scholarly journals Single individual structural variant detection uncovers widespread hemizygosity in molluscs

2021 ◽  
Vol 376 (1825) ◽  
Author(s):  
Andrew D. Calcino ◽  
Nathan J. Kenny ◽  
Marco Gerdol
Keyword(s):  
Gene Families ◽  
Genomic Sequencing ◽  
Single Individual ◽  
Genomic Evolution ◽  
Future Directions ◽  
Individual Gene ◽  
Complete Genomes ◽  
Variant Detection ◽  
Firm Evidence ◽  
Complete Genomic

The advent of complete genomic sequencing has opened a window into genomic phenomena obscured by fragmented assemblies. A good example of these is the existence of hemizygous regions of autosomal chromosomes, which can result in marked differences in gene content between individuals within species. While these hemizygous regions, and presence/absence variation of genes that can result, are well known in plants, firm evidence has only recently emerged for their existence in metazoans. Here, we use recently published, complete genomes from wild-caught molluscs to investigate the prevalence of hemizygosity across a well-known and ecologically important clade. We show that hemizygous regions are widespread in mollusc genomes, not clustered in individual chromosomes, and often contain genes linked to transposition, DNA repair and stress response. With targeted investigations of HSP70-12 and C1qDC , we also show how individual gene families are distributed within pan-genomes. This work suggests that extensive pan-genomes are widespread across the conchiferan Mollusca, and represent useful tools for genomic evolution, allowing the maintenance of additional genetic diversity within the population. As genomic sequencing and re-sequencing becomes more routine, the prevalence of hemizygosity, and its impact on selection and adaptation, are key targets for research across the tree of life. This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.

scholarly journals Single individual structural variant detection uncovers widespread hemizygosity in molluscs

2020 ◽  
Author(s):  
Andrew D Calcino ◽  
Nathan J Kenny ◽  
Marco Gerdol
Keyword(s):  
Genetic Diversity ◽  
Gene Families ◽  
Genomic Sequencing ◽  
Single Individual ◽  
Genomic Evolution ◽  
Individual Gene ◽  
Complete Genomes ◽  
Variant Detection ◽  
Firm Evidence ◽  
Complete Genomic

AbstractThe advent of complete genomic sequencing has opened a window into genomic phenomena obscured by fragmented assemblies. A good example of these is the existence of hemizygous regions of autosomal chromosomes, which can result in marked differences in gene content between individuals within species. While these hemizygous regions, and presence/absence variation of genes that can result, are well known in plants, firm evidence has only recently emerged for their existence in metazoans.Here we use recently published, complete genomes from wild-caught molluscs to investigate the prevalence of hemizygosity and pan-genomes across a well-known and ecologically important clade. We show that hemizygous regions are widespread in mollusc genomes, not clustered in individual chromosomes, and often contain genes linked to transposition, DNA repair and stress response. With targeted investigations of HSP70-12 and C1qDC, we also show how individual gene families are distributed within pan-genomes.This work suggests that pan-genomes are widespread across the conchiferan Mollusca, and represent useful tools for genomic evolution, allowing the maintenance of additional genetic diversity within the population. As genomic sequencing and re-sequencing becomes more routine, the prevalence of hemizygosity, and its impact on selection and adaptation, are key targets for research across the tree of life.

scholarly journals Complex Molecular Evolution and Expression of Expansin Gene Families in Three Basic Diploid Species of Brassica

2020 ◽  
Vol 21 (10) ◽  
pp. 3424 ◽  
Author(s):  
Weimiao Liu ◽  
Tianqi Lyu ◽  
Liai Xu ◽  
Ziwei Hu ◽  
Xingpeng Xiong ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Cell Walls ◽  
Plant Cell Wall ◽  
Diploid Species ◽  
Brassica Species ◽  
Gene Families ◽  
Structural Proteins ◽  
Development Processes ◽  
Positive Correlations ◽  
Complete Genomic

