scholarly journals The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Josué Barrera-Redondo ◽  
Guillermo Sánchez-de la Vega ◽  
Jonás A. Aguirre-Liguori ◽  
Gabriela Castellanos-Morales ◽  
Yocelyn T. Gutiérrez-Guerrero ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Population Level ◽  
Growth Hormones ◽  
Comparative Genomic ◽  
Structural Variants ◽  
Closely Related Species ◽  
Level Data ◽  
Genomic Analyses ◽  
Genotype By Sequencing ◽  
Regulation Of Growth

AbstractDespite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

scholarly journals A wild Cucurbita genome reveals the role of structural variants and introgression in domestication

2020 ◽  
Author(s):  
Josué Barrera-Redondo ◽  
Guillermo Sánchez-de la Vega ◽  
Jonás A. Aguirre-Liguori ◽  
Gabriela Castellanos-Morales ◽  
Yocelyn T. Gutiérrez-Guerrero ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Population Level ◽  
Comparative Genomic ◽  
Structural Variants ◽  
Closely Related Species ◽  
Level Data ◽  
Genomic Analyses ◽  
Genotype By Sequencing ◽  
Regulation Of Growth

AbstractDespite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first wild Cucurbita genome at a chromosome level. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We uncovered candidate domestication genes that are involved in the synthesis and regulation of growth hormones, plant defense mechanisms, flowering time and seed development. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

scholarly journals Functional endogenous viral elements in the genome of the parasitoid wasp Cotesia congregata : insights into the evolutionary dynamics of bracoviruses

2013 ◽  
Vol 368 (1626) ◽  
pp. 20130047 ◽  
Author(s):  
Annie Bézier ◽  
Faustine Louis ◽  
Séverine Jancek ◽  
Georges Periquet ◽  
Julien Thézé ◽  
...  
Keyword(s):  
Virulence Genes ◽  
Evolutionary Dynamics ◽  
Genomic Organization ◽  
Parasitoid Wasp ◽  
Comparative Genomic ◽  
Conserved Synteny ◽  
Closely Related Species ◽  
Cotesia Congregata ◽  
Genomic Analyses ◽  
Endogenous Viral Elements

Bracoviruses represent the most complex endogenous viral elements (EVEs) described to date. Nudiviral genes have been hosted within parasitoid wasp genomes since approximately 100 Ma. They play a crucial role in the wasp life cycle as they produce bracovirus particles, which are injected into parasitized lepidopteran hosts during wasp oviposition. Bracovirus particles encapsidate multiple dsDNA circles encoding virulence genes. Their expression in parasitized caterpillars is essential for wasp parasitism success. Here, we report on the genomic organization of the proviral segments (i.e. master sequences used to produce the encapsidated dsDNA circles) present in the Cotesia congregata parasitoid wasp genome. The provirus is composed of a macrolocus, comprising two-thirds of the proviral segments and of seven dispersed loci, each containing one to three segments. Comparative genomic analyses with closely related species gave insights into the evolutionary dynamics of bracovirus genomes. Conserved synteny in the different wasp genomes showed the orthology of the proviral macrolocus across different species. The nudiviral gene odv-e66-like1 is conserved within the macrolocus, suggesting an ancient co-localization of the nudiviral genome and bracovirus proviral segments. By contrast, the evolution of proviral segments within the macrolocus has involved a series of lineage-specific duplications.

scholarly journals Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species

2020 ◽  
Vol 8 (11) ◽  
pp. 1720
Author(s):  
Gabriele Andrea Lugli ◽  
Chiara Tarracchini ◽  
Giulia Alessandri ◽  
Christian Milani ◽  
Leonardo Mancabelli ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Ursus Arctos ◽  
Primate Species ◽  
Comparative Genomic ◽  
Glycosyl Hydrolases ◽  
Genomic Variability ◽  
Fecal Samples ◽  
Genomic Analyses ◽  
Conserved Genes ◽  
Genetic Features

