scholarly journals Research gaps and new insights in the intriguing evolution of Drosophila seminal proteins

2021 ◽  
Author(s):  
Juan Hurtado ◽  
Francisca Cunha Almeida ◽  
Silvina Anahí Belliard ◽  
Santiago Revale ◽  
Esteban Hasson
Keyword(s):  
Seminal Fluid ◽  
Current Knowledge ◽  
Comparative Genomic ◽  
Genomic Information ◽  
Research Gaps ◽  
Seminal Fluid Proteins ◽  
Open Questions ◽  
Starting Point ◽  
Genomic Analyses ◽  
Multiple Species

While the striking effects that seminal fluid proteins (SFPs) exert on females are fairly conserved among Diptera, they exhibit remarkable evolutionary lability. Consequently, most SFPs lack detectable homologs among the repertoire of SFPs of phylogenetically distant species. How such a rapidly changing proteome "manages" to conserve functions across taxa is a fascinating question. However, this and other pivotal aspects of SFPs' evolution remain elusive because discoveries on these proteins have been mainly restricted to the model D. melanogaster. Here, we provide an overview of the current knowledge on the inter-specific divergence of Drosophila SFPs and compile the increasing amount of relevant genomic information from multiple species. Capitalizing the accumulated knowledge in D. melanogaster, we present novel sets of high-confidence SFP candidates and transcription factors presumptively involved in regulating the expression of SFPs. We also address open questions by performing comparative genomic analyses that failed to support the existence of conserved SFPs shared by most dipterans and indicated that gene co-option is the most frequent mechanism accounting for the origin of Drosophila SFP-coding genes. We hope our update establishes a starting point to integrate, as more species are assayed for SFPs, further data and thus, to widen the understanding of the intricate evolution of these proteins.

scholarly journals Genome Organization and Pathogenicity of Corynebacterium diphtheriae C7(−) and PW8 Strains

2010 ◽  
Vol 78 (9) ◽  
pp. 3791-3800 ◽  
Author(s):  
Masaaki Iwaki ◽  
Takako Komiya ◽  
Akihiko Yamamoto ◽  
Akiko Ishiwa ◽  
Noriyo Nagata ◽  
...  
Keyword(s):  
Soviet Union ◽  
Genome Organization ◽  
Former Soviet Union ◽  
Current Knowledge ◽  
Corynebacterium Diphtheriae ◽  
Comparative Genomic ◽  
Genomic Information ◽  
Great Heterogeneity ◽  
Large Outbreak ◽  
Genomic Regions

ABSTRACT Corynebacterium diphtheriae is the causative agent of diphtheria. In 2003, the complete genomic nucleotide sequence of an isolate (NCTC13129) from a large outbreak in the former Soviet Union was published, in which the presence of 13 putative pathogenicity islands (PAIs) was demonstrated. In contrast, earlier work on diphtheria mainly employed the C7(−) strain for genetic analysis; therefore, current knowledge of the molecular genetics of the bacterium is limited to that strain. However, genomic information on the NCTC13129 strain has scarcely been compared to strain C7(−). Another important C. diphtheriae strain is Park-Williams no. 8 (PW8), which has been the only major strain used in toxoid vaccine production and for which genomic information also is not available. Here, we show by comparative genomic hybridization that at least 37 regions from the reference genome, including 11 of the 13 PAIs, are considered to be absent in the C7(−) genome. Despite this, the C7(−) strain still retained signs of pathogenicity, showing a degree of adhesion to Detroit 562 cells, as well as the formation of and persistence in abscesses in animal skin comparable to that of the NCTC13129 strain. In contrast, the PW8 strain, suggested to lack 14 genomic regions, including 3 PAIs, exhibited more reduced signs of pathogenicity. These results, together with great diversity in the presence of the 37 genomic regions among various C. diphtheriae strains shown by PCR analyses, suggest great heterogeneity of this pathogen, not only in genome organization, but also in pathogenicity.