Expansins are a kind of structural proteins of the plant cell wall, and they enlarge cells by loosening the cell walls. Therefore, expansins are involved in many growth and development processes. The complete genomic sequences of Brassica rapa, Brassica oleracea and Brassica nigra provide effective platforms for researchers to study expansin genes, and can be compared with analogues in Arabidopsis thaliana. This study identified and characterized expansin families in B. rapa, B. oleracea, and B. nigra. Through the comparative analysis of phylogeny, gene structure, and physicochemical properties, the expansin families were divided into four subfamilies, and then their expansion patterns and evolution details were explored accordingly. Results showed that after the three species underwent independent evolution following their separation from A. thaliana, the expansin families in the three species had increased similarities but fewer divergences. By searching divergences of promoters and coding sequences, significant positive correlations were revealed among orthologs in A. thaliana and the three basic species. Subsequently, differential expressions indicated extensive functional divergences in the expansin families of the three species, especially in reproductive development. Hence, these results support the molecular evolution of basic Brassica species, potential functions of these genes, and genetic improvement of related crops.

scholarly journals Localized Gene-Specific Induction of Accessibility to V(D)j Recombination Induced by E2a and Early B Cell Factor in Nonlymphoid Cells

2001 ◽  
Vol 194 (5) ◽  
pp. 645-656 ◽  
Author(s):  
Peter Goebel ◽  
Noel Janney ◽  
Joaquín R. Valenzuela ◽  
William J. Romanow ◽  
Cornelis Murre ◽  
...  
Keyword(s):  
B Cell ◽  
Ectopic Expression ◽  
Gene Families ◽  
Individual Gene ◽  
Germline Transcription ◽  
Specific Induction ◽  
Recombination Activating Gene ◽  
Direct Targeting ◽  
B Cell Precursors ◽  
Early B Cell Factor

Accessibility of immunoglobulin (Ig) gene segments to V(D)J recombination is highly regulated and is normally only achieved in B cell precursors. We previously showed that ectopic expression of E2A or early B cell factor (EBF) with recombination activating gene (RAG) induces rearrangement of IgH and IgL genes in nonlymphoid cells. VκI genes throughout the locus were induced to rearrange after transfection with E2A, suggesting that the entire Vκ locus was accessible. However, here we show that Ig loci are not opened globally but that recombination is localized. Gene families are interspersed in the DH, Vκ, and Vλ loci, and we show that certain families and individual genes undergo high levels of recombination after ectopic expression of E2A or EBF, while other families within the same locus are not induced to rearrange. Furthermore, in some families, induction of germline transcription correlates with the level of induced recombination, while in others there is no correlation, suggesting that recombination is not simply initiated by induction of germline transcription. The induced repertoire seen at 24 hours does not change significantly over time indicating the absence of many secondary rearrangements and also suggesting a direct targeting mechanism. We propose that accessibility occurs in a local manner, and that binding sites for factors facilitating accessibility are therefore likely to be associated with individual gene segments.

scholarly journals Role of Recombination in the Evolution of Host Specialization Within Bean yellow mosaic virus

2009 ◽  
Vol 99 (5) ◽  
pp. 512-518 ◽  
Author(s):  
S. J. Wylie ◽  
R. A. C. Jones
Keyword(s):  
Coat Protein ◽  
Mosaic Virus ◽  
Genetic Recombination ◽  
Bean Yellow Mosaic Virus ◽  
Host Specialization ◽  
Yellow Mosaic Virus ◽  
Complete Genomes ◽  
Tentative Evidence ◽  
Firm Evidence

Seven complete genomes and 64 coat protein gene sequences belonging to Bean yellow mosaic virus (BYMV) isolates from different continents were examined for evidence of genetic recombination using six different recombination-detection programs. In the seven complete genomes and a single complete genome of the related virus Clover yellow vein virus (ClYVV), evidence for eight recombination patterns was found by four or more programs, giving firm evidence of their presence, and five additional recombination patterns were detected by three or fewer programs, giving tentative evidence of their occurrence. When the nucleotide sequences of 64 BYMV and one ClYVV coat protein genes were analyzed, three firm recombination patterns were detected in 21 isolates (32%). With another six isolates (9%), tentative evidence was found for three further recombination patterns. Of the 19 firm or tentative recombination patterns detected within and between strain groups of BYMV, and with ClYVV, 12 involved a generalist group of isolates as a parent but none of the other BYMV groups acted as parents more than six times. These findings suggest that recombination played an important role in the evolution of BYMV strain groups that specialize in infecting particular groups of domesticated plants.