Members of the Bifidobacterium dentium species are usually identified in the oral cavity of humans and associated with the development of plaque and dental caries. Nevertheless, they have also been detected from fecal samples, highlighting a widespread distribution among mammals. To explore the genetic variability of this species, we isolated and sequenced the genomes of 18 different B. dentium strains collected from fecal samples of several primate species and an Ursus arctos. Thus, we investigated the genomic variability and metabolic abilities of the new B. dentium isolates together with 20 public genome sequences. Comparative genomic analyses provided insights into the vast metabolic repertoire of the species, highlighting 19 glycosyl hydrolases families shared between each analyzed strain. Phylogenetic analysis of the B. dentium taxon, involving 1140 conserved genes, revealed a very close phylogenetic relatedness among members of this species. Furthermore, low genomic variability between strains was also confirmed by an average nucleotide identity analysis showing values higher than 98.2%. Investigating the genetic features of each strain, few putative functional mobile elements were identified. Besides, a consistent occurrence of defense mechanisms such as CRISPR–Cas and restriction–modification systems may be responsible for the high genome synteny identified among members of this taxon.

scholarly journals Population-Level Prevalence, Bother, and Treatment Behavior for Urinary Incontinence in an Eastern European Country: Findings from the LUTS POLAND Study

2021 ◽  
Vol 10 (11) ◽  
pp. 2314
Author(s):  
Mikolaj Przydacz ◽  
Marcin Chlosta ◽  
Piotr Chlosta
Keyword(s):  
Quality Of Life ◽  
Urinary Incontinence ◽  
Rural Areas ◽  
Eastern European Country ◽  
Population Level ◽  
Eastern European ◽  
Level Data ◽  
Urban And Rural Areas ◽  
Eastern European Countries

Objectives: Population-level data are lacking for urinary incontinence (UI) in Central and Eastern European countries. Therefore, the objective of this study was to estimate the prevalence, bother, and behavior regarding treatment for UI in a population-representative group of Polish adults aged ≥ 40 years. Methods: Data for this epidemiological study were derived from the larger LUTS POLAND project, in which a group of adults that typified the Polish population were surveyed, by telephone, about lower urinary tract symptoms. Respondents were classified by age, sex, and place of residence. UI was assessed with a standard protocol and established International Continence Society definitions. Results: The LUTS POLAND survey included 6005 completed interviews. The prevalence of UI was 14.6–25.4%; women reported a greater occurrence compared with men (p < 0.001). For both sexes, UI prevalence increased with age. Stress UI was the most common type of UI in women, and urgency UI was the most prevalent in men. We did not find a difference in prevalence between urban and rural areas. Individuals were greatly bothered by UI. For women, mixed UI was the most bothersome, whereas for men, leak for no reason was most annoying. More than half of respondents (51.4–62.3%) who reported UI expressed anxiety about the effect of UI on their quality of life. Nevertheless, only around one third (29.2–38.1%) of respondents with UI sought treatment, most of whom received treatment. Persons from urban and rural areas did not differ in the degrees of treatment seeking and treatment receiving. Conclusion: Urinary incontinence was prevalent and greatly bothersome among Polish adults aged ≥ 40 years. Consequently, UI had detrimental effects on quality of life. Nonetheless, most affected persons did not seek treatment. Therefore, we need to increase population awareness in Poland about UI and available treatment methods, and we need to ensure adequate allocation of government and healthcare system resources.

