scholarly journals Small genome, big insights

Nature ◽  
2004 ◽  
Vol 431 (7011) ◽  
pp. 916-917 ◽  
Author(s):  
John Mulley ◽  
Peter Holland
Keyword(s):  
Small Genome

scholarly journals The Occurrence of Genetic Recombination between Viruses and Human, it's Possible Influence on Vaccination

2020 ◽  
Vol 18 (6) ◽  
pp. 4-14 ◽  
Author(s):  
E. P. Kharchenko
Keyword(s):  
Genetic Information ◽  
Genetic Recombination ◽  
Protein Sequences ◽  
Virus Protein ◽  
Computer Study ◽  
Data Bases ◽  
Small Genome ◽  
After Effects ◽  
The Past ◽  
Human Proteins

Relevance. The genetic recombination between viruses and men is known long ago. It can be divided on relict and ontogenic ones. For the host the recombination may display different consequences the nature of which is not exposed explicitly.Aim is to analyze (on the base of computer comparison of the primary structure of viral and human proteins ) the occurrence of twodirectional recombination by small genome fragments between viruses and men and describe its possible after-effects.Materials and methods. For this computer study human and virus protein sequences were used from data bases available in INTERNET.Results. It was indicated that recombination (cryptical and explicit) by small genome fragments between viruses and men occurred many times in the past and many viruses pathogenic for men were involved in it.Conclusion. The bioinformatics approach allows to look at the past of viruses and men and find the traces of genetic information changes between them that may predetermine the effects of vaccines and diagnostic immune tests.

scholarly journals Genomic Survey, Transcriptome, and Metabolome Analysis of Apocynum venetum and Apocynum hendersonii to Reveal Major Flavonoid Biosynthesis Pathways

Metabolites ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 296 ◽  
Author(s):  
Gang Gao ◽  
Ping Chen ◽  
Jikang Chen ◽  
Kunmei Chen ◽  
Xiaofei Wang ◽  
...  
Keyword(s):  
Morphological Difference ◽  
Flavonoid Biosynthesis ◽  
Flavonoid Content ◽  
Metabolome Analysis ◽  
Total Anthocyanin ◽  
Small Genome ◽  
Genome Survey ◽  
Metabolite Profiles ◽  
Apocynum Venetum ◽  
Gene Expression Levels

Apocynum plants, especially A. venetum and A. hendersonii, are rich in flavonoids. In the present study, a whole genome survey of the two species was initially carried out to optimize the flavonoid biosynthesis-correlated gene mining. Then, the metabolome and transcriptome analyses were combined to elucidate the flavonoid biosynthesis pathways. Both species have small genome sizes of 232.80 Mb (A. venetum) and 233.74 Mb (A. hendersonii) and showed similar metabolite profiles with flavonols being the main differentiated flavonoids between the two specie. Positive correlation of gene expression levels (flavonone-3 hydroxylase, anthocyanidin reductase, and flavonoid 3-O-glucosyltransferase) and total flavonoid content were observed. The contents of quercitrin, hyperoside, and total anthocyanin in A. venetum were found to be much higher than in A. hendersonii, and such was thought to be the reason for the morphological difference in color of A. venetum and A. hendersonii. This study provides valuable genomic and metabolome information for understanding of A. venetum and A. hendersonii, and lays a foundation for elucidating Apocynum genus plant flavonoid biosynthesis.

scholarly journals Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences

2016 ◽  
Vol 48 (1) ◽  
Author(s):  
Mekki Boussaha ◽  
Pauline Michot ◽  
Rabia Letaief ◽  
Chris Hozé ◽  
Sébastien Fritz ◽  
...  
Keyword(s):  
Whole Genome ◽  
Large Collection ◽  
Genome Sequences ◽  
Small Genome ◽  
Genome Variations

scholarly journals Hundreds of Flagellar Basal Bodies Cover the Cell Surface of the Endosymbiotic Bacterium Buchnera aphidicola sp. Strain APS

2006 ◽  
Vol 188 (18) ◽  
pp. 6539-6543 ◽  
Author(s):  
Kazuki Maezawa ◽  
Shuji Shigenobu ◽  
Hisaaki Taniguchi ◽  
Takeo Kubo ◽  
Shin-ichi Aizawa ◽  
...  
Keyword(s):  
Cell Surface ◽  
Basal Bodies ◽  
Endosymbiotic Bacterium ◽  
Symbiotic System ◽  
Buchnera Aphidicola ◽  
Flagellin Gene ◽  
Small Genome ◽  
Late Genes ◽  
Flagellar Proteins ◽  
Flagellar Genes

ABSTRACT Buchnera aphidicola is the endosymbiotic bacterium of the pea aphid. Due to its small genome size, Buchnera lacks many essential genes for autogenous life but obtains nutrients from the host. Although the Buchnera cell is nonmotile, it retains clusters of flagellar genes that lack the late genes necessary for motility, including the flagellin gene. In this study, we show that the flagellar genes are actually transcribed and translated and that the Buchnera cell surface is covered with hundreds of hook-basal-body (HBB) complexes. The abundance of HBB complexes suggests a role other than motility. We discuss the possibility that the HBB complex may serve as a protein transporter not only for the flagellar proteins but also for other proteins to maintain the symbiotic system.