scholarly journals Evolutionary insights into Bean common mosaic necrosis virus and Cowpea aphid borne mosaic virus using global isolates and thirteen new near complete genomes from Kenya

2018 ◽  
Author(s):  
James M Wainaina ◽  
Laura Kubatko ◽  
Jagger Harvey ◽  
Elijah Ateka ◽  
Timothy Makori ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Selection Pressure ◽  
Sub Saharan Africa ◽  
Phylogenomic Analysis ◽  
Gene Trees ◽  
Necrosis Virus ◽  
Individual Gene ◽  
Viral Genomes ◽  
Cowpea Aphid ◽  
Complete Genomes

AbstractPlant viral diseases are one of the major limitations in legume production within sub Saharan Africa (SSA), as they account for up to 100 % in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out. The main aim was to gain insights into the selection pressure and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV), within symptomatic common beans and cowpeas. Eleven near complete genomes of BCMNV and two for CABMV sequences were obtained from SSA. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes was carried out. Three distinct well-supported clades were identified across the whole genome tree, and were in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. These results will contribute greatly to the knowledge gap surrounding the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and support the current breeding efforts towards resistance for BCMNV and CABMV.

Molecular Characterization of the Tubulin-Related Gene Families in Herbicide Resistant and Susceptible Goosegrass (Eleusine indica)

Weed Science ◽  
1995 ◽  
Vol 43 (1) ◽  
pp. 28-33 ◽  
Author(s):  
Kirankumar S. Mysore ◽  
Wm. Vance Baird
Keyword(s):  
Tandem Repeats ◽  
Gene Families ◽  
Related Gene ◽  
Tubulin Gene ◽  
Individual Gene ◽  
Large Deletions ◽  
Tubulin Genes ◽  
Significant Difference ◽  
The Difference ◽  
Tubulin Protein

Goosegrass, wide spread throughout the tropics and subtropics, is one of the most noxious weeds known. Recently, biotypes of goosegrass have been found resistant to the dinitroaniline herbicides. An alteration in the structure/composition of a tubulin protein has been postulated as an explanation for the hyperstable microtubules and the resistant phenotype. Our study was initiated to investigate the structure of the alpha (α)-, beta (β)- and gamma (γ)-tubulin related gene sequences in resistant, intermediately resistant, and susceptible biotypes. Heterologous tubulin gene clones were used as probes of restriction endonuclease-digested genomic DNA from each biotype, to determine gene size and copy number and to screen for restriction fragment length polymorphisms. The tubulin genes are organized into gene families. There are three to five α-tubulin genes, four to seven β-tubulin genes, and four to eight γ-tubulin genes. There was no evidence of multiple copies or tandem repeats of any individual gene sequence. Although RFLPs were observed, no significant difference in the banding pattern between the resistant and the susceptible biotypes was found for either α-, β-, or γ-tubulin gene families. Therefore, it is unlikely that the difference between the herbicide-response phenotypes can be attributed to large deletions or insertions in a tubulin gene.

What Do Evolutionary Models Teach Us About Sensitive Periods in Psychological Development?

2017 ◽  
Vol 22 (3) ◽  
pp. 141-150 ◽  
Author(s):  
Willem E. Frankenhuis ◽  
R. Chris Fraley
Keyword(s):  
Empirical Research ◽  
Psychological Development ◽  
Single Individual ◽  
Evolutionary Models ◽  
Formal Models ◽  
Future Directions ◽  
Developmental Processes ◽  
Sensitive Periods

Abstract. Sensitive periods in development are widespread in nature. Many psychologists and biologists regard sensitive periods as byproducts of developmental processes. Although this view may be correct in some cases, it is unlikely to be the whole story. There is large variation in sensitive periods (a) between species in the same trait ( Beecher & Brenowitz, 2005 ), (b) between individuals of the same species ( Frankenhuis, Panchanathan, & Belsky, 2016 ), and (c) between different traits within a single individual ( Zeanah, Gunnar, McCall, Kreppner, & Fox, 2011 ). In this article, we discuss recent insights provided by formal models of the evolution of sensitive periods. These models help to identify the conditions in which sensitive periods are likely to evolve, and make predictions about the factors that affect their development. We conclude by discussing future directions for empirical research.

