Targeted Genotyping of a Whole-Gene Repertoire by an Ultrahigh-Multiplex and Flexible HD-Marker Approach

AbstractTepary bean (Phaseolus acutifolis A. Gray), native to the Sonoran Desert, is highly adapted to heat and drought. It is a sister species of common bean (Phaseolus vulgaris L.), the most important legume protein source for direct human consumption, and whose production is threatened by climate change. Here, we report on the tepary genome including exploration of possible mechanisms for resilience to moderate heat stress and a reduced disease resistance gene repertoire, consistent with adaptation to arid and hot environments. Extensive collinearity and shared gene content among these Phaseolus species will facilitate engineering climate adaptation in common bean, a key food security crop, and accelerate tepary bean improvement.

Download Full-text

A Deadly Cargo: Gene Repertoire of Cytotoxic Effector Proteins in the Camelidae

Genes ◽

10.3390/genes12020304 ◽

2021 ◽

Vol 12 (2) ◽

pp. 304

Author(s):

Ján Futas ◽

Jan Oppelt ◽

Pamela Anna Burger ◽

Petr Horin

Keyword(s):

Cytotoxic T Cells ◽

Effector Proteins ◽

Target Cells ◽

Gene Repertoire ◽

Interspecific Differences ◽

Genes Encoding ◽

Bactrian Camels ◽

Pore Forming Proteins ◽

Sequence Similarities ◽

Cytotoxic Effector

Cytotoxic T cells and natural killer cells can kill target cells based on their expression and release of perforin, granulysin, and granzymes. Genes encoding these molecules have been only poorly annotated in camelids. Based on bioinformatic analyses of genomic resources, sequences corresponding to perforin, granulysin, and granzymes were identified in genomes of camelids and related ungulate species, and annotation of the corresponding genes was performed. A phylogenetic tree was constructed to study evolutionary relationships between the species analyzed. Re-sequencing of all genes in a panel of 10 dromedaries and 10 domestic Bactrian camels allowed analyzing their individual genetic polymorphisms. The data showed that all extant Old World camelids possess functional genes for two pore-forming proteins (PRF1, GNLY) and six granzymes (GZMA, GZMB, GZMH, GZMK, GZMM, and GZMO). All these genes were represented as single copies in the genome except the GZMH gene exhibiting interspecific differences in the number of loci. High protein sequence similarities with other camelid and ungulate species were observed for GZMK and GZMM. The protein variability in dromedaries and Bactrian camels was rather low, except for GNLY and chymotrypsin-like granzymes (GZMB, GZMH).

Download Full-text

The Giardia lamblia vsp gene repertoire: characteristics, genomic organization, and evolution

BMC Genomics ◽

10.1186/1471-2164-11-424 ◽

2010 ◽

Vol 11 (1) ◽

pp. 424 ◽

Cited By ~ 50

Author(s):

Rodney D Adam ◽

Anuranjini Nigam ◽

Vishwas Seshadri ◽

Craig A Martens ◽

Gregory A Farneth ◽

...

Keyword(s):

Giardia Lamblia ◽

Genomic Organization ◽

Gene Repertoire

Download Full-text

Evolutionary Analysis of Cystatins of Early-Emerging Metazoans Reveals a Novel Subtype in Parasitic Cnidarians

Biology ◽

10.3390/biology10020110 ◽

2021 ◽

Vol 10 (2) ◽

pp. 110

Author(s):

Pavla Bartošová-Sojková ◽

Jiří Kyslík ◽

Gema Alama-Bermejo ◽

Ashlie Hartigan ◽

Stephen D. Atkinson ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Gene Organization ◽

