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 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 Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Jaewon Lim ◽  
Hong-Tae Park ◽  
Seyoung Ko ◽  
Hyun-Eui Park ◽  
Gyumin Lee ◽  
...  
Keyword(s):  
Mycobacterium Avium ◽  
Phenotypic Diversity ◽  
Control Strategies ◽  
Genomic Diversity ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Genomic Features ◽  
Phenotypic Differences ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
Type Strains

AbstractMycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits.

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 Consistent sex ratio bias of individual female dragon lizards

2006 ◽  
Vol 2 (4) ◽  
pp. 569-572 ◽  
Author(s):  
Tobias Uller ◽  
Beth Mott ◽  
Gaetano Odierna ◽  
Mats Olsson
Keyword(s):  
Genetic Variation ◽  
Sex Ratio ◽  
Incubation Temperature ◽  
Sex Ratios ◽  
Phenotypic Traits ◽  
Female Size ◽  
Offspring Sex Ratio ◽  
Phenotypic Differences ◽  
Sex Ratio Bias ◽  
Offspring Sex

Sex ratio evolution relies on genetic variation in either the phenotypic traits that influence sex ratios or sex-determining mechanisms. However, consistent variation among females in offspring sex ratio is rarely investigated. Here, we show that female painted dragons ( Ctenophorus pictus ) have highly repeatable sex ratios among clutches within years. A consistent effect of female identity could represent stable phenotypic differences among females or genetic variation in sex-determining mechanisms. Sex ratios were not correlated with female size, body condition or coloration. Furthermore, sex ratios were not influenced by incubation temperature. However, the variation among females resulted in female-biased mean population sex ratios at hatching both within and among years.

scholarly journals Comparative Transcriptomic Approach To Investigate Differences in Wine Yeast Physiology and Metabolism during Fermentation

2009 ◽  
Vol 75 (20) ◽  
pp. 6600-6612 ◽  
Author(s):  
Debra Rossouw ◽  
Roberto Olivares-Hernandes ◽  
Jens Nielsen ◽  
Florian F. Bauer
Keyword(s):  
Stress Responses ◽  
Metabolic Regulation ◽  
Wine Yeast ◽  
Molecular Networks ◽  
Comparative Approach ◽  
Phenotypic Traits ◽  
Phenotypic Differences ◽  
Yeast Strains ◽  
Industrial Strains ◽  
Different Strains

ABSTRACT Commercial wine yeast strains of the species Saccharomyces cerevisiae have been selected to satisfy many different, and sometimes highly specific, oenological requirements. As a consequence, more than 200 different strains with significantly diverging phenotypic traits are produced globally. This genetic resource has been rather neglected by the scientific community because industrial strains are less easily manipulated than the limited number of laboratory strains that have been successfully employed to investigate fundamental aspects of cellular biology. However, laboratory strains are unsuitable for the study of many phenotypes that are of significant scientific and industrial interest. Here, we investigate whether a comparative transcriptomics and phenomics approach, based on the analysis of five phenotypically diverging industrial wine yeast strains, can provide insights into the molecular networks that are responsible for the expression of such phenotypes. For this purpose, some oenologically relevant phenotypes, including resistance to various stresses, cell wall properties, and metabolite production of these strains were evaluated and aligned with transcriptomic data collected during alcoholic fermentation. The data reveal significant differences in gene regulation between the five strains. While the genetic complexity underlying the various successive stress responses in a dynamic system such as wine fermentation reveals the limits of the approach, many of the relevant differences in gene expression can be linked to specific phenotypic differences between the strains. This is, in particular, the case for many aspects of metabolic regulation. The comparative approach therefore opens new possibilities to investigate complex phenotypic traits on a molecular level.

Egg size, fecundity, and development rate of two introduced New Zealand chinook salmon (Oncorhynchus tshawytscha) populations

1998 ◽  
Vol 55 (8) ◽  
pp. 1946-1953 ◽  
Author(s):  
Michael T Kinnison ◽  
Martin J Unwin ◽  
William K Hershberger ◽  
Thomas P Quinn
Keyword(s):  
New Zealand ◽  
Chinook Salmon ◽  
Egg Size ◽  
Oncorhynchus Tshawytscha ◽  
Gonadosomatic Index ◽  
Phenotypic Traits ◽  
Egg Weight ◽  
Phenotypic Differences ◽  
Development Rates ◽  
Temperature Records

Interpopulation differences in several adult phenotypic traits suggest that New Zealand (NZ) chinook salmon (Oncorhynchus tshawytscha) are evolving into distinct populations. To further investigate this hypothesis, we compared egg sizes, fecundities, and early development rates of chinook from two NZ streams. The two NZ study populations differed in size-adjusted egg weight and gonadosomatic index, but not in size-adjusted fecundity. Egg weight, fecundity, and gonadosomatic index values for both NZ populations were different than values for chinook from Battle Creek, California, the population regarded as the ancestral NZ stock. In contrast, there was little evidence of divergence in juvenile development. Time to hatching did not differ between the two NZ study populations and heritability estimates were small with large standard errors. Evidence of a small difference in alevin growth rate may have represented an effect of yolk conversion mechanics related to egg size. Despite the similarity in development rates under shared conditions, modeling based on temperature records suggests that emergence dates in the two NZ streams may differ by 4-6 weeks, yielding significant phenotypic differences.

scholarly journals Malus sieversii: A Diverse Central Asian Apple Species in the USDA-ARS National Plant Germplasm System