Research gaps and new insights in the evolution of Drosophila seminal fluid proteins

2021 ◽  
Author(s):  
H. Juan ◽  
C. Almeida Francisca ◽  
B. S. Anahí ◽  
R. Santiago ◽  
H. Esteban
Keyword(s):  
Seminal Fluid ◽  
Research Gaps ◽  
Seminal Fluid Proteins

scholarly journals Beyond Sperm and Male Accessory Gland Proteins: Exploring Insect Reproductive Metabolomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Francesca Scolari ◽  
Fathiya M. Khamis ◽  
Diana Pérez-Staples
Keyword(s):  
Large Scale ◽  
Reproductive Tract ◽  
Seminal Fluid ◽  
Metabolite Identification ◽  
Accessory Gland ◽  
Agricultural Pests ◽  
Accessory Gland Proteins ◽  
Seminal Fluid Proteins ◽  
Technological Advances ◽  
Multiple Species

Insect seminal fluid, the non-sperm component of the ejaculate, comprises a variegated set of molecules, including, but not limited to, lipids, proteins, carbohydrates, salts, hormones, nucleic acids, and vitamins. The identity and functional role of seminal fluid proteins (SFPs) have been widely investigated, in multiple species. However, most of the other small molecules in insect ejaculates remain uncharacterized. Metabolomics is currently adopted to deepen our understanding of complex biological processes and in the last 15years has been applied to answer different physiological questions. Technological advances in high-throughput methods for metabolite identification such as mass spectrometry and nuclear magnetic resonance (NMR) are now coupled to an expanded bioinformatics toolbox for large-scale data analysis. These improvements allow for the processing of smaller-sized samples and for the identification of hundreds to thousands of metabolites, not only in Drosophila melanogaster but also in disease vectors, animal, and agricultural pests. In this review, we provide an overview of the studies that adopted metabolomics-based approaches in insects, with a particular focus on the reproductive tract (RT) of both sexes and the ejaculate. Progress in the field of metabolomics will contribute not only to achieve a deeper understanding of the composition of insect ejaculates and how they are affected by endogenous and exogenous factors, but also to provide increasingly powerful tools to decipher the identity and molecular interactions between males and females during and after mating.

scholarly journals iHam and pyHam: visualizing and processing hierarchical orthologous groups

2018 ◽  
Vol 35 (14) ◽  
pp. 2504-2506 ◽  
Author(s):  
Clément-Marie Train ◽  
Miguel Pignatelli ◽  
Adrian Altenhoff ◽  
Christophe Dessimoz
Keyword(s):  
Gene Family ◽  
Evolutionary History ◽  
Gene Families ◽  
Comparative Genomic ◽  
Last Common Ancestor ◽  
Analysis Method ◽  
Ancestral Gene ◽  
Genomic Analyses ◽  
History Of ◽  
Multiple Species

Abstract Summary The evolutionary history of gene families can be complex due to duplications and losses. This complexity is compounded by the large number of genomes simultaneously considered in contemporary comparative genomic analyses. As provided by several orthology databases, hierarchical orthologous groups (HOGs) are sets of genes that are inferred to have descended from a common ancestral gene within a species clade. This implies that the set of HOGs defined for a particular clade correspond to the ancestral genes found in its last common ancestor. Furthermore, by keeping track of HOG composition along the species tree, it is possible to infer the emergence, duplications and losses of genes within a gene family of interest. However, the lack of tools to manipulate and analyse HOGs has made it difficult to extract, display and interpret this type of information. To address this, we introduce interactive HOG analysis method, an interactive JavaScript widget to visualize and explore gene family history encoded in HOGs and python HOG analysis method, a python library for programmatic processing of genes families. These complementary open source tools greatly ease adoption of HOGs as a scalable and interpretable concept to relate genes across multiple species. Availability and implementation iHam’s code is available at https://github.com/DessimozLab/iHam or can be loaded dynamically. pyHam’s code is available at https://github.com/DessimozLab/pyHam and or via the pip package ‘pyham’.

scholarly journals The Drosophila seminal proteome and its role in postcopulatory sexual selection