Gene Repertoire ◽

Evolutionary Analysis ◽

Ancestral Gene ◽

Protein Architecture ◽

Basal Metazoan ◽

Cystatin Gene ◽

Evolutionary Aspects

The evolutionary aspects of cystatins are greatly underexplored in early-emerging metazoans. Thus, we surveyed the gene organization, protein architecture, and phylogeny of cystatin homologues mined from 110 genomes and the transcriptomes of 58 basal metazoan species, encompassing free-living and parasite taxa of Porifera, Placozoa, Cnidaria (including Myxozoa), and Ctenophora. We found that the cystatin gene repertoire significantly differs among phyla, with stefins present in most of the investigated lineages but with type 2 cystatins missing in several basal metazoan groups. Similar to liver and intestinal flukes, myxozoan parasites possess atypical stefins with chimeric structure that combine motifs of classical stefins and type 2 cystatins. Other early metazoan taxa regardless of lifestyle have only the classical representation of cystatins and lack multi-domain ones. Our comprehensive phylogenetic analyses revealed that stefins and type 2 cystatins clustered into taxonomically defined clades with multiple independent paralogous groups, which probably arose due to gene duplications. The stefin clade split between the subclades of classical stefins and the atypical stefins of myxozoans and flukes. Atypical stefins represent key evolutionary innovations of the two parasite groups for which their origin might have been linked with ancestral gene chimerization, obligate parasitism, life cycle complexity, genome reduction, and host immunity.

Download Full-text

Evolution of the tyrosinase gene family in bivalve molluscs: Independent expansion of the mantle gene repertoire

Acta Biomaterialia ◽

10.1016/j.actbio.2014.03.031 ◽

2014 ◽

Vol 10 (9) ◽

pp. 3855-3865 ◽

Cited By ~ 43

Author(s):

Felipe Aguilera ◽

Carmel McDougall ◽

Bernard M. Degnan

Keyword(s):

Gene Family ◽

Gene Repertoire ◽

Bivalve Molluscs ◽

Tyrosinase Gene ◽

Independent Expansion

Download Full-text

The mutational landscape of human olfactory G protein-coupled receptors

BMC Biology ◽

10.1186/s12915-021-00962-0 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Ramón Cierco Jimenez ◽

Nil Casajuana-Martin ◽

Adrián García-Recio ◽

Lidia Alcántara ◽

Leonardo Pardo ◽

...

Keyword(s):

G Protein ◽

Olfactory Receptors ◽

Activation Mechanism ◽

Gene Repertoire ◽

Structural Level ◽

Ongoing Research ◽

Wide Range ◽

Natural Variants ◽

The Impact ◽

G Protein Coupled

Abstract Background Olfactory receptors (ORs) constitute a large family of sensory proteins that enable us to recognize a wide range of chemical volatiles in the environment. By contrast to the extensive information about human olfactory thresholds for thousands of odorants, studies of the genetic influence on olfaction are limited to a few examples. To annotate on a broad scale the impact of mutations at the structural level, here we analyzed a compendium of 119,069 natural variants in human ORs collected from the public domain. Results OR mutations were categorized depending on their genomic and protein contexts, as well as their frequency of occurrence in several human populations. Functional interpretation of the natural changes was estimated from the increasing knowledge of the structure and function of the G protein-coupled receptor (GPCR) family, to which ORs belong. Our analysis reveals an extraordinary diversity of natural variations in the olfactory gene repertoire between individuals and populations, with a significant number of changes occurring at the structurally conserved regions. A particular attention is paid to mutations in positions linked to the conserved GPCR activation mechanism that could imply phenotypic variation in the olfactory perception. An interactive web application (hORMdb, Human Olfactory Receptor Mutation Database) was developed for the management and visualization of this mutational dataset. Conclusion We performed topological annotations and population analysis of natural variants of human olfactory receptors and provide an interactive application to explore human OR mutation data. We envisage that the utility of this information will increase as the amount of available pharmacological data for these receptors grow. This effort, together with ongoing research in the study of genetic changes in other sensory receptors could shape an emerging sensegenomics field of knowledge, which should be considered by food and cosmetic consumer product manufacturers for the benefit of the general population.

