides an opportunity to gain comparative insights on their unique evolutionary adaptations. However, genome-wide comparative analyses are very sensitive to errors in genome sequences and thus require accurate genomic assemblies for reliable evolutionary insights. In this study, while analyzing the tiger genome, we found almost one million erroneous substitutions in the coding and non-coding region of the genome affecting 4,472 genes, hence, biasing the current understanding of tiger evolution. Moreover, these errors produced several misleading observations in previous studies. Thus, to gain insights into the tiger evolution, we corrected the erroneous bases in the genome assembly and gene set of tiger, which was also validated by resequencing of a Bengal tiger genome and transcriptome. A comprehensive evolutionary analysis was performed using 10,920 orthologs from nine mammalian species including the corrected gene sets of tiger and leopard, and using five different methods at three hierarchical levels i.e. felids, Panthera, and tiger. The unique genetic changes in tiger revealed that the genes showing the signatures of adaptation in tiger were enriched in development and neuronal functioning. Specifically, the genes belonging to Notch signalling pathway, which is among the most conserved pathways involved in embryonic and neuronal development, were found to be significantly diverged in tiger in comparison to the other mammals. Our findings suggest the role of adaptive evolution in neuronal functions and development processes, which correlates well with the presence of exceptional traits such as sensory perception, strong neuro-muscular coordination, and hypercarnivorous behavior in tiger.

scholarly journals The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation

2016 ◽  
Author(s):  
John C. Schwartz ◽  
Mark S. Gibson ◽  
Dorothea Heimeier ◽  
Sergey Koren ◽  
Adam M. Phillippy ◽  
...  
Keyword(s):  
Natural Killer ◽  
Nk Cell ◽  
Balancing Selection ◽  
Mammalian Species ◽  
Draft Genome ◽  
Allelic Polymorphism ◽  
High Quality ◽  
Lectin Receptors ◽  
Differential Outcomes ◽  
Genome Assemblies

ABSTRACTNatural killer (NK) cells are a diverse population of lymphocytes with a range of biological roles including essential immune functions. NK cell diversity is created by the differential expression of cell surface receptors which modulate activation and function, including multiple subfamilies of C-type lectin receptors encoded within the NK gene complex (NKC). Little is known about the gene content of the NKC beyond rodent and primate lineages, other than it appears to be extremely variable between mammalian groups. We compared the NKC structure between mammalian species using new high quality draft genome assemblies for cattle and goat, re-annotated sheep, pig and horse genome assemblies and the published human, rat and mouse lemur NKC. The major NKC genes are largely in syntenic positions in all eight species, with significant independent expansions and deletions between species, allowing us to present a model for NKC evolution during mammalian radiation. The ruminant species, cattle and goats, have independently evolved a second KLRC locus flanked by KLRA and KLRJ and a novel KLRH-like gene has acquired an activating tail. This novel gene has duplicated several times within cattle, while other activating receptor genes have been selectively disrupted. Targeted genome enrichment in cattle identified varying levels of allelic polymorphism between these NKC genes concentrated in the predicted extracellular ligand binding domains. This novel recombination and allelic polymorphism is consistent with NKC evolution under balancing selection, suggesting this diversity influences individual immune responses and may impact on differential outcomes of pathogen infection and vaccination.

scholarly journals The Genomes of the Livebearing Fish Species Poeciliopsis retropinna and Poeciliopsis turrubarensis Reflect Their Different Reproductive Strategies

2020 ◽  
Vol 37 (5) ◽  
pp. 1376-1386
Author(s):  
Henri van Kruistum ◽  
Michael W Guernsey ◽  
Julie C Baker ◽  
Susan L Kloet ◽  
Martien A M Groenen ◽  
...  
Keyword(s):  
Positive Selection ◽  
Mammalian Species ◽  
Rapid Evolution ◽  
Gene Duplications ◽  
Genome Wide ◽  
Single Instance ◽  
A Genome ◽  
Livebearing Fish ◽  
Genome Assemblies ◽  
Genome Wide Scan

Abstract The evolution of a placenta is predicted to be accompanied by rapid evolution of genes involved in processes that regulate mother–offspring interactions during pregnancy, such as placenta formation, embryonic development, and nutrient transfer to offspring. However, these predictions have only been tested in mammalian species, where only a single instance of placenta evolution has occurred. In this light, the genus Poeciliopsis is a particularly interesting model for placenta evolution, because in this genus a placenta has evolved independently from the mammalian placenta. Here, we present and compare genome assemblies of two species of the livebearing fish genus Poeciliopsis (family Poeciliidae) that differ in their reproductive strategy: Poeciliopsis retropinna which has a well-developed complex placenta and P. turrubarensis which lacks a placenta. We applied different assembly strategies for each species: PacBio sequencing for P. retropinna (622-Mb assembly, scaffold N50 of 21.6 Mb) and 10× Genomics Chromium technology for P. turrubarensis (597-Mb assembly, scaffold N50 of 4.2 Mb). Using the high contiguity of these genome assemblies and near-completeness of gene annotations to our advantage, we searched for gene duplications and performed a genome-wide scan for genes evolving under positive selection. We find rapid evolution in major parts of several molecular pathways involved in parent–offspring interaction in P. retropinna, both in the form of gene duplications as well as positive selection. We conclude that the evolution of the placenta in the genus Poeciliopsis is accompanied by rapid evolution of genes involved in similar genomic pathways as found in mammals.

scholarly journals Long-read sequencing improves assembly of Trichinella genomes 10-fold, revealing substantial synteny between lineages diverged over 7 million years

Parasitology ◽  
2017 ◽  
Vol 144 (10) ◽  
pp. 1302-1315 ◽  
Author(s):  
PETER C. THOMPSON ◽  
DANTE S. ZARLENGA ◽  
MING-YUAN LIU ◽  
BENJAMIN M. ROSENTHAL
Keyword(s):  
Reference Genome ◽  
Trichinella Spiralis ◽  
Evolutionary Genetics ◽  
Invasion Biology ◽  
Phenotypic Traits ◽  
Draft Assembly ◽  
Long Read ◽  
Genome Assemblies ◽  
First Time ◽  
Insight Into

SUMMARYGenome assemblies can form the basis of comparative analyses fostering insight into the evolutionary genetics of a parasite's pathogenicity, host–pathogen interactions, environmental constraints and invasion biology; however, the length and complexity of many parasite genomes has hampered the development of well-resolved assemblies. In order to improve Trichinella genome assemblies, the genome of the sylvatic encapsulated species Trichinella murrelli was sequenced using third-generation, long-read technology and, using syntenic comparisons, scaffolded to a reference genome assembly of Trichinella spiralis, markedly improving both. A high-quality draft assembly for T. murrelli was achieved that totalled 63·2 Mbp, half of which was condensed into 26 contigs each longer than 571 000 bp. When compared with previous assemblies for parasites in the genus, ours required 10-fold fewer contigs, which were five times longer, on average. Better assembly across repetitive regions also enabled resolution of 8 Mbp of previously indeterminate sequence. Furthermore, syntenic comparisons identified widespread scaffold misassemblies in the T. spiralis reference genome. The two new assemblies, organized for the first time into three chromosomal scaffolds, will be valuable resources for future studies linking phenotypic traits within each species to their underlying genetic bases.

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