scholarly journals Comparative Genomic and Morphological Analyses of Listeria Phages Isolated from Farm Environments

2014 ◽  
Vol 80 (15) ◽  
pp. 4616-4625 ◽  
Author(s):  
Thomas Denes ◽  
Kitiya Vongkamjan ◽  
Hans-Wolfgang Ackermann ◽  
Andrea I. Moreno Switt ◽  
Martin Wiedmann ◽  
...  
Keyword(s):  
New York ◽  
Dairy Farm ◽  
Morphological Diversity ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
The Novel ◽  
Important Food ◽  
Content Type ◽  
Small Genome ◽  
Food Borne

ABSTRACTThe genusListeriais ubiquitous in the environment and includes the globally important food-borne pathogenListeria monocytogenes. While the genomic diversity ofListeriahas been well studied, considerably less is known about the genomic and morphological diversity ofListeriabacteriophages. In this study, we sequenced and analyzed the genomes of 14Listeriaphages isolated mostly from New York dairy farm environments as well as one relatedEnterococcus faecalisphage to obtain information on genome characteristics and diversity. We also examined 12 of the phages by electron microscopy to characterize their morphology. TheseListeriaphages, based on gene orthology and morphology, together with previously sequencedListeriaphages could be classified into five orthoclusters, including one novel orthocluster. One orthocluster (orthocluster I) consists of large-genome (∼135-kb) myoviruses belonging to the genus “Twort-like viruses,” three orthoclusters (orthoclusters II to IV) contain small-genome (36- to 43-kb) siphoviruses with icosahedral heads, and the novel orthocluster V contains medium-sized-genome (∼66-kb) siphoviruses with elongated heads. A novel orthocluster (orthocluster VI) ofE. faecalisphages, with medium-sized genomes (∼56 kb), was identified, which grouped together and shares morphological features with the novelListeriaphage orthocluster V. This new group of phages (i.e., orthoclusters V and VI) is composed of putative lytic phages that may prove to be useful in phage-based applications for biocontrol, detection, and therapeutic purposes.

scholarly journals No ‘small genome attraction’ artifact: A response to Harish et al. ‘Did viruses evolve as a distinct supergroup from common ancestors of cells?’

2016 ◽  
Author(s):  
Arshan Nasir ◽  
Kyung Mo Kim ◽  
Gustavo Caetano-Anollés
Keyword(s):  
Phylogenetic Trees ◽  
Recent Literature ◽  
Viral Evolution ◽  
Tree Of Life ◽  
Tree Topology ◽  
Tree Reconstruction ◽  
Small Genome ◽  
Cellular Origin ◽  
Common Ancestors

In a recent eLetter and associated preprint, Harish, Abroi, Gough and Kurland criticized our structural phylogenomic methods, which support the early cellular origin of viruses. Their claims include the argument that the rooting of our trees is artifactual and distorted by small genome (proteome) size. Here we uncover their aprioristic reasoning, which mingles with misunderstandings and misinterpretations of cladistic methodology. To demonstrate, we labeled the phylogenetic positions of the smallest proteomes in our phylogenetic trees and confirm that the smallest genomes were neither attracted towards the root nor caused any distortions in the four-supergroup tree of life. Their results therefore stem from confusing outgroups with ancestors and handpicking problematic taxa to distort tree reconstruction. In doing so, they ignored the details of our rooting method, taxa sampling rationale, the plethora of evidence given in our study supporting the ancient origin of the viral supergroup and also recent literature on viral evolution. Indeed, our tree of life uncovered many viral monophyletic groups consistent with ICTV classifications and showed remarkable evolutionary tracings of virion morphotypes onto a revealing tree topology.

scholarly journals Beware of Mycoplasma Anti-immunoglobulin Strategies

mBio ◽  
2021 ◽  
Author(s):  
Yonathan Arfi ◽  
Carole Lartigue ◽  
Pascal Sirand-Pugnet ◽  
Alain Blanchard
Keyword(s):  
Host Species ◽  
Small Genome ◽  
Obligate Parasites ◽  
Wide Range

Mycoplasmas are small, genome-reduced bacteria. They are obligate parasites that can be found in a wide range of host species, including the majority of livestock animals and humans.

scholarly journals Complete Genome Sequence of Proteus mirabilis Phage Myduc

2019 ◽  
Vol 8 (47) ◽  
Author(s):  
Jennifer Tran ◽  
Lauren Lessor ◽  
Chandler O’Leary ◽  
Jason Gill ◽  
Mei Liu
Keyword(s):  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Genome Sequence ◽  
Proteus Mirabilis ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Nosocomial Pathogen ◽  
Content Type ◽  
Small Genome ◽  
Tract Infections

Proteus mirabilis as a nosocomial pathogen is often the cause of urinary tract infections. This announcement describes the complete genome sequence of a P. mirabilis myophage named Myduc. Phage Myduc is related to Enterobacteria phage phiEcoM-GJ1, which belongs to a group of myophages with small genome sizes (52,000 to 56,000 bp) possessing a T7-like RNA polymerase.

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