Download Full-text

The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia

BMC Biology ◽

10.1186/s12915-020-00943-9 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Hao Song ◽

Ximing Guo ◽

Lina Sun ◽

Qianghui Wang ◽

Fengming Han ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Tandem Duplication ◽

Expression Patterns ◽

Hard Clam ◽

Gene Repertoire ◽

Single Chromosome ◽

Inhibitors Of Apoptosis ◽

History Of ◽

Evolutionary Success

Abstract Background Inhibitors of apoptosis (IAPs) are critical regulators of programmed cell death that are essential for development, oncogenesis, and immune and stress responses. However, available knowledge regarding IAP is largely biased toward humans and model species, while the distribution, function, and evolutionary novelties of this gene family remain poorly understood in many taxa, including Mollusca, the second most speciose phylum of Metazoa. Results Here, we present a chromosome-level genome assembly of an economically significant bivalve, the hard clam Mercenaria mercenaria, which reveals an unexpected and dramatic expansion of the IAP gene family to 159 members, the largest IAP gene repertoire observed in any metazoan. Comparative genome analysis reveals that this massive expansion is characteristic of bivalves more generally. Reconstruction of the evolutionary history of molluscan IAP genes indicates that most originated in early metazoans and greatly expanded in Bivalvia through both lineage-specific tandem duplication and retroposition, with 37.1% of hard clam IAPs located on a single chromosome. The expanded IAPs have been subjected to frequent domain shuffling, which has in turn shaped their architectural diversity. Further, we observed that extant IAPs exhibit dynamic and orchestrated expression patterns among tissues and in response to different environmental stressors. Conclusions Our results suggest that sophisticated regulation of apoptosis enabled by the massive expansion and diversification of IAPs has been crucial for the evolutionary success of hard clam and other molluscan lineages, allowing them to cope with local environmental stresses. This study broadens our understanding of IAP proteins and expression diversity and provides novel resources for studying molluscan biology and IAP function and evolution.

Download Full-text

Marine Prasinovirus Genomes Show Low Evolutionary Divergence and Acquisition of Protein Metabolism Genes by Horizontal Gene Transfer

Journal of Virology ◽

10.1128/jvi.01123-10 ◽

2010 ◽

Vol 84 (24) ◽

pp. 12555-12563 ◽

Cited By ~ 57

Author(s):

Hervé Moreau ◽

Gwenael Piganeau ◽

Yves Desdevises ◽

Richard Cooke ◽

Evelyne Derelle ◽

...

Keyword(s):

Gene Transfer ◽

Viral Evolution ◽

Genome Comparison ◽

Evolutionary Divergence ◽

Gene Repertoire ◽

Whole Genomes ◽

Complete Sequences ◽

Virus Genomes ◽

High Degree ◽

Ostreococcus Lucimarinus

ABSTRACT Although marine picophytoplankton are at the base of the global food chain, accounting for half of the planetary primary production, they are outnumbered 10 to 1 and are largely controlled by hugely diverse populations of viruses. Eukaryotic microalgae form a ubiquitous and particularly dynamic fraction of such plankton, with environmental clone libraries from coastal regions sometimes being dominated by one or more of the three genera Bathycoccus, Micromonas, and Ostreococcus (class Prasinophyceae). The complete sequences of two double-stranded (dsDNA) Bathycoccus, one dsDNA Micromonas, and one new dsDNA Ostreococcus virus genomes are described. Genome comparison of these giant viruses revealed a high degree of conservation, both for orthologous genes and for synteny, except for one 36-kb inversion in the Ostreococcus lucimarinus virus and two very large predicted proteins in Bathycoccus prasinos viruses. These viruses encode a gene repertoire of certain amino acid biosynthesis pathways never previously observed in viruses that are likely to have been acquired from lateral gene transfer from their host or from bacteria. Pairwise comparisons of whole genomes using all coding sequences with homologous counterparts, either between viruses or between their corresponding hosts, revealed that the evolutionary divergences between viruses are lower than those between their hosts, suggesting either multiple recent host transfers or lower viral evolution rates.

Download Full-text