2020 ◽  
Vol 375 (1813) ◽  
pp. 20200072 ◽  
Author(s):  
Stuart Wigby ◽  
Nora C. Brown ◽  
Sarah E. Allen ◽  
Snigdha Misra ◽  
Jessica L. Sitnik ◽  
...  
Keyword(s):  
Sexual Selection ◽  
Sperm Competition ◽  
Seminal Fluid ◽  
Current Knowledge ◽  
Future Research ◽  
Seminal Fluid Proteins ◽  
Scale Functions ◽  
Postcopulatory Sexual Selection ◽  
Evolutionary Force ◽  
Protein Classes

Postcopulatory sexual selection (PCSS), comprised of sperm competition and cryptic female choice, has emerged as a widespread evolutionary force among polyandrous animals. There is abundant evidence that PCSS can shape the evolution of sperm. However, sperm are not the whole story: they are accompanied by seminal fluid substances that play many roles, including influencing PCSS. Foremost among seminal fluid models is Drosophila melanogaster , which displays ubiquitous polyandry, and exhibits intraspecific variation in a number of seminal fluid proteins (Sfps) that appear to modulate paternity share. Here, we first consolidate current information on the identities of D. melanogaster Sfps. Comparing between D. melanogaster and human seminal proteomes, we find evidence of similarities between many protein classes and individual proteins, including some D. melanogaster Sfp genes linked to PCSS, suggesting evolutionary conservation of broad-scale functions. We then review experimental evidence for the functions of D. melanogaster Sfps in PCSS and sexual conflict. We identify gaps in our current knowledge and areas for future research, including an enhanced identification of PCSS-related Sfps, their interactions with rival sperm and with females, the role of qualitative changes in Sfps and mechanisms of ejaculate tailoring. This article is part of the theme issue ‘Fifty years of sperm competition’.

scholarly journals Factors Influencing the Reproductive Ability of Male Bees: Current Knowledge and Further Directions

Insects ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 529
Author(s):  
Huiyue Zhao ◽  
Shibonage K. Mashilingi ◽  
Yanjie Liu ◽  
Jiandong An
Keyword(s):  
Seminal Fluid ◽  
Current Knowledge ◽  
Sperm Quality ◽  
Sperm Count ◽  
Vital Role ◽  
Natural Ecosystems ◽  
Related Factors ◽  
Seminal Fluid Proteins ◽  
Reproductive Behaviors ◽  
Reproductive Ability

Bumblebees and honeybees are very important pollinators and play a vital role in agricultural and natural ecosystems. The quality of their colonies is determined by the queens and the reproductive drones of mother colonies, and mated drones transmit semen, including half of the genetic materials, to queens and enhance their fertility. Therefore, factors affecting drone fecundity will also directly affect progeny at the colony level. Here, we review environmental and bee-related factors that are closely related to drone reproductive ability. The environmental factors that mainly affect the sperm count and the viability of males include temperature, nutrients and pesticides. In addition, the inherent characteristics of male bees, such as body size, weight, age, seminal fluid proteins and proteins of the spermathecal fluid, contribute to mating success, sperm quality during long-term storage in the spermathecae and the reproductive behaviors of queens. Based on the results of previous studies, we also suggest that the effects of somatotype dimorphism in bumblebee males on sperm quality and queen fecundity and the indispensable and exploitable function of gland proteins in the fecundity of males and queens should be given more attention in further studies.

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.

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

The DEAH helicase DHX36 and its role in G-quadruplex-dependent processes

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Philipp Schult ◽  
Katrin Paeschke
Keyword(s):  
Current Knowledge ◽  
Future Research ◽  
Transcriptional Level ◽  
Cellular Functions ◽  
Multiple Functions ◽  
Open Questions ◽  
G Quadruplex ◽  
Cellular Pathways ◽  
Nucleic Acid Structures ◽  
Dependent Processes

AbstractDHX36 is a member of the DExD/H box helicase family, which comprises a large number of proteins involved in various cellular functions. Recently, the function of DHX36 in the regulation of G-quadruplexes (G4s) was demonstrated. G4s are alternative nucleic acid structures, which influence many cellular pathways on a transcriptional and post-transcriptional level. In this review we provide an overview of the current knowledge about DHX36 structure, substrate specificity, and mechanism of action based on the available models and crystal structures. Moreover, we outline its multiple functions in cellular homeostasis, immunity, and disease. Finally, we discuss the open questions and provide potential directions for future research.

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