Genomic features and insights into the biology of Mycoplasma fermentans

Microbiology ◽  
2011 ◽  
Vol 157 (3) ◽  
pp. 760-773 ◽  
Author(s):  
Hagai Rechnitzer ◽  
Elzbieta Brzuszkiewicz ◽  
Axel Strittmatter ◽  
Heiko Liesegang ◽  
Inna Lysnyansky ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Genomic Sequence ◽  
Gene Families ◽  
Hypothetical Proteins ◽  
Protein Coding ◽  
Mycoplasma Fermentans ◽  
Coding Sequences ◽  
Transporter Family ◽  
Genes Encoding ◽  
Complete Genomic

We present the complete genomic sequence of Mycoplasma fermentans, an organism suggested to be associated with the pathogenesis of rheumatoid arthritis in humans. The genome is composed of 977 524 bp and has a mean G+C content of 26.95 mol%. There are 835 predicted protein-coding sequences and a mean coding density of 87.6 %. Functions have been assigned to 58.8 % of the predicted protein-coding sequences, while 18.4 % of the proteins are conserved hypothetical proteins and 22.8 % are hypothetical proteins. In addition, there are two complete rRNA operons and 36 tRNA coding sequences. The largest gene families are the ABC transporter family (42 members), and the functionally heterogeneous group of lipoproteins (28 members), which encode the characteristic prokaryotic cysteine ‘lipobox’. Protein secretion occurs through a pathway consisting of SecA, SecD, SecE, SecG, SecY and YidC. Some highly conserved eubacterial proteins, such as GroEL and GroES, are notably absent. The genes encoding DnaK-DnaJ-GrpE and Tig, forming the putative complex of chaperones, are intact, providing the only known control over protein folding. Eighteen nucleases and 17 proteases and peptidases were detected as well as three genes for the thioredoxin-thioreductase system. Overall, this study presents insights into the physiology of M. fermentans, and provides several examples of the genetic basis of systems that might function as virulence factors in this organism.

scholarly journals Complete Genomic Sequence of an Avian Pathogenic Escherichia coli Strain of Serotype O7:HNT

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Renato P. Maluta ◽  
Bryon Nicholson ◽  
Catherine M. Logue ◽  
Lisa K. Nolan ◽  
Thaís C. G. Rojas ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genomic Sequence ◽  
Complete Sequence ◽  
Coli Strain ◽  
Sequence Type ◽  
Complete Genomic Sequence ◽  
Avian Pathogenic Escherichia Coli ◽  
Pathogenic Escherichia Coli ◽  
Complete Genomes ◽  
Complete Genomic

Avian pathogenic Escherichia coli (APEC) is associated with colibacillosis in poultry. Here, we present the first complete sequence of an APEC strain of the O7:HNT serotype and ST73 sequence type, isolated from a broiler with cellulitis. Complete genomes of APEC with distinct genetic backgrounds may be useful for comparative analysis.

scholarly journals The Highest Cited Papers in Brucellosis: Identification Using Two Databases and Review of the Papers’ Major Findings

2018 ◽  
Vol 2018 ◽  
pp. 1-10
Author(s):  
Faris Ghalib Bakri ◽  
Hamzah M. AlQadiri ◽  
Marwan Hmoud Adwan
Keyword(s):  
Basic Science ◽  
Web Of Science ◽  
Brucella Melitensis ◽  
Citation Count ◽  
The Other ◽  
Genomic Sequencing ◽  
Citation Classics ◽  
Complete Genomic

Citation classics represent the highest impact work in a given field. We aim to identify and analyze the most frequently cited papers on brucellosis. We used the databases Scopus and Web of Science to determine the most frequently cited papers. The most cited fifty papers in each database were identified. We then ranked the papers according to the highest citation count recorded from any of the two databases. The most frequently cited paper received 964 citations and was by DelVecchio VG et al. reporting the complete genomic sequencing ofBrucella melitensis. The papers were published in 30 journals led by the “Infection and Immunity” journal and the “Veterinary Microbiology” journal (each had 7 papers). Citation classics in brucellosis were all in English except one in French and were mostly of basic science type. In addition, we noticed that 12 articles that were identified among the highest fifty articles in one database were missed by the other database and vice versa. Therefore, we suggest that searching in more than one database would detect additional citation classics.

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