Complete chloroplast genomes of Leptodermis scabrida complex: comparative genomic analyses and phylogenetic relationships

Gene ◽  
2021 ◽  
pp. 145715
Author(s):  
Ying Zhang ◽  
Zhengfeng Wang ◽  
Yanan Guo ◽  
Sheng Chen ◽  
Xianyi Xu ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Comparative Genomic ◽  
Chloroplast Genomes ◽  
Genomic Analyses

Evidence from comparative genomic analyses indicating that Lactobacillus-mediated irritable bowel syndrome alleviation is mediated by the conjugated linoleic acid synthesis

2021 ◽  
Author(s):  
Yang Liu ◽  
Wei Xiao ◽  
Leilei Yu ◽  
Fengwei Tian ◽  
Gang Wang ◽  
...  
Keyword(s):  
Irritable Bowel Syndrome ◽  
Linoleic Acid ◽  
Gut Microbiota ◽  
Acid Synthesis ◽  
Comparative Genomic ◽  
Low Grade ◽  
Genomic Analyses ◽  
Irritable Bowel ◽  
Low Grade Inflammation ◽  
Gut Microbiota Dysbiosis

Irritable bowel syndrome (IBS) is a chronic intestinal disorder accompanied by low-grade inflammation, visceral hypersensitivity, and gut microbiota dysbiosis. Several studies have indicated that Lactobacillus supplementation can help to alleviate...

scholarly journals Comparative genomic analyses of a virulent pseudorabies virus and a series of its in vitro passaged strains

2018 ◽  
Vol 15 (1) ◽  
Author(s):  
Chao Ye ◽  
Jiqiang Wu ◽  
Wu Tong ◽  
Tongling Shan ◽  
Xuefei Cheng ◽  
...  
Keyword(s):  
Pseudorabies Virus ◽  
Comparative Genomic ◽  
Genomic Analyses

scholarly journals Rapid evolution and molecular convergence in cryptorchidism-related genes associated with inherently undescended testes in mammals

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Simin Chai ◽  
Ran Tian ◽  
Juanjuan Bi ◽  
Shixia Xu ◽  
Guang Yang ◽  
...  
Keyword(s):  
Muscle Development ◽  
Rapid Evolution ◽  
Genetic Material ◽  
Comparative Genomic ◽  
Testicular Descent ◽  
Ancestral State ◽  
Undescended Testes ◽  
Genomic Analyses ◽  
Genetic Mechanisms ◽  
Molecular Convergence

Abstract Background The mammalian testis is an important male exocrine gland and spermatozoa-producing organ that usually lies in extra-abdominal scrotums to provide a cooler environment for spermatogenesis and sperm storage. Testicles sometimes fail to descend, leading to cryptorchidism. However, certain groups of mammals possess inherently ascrotal testes (i.e. testes that do not descend completely or at all) that have the same physiological functions as completely descended scrotal testes. Although several anatomical and hormonal factors involved in testicular descent have been studied, there is still a paucity of comprehensive research on the genetic mechanisms underlying the evolution of testicular descent in mammals and how mammals with ascrotal testes maintain their reproductive health. Results We performed integrative phenotypic and comparative genomic analyses of 380 cryptorchidism-related genes and found that the mammalian ascrotal testes trait is derived from an ancestral scrotal state. Rapidly evolving genes in ascrotal mammals were enriched in the Hedgehog pathway—which regulates Leydig cell differentiation and testosterone secretion—and muscle development. Moreover, some cryptorchidism-related genes in ascrotal mammals had undergone positive selection and contained specific mutations and indels. Genes harboring convergent/parallel amino acid substitutions between ascrotal mammals were enriched in GTPase functions. Conclusions Our results suggest that the scrotal testis is an ancestral state in mammals, and the ascrotal phenotype was derived multiple times in independent lineages. In addition, the adaptive evolution of genes involved in testicular descent and the development of the gubernaculum contributed to the evolution of ascrotal testes. Accurate DNA replication, the proper segregation of genetic material, and appropriate autophagy are the potential mechanisms for maintaining physiological normality during spermatogenesis in ascrotal mammals. Furthermore, the molecular convergence of GTPases is probably a mechanism in the ascrotal testes of different mammals. This study provides novel insights into the evolution of the testis and scrotum in mammals and contributes to a better understanding of the pathogenesis of cryptorchidism in humans.

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