HortScience ◽  
2013 ◽  
Vol 48 (12) ◽  
pp. 1440-1444 ◽  
Author(s):  
Gayle M. Volk ◽  
Adam D. Henk ◽  
Christopher M. Richards ◽  
Philip L. Forsline ◽  
C. Thomas Chao
Keyword(s):  
Single Gene ◽  
Phenotypic Trait ◽  
Phenotypic Traits ◽  
Gene Pools ◽  
Phenotypic Differences ◽  
Plant Germplasm ◽  
Malus Sieversii ◽  
Central Asian ◽  
National Plant Germplasm System ◽  
Anthocyanin Production

There are several Central Asian Malus species and varieties in the USDA-ARS National Plant Germplasm System (NPGS) apple collection. Malus sieversii is the most comprehensively collected species native to Central Asia. Other taxa such as M. sieversii var. kirghisorum, M. sieversii var. turkmenorum, M. pumila, and M. pumila var. niedzwetzkyana have primarily been donated to the collection by other institutions and arboreta. We sought to determine if genetic and/or phenotypic differences among the individuals that make up the gene pools of these taxa in the NPGS exhibit unique characteristics. Genetic data, based on microsatellite analyses, suggested that the diversity within each taxa is significantly greater than that among taxa. Trait data also revealed very few differences among taxa, the primary characteristic being the dark red fruit coloration and tinted flesh color of the accessions assigned to M. pumila var. niedzwetzkyana resulting from a known single-gene mutation in anthocyanin production. We found that M. sieversii is a highly diverse species with a range in genetic and phenotypic trait variation that includes the characteristics of the other Central Asian taxa of interest. We conclude that the gene pools that comprise the accessions within the NPGS Central Asian Malus collection are highly overlapping with respect to both phenotypic traits and genotypic characters.

scholarly journals Analysis of female song provides insight into the evolution of sex differences in a widely studied songbird

2020 ◽  
Author(s):  
Matthew R. Wilkins ◽  
Karan J. Odom ◽  
Lauryn Benedict ◽  
Rebecca J. Safran
Keyword(s):  
Sex Differences ◽  
Sexual Differentiation ◽  
Animal Communication ◽  
Phenotypic Traits ◽  
Phenotypic Differences ◽  
Female Song ◽  
Fitness Consequences ◽  
Song Production ◽  
Foundational Research ◽  
Patterns And Processes

ABSTRACTUnderstanding the patterns and processes related to sexual dimorphism and sex differences in diverse animal taxa is a foundational research topic in ecology and evolution. Within the realm of animal communication, studies have traditionally focused on male signals, assuming that female choice and male-male competition have promoted sex differences via elaboration of male traits, but selection on females also has the potential to drive sexual differentiation in signals. Here, we describe female song in barn swallows (Hirundo rustica erythrogaster) for the first time, report rates of female song production, and couple song data with plumage data to explore the relative degree to which sex differences in phenotypic traits are consistent with contemporary selection on males versus females. During previous intensive study of male song over two years, we opportunistically recorded songs for 15 females, with matched phenotypic and fitness data. We randomly selected 15 high-quality samples from our larger male dataset to test whether sex differences in song and plumage are more strongly associated with fledgling success for females or genetic paternity for males. Analyses included 35 potential sexual signals including 22 song parameters and 13 plumage traits. Outcomes indicate that: female songs were used in multiple contexts, restricted primarily to the beginning of the breeding season; song traits showed greater sexual differentiation than visual plumage traits; and trait correlations with reproductive success in females, rather than males, predicted sex-based differences in song and plumage. These results are consistent with phylogenetic studies showing that sex-based phenotypic differences are driven by changes in females, highlighting the potential role of female trait evolution in explaining patterns of sexual differentiation. To achieve a better understanding of sex differences and dimorphism, we require comprehensive studies that measure the same traits in males and females and their fitness consequences.

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 Decoupling the variances of heterosis and inbreeding effects is evidenced in yeast’s life-history and proteomic traits

2018 ◽  
Author(s):  
M. Petrizzelli ◽  
D. de Vienne ◽  
C. Dillmann
Keyword(s):  
Life History ◽  
Alcoholic Fermentation ◽  
Real Data ◽  
Diallel Cross ◽  
Hybrid Vigor ◽  
Phenotypic Traits ◽  
Phenotypic Differences ◽  
Clear Cut ◽  
Specific Effects ◽  
Common Parent

ABSTRACTHeterosis (hybrid vigor) and inbreeding depression, commonly considered as corollary phenomena, could nevertheless be decoupled under certain assumptions according to theoretical population genetics works. In order to explore this issue on real data, we analyzed the components of genetic variation in a population derived from a half-diallel cross between strains fromSaccharomyces cerevisiaeandS. uvarum, two related yeast species involved in alcoholic fermentation. A large number of phenotypic traits, either molecular (coming from quantitative proteomics) or related to fermentation and life-history, were measured during alcoholic fermentation. Because the parental strains were included in the design, we were able to distinguish between inbreeding effects, which measures phenotypic differences between inbred and hybrids, and heterosis, which measures phenotypic differences between a specific hybrid and the other hybrids sharing a common parent. The sources of phenotypic variation differed depending on the temperature, indicating the predominance of genotype by environment interactions. Decomposing the total genetic variance into variances of additive (intra- and inter-specific) effects, of inbreeding effects and of heterosis (intra- and inter-specific) effects, we showed that the distribution of variance components defined clear-cut groups of proteins and traits. Moreover, it was possible to cluster fermentation and life-history traits into most proteomic groups. Within groups, we observed positive, negative or null correlations between the variances of heterosis and inbreeding effects. To our knowledge, such a decoupling had never been experimentally demonstrated. This result suggests that, despite a common evolutionary history of individuals within a species, the different types of traits have been subject to different selective pressures.

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