scholarly journals Comparative genomics and genome evolution in yeasts

2006 ◽  
Vol 361 (1467) ◽  
pp. 403-412 ◽  
Author(s):  
Kenneth H Wolfe
Keyword(s):  
Comparative Genomics ◽  
Genome Evolution ◽  
Model System ◽  
Genome Sequences ◽  
Broad Perspective ◽  
Sequence Identity ◽  
Species Pairs ◽  
Genomics Research ◽  
Protein Sequence Identity ◽  
Low Levels

Yeasts provide a powerful model system for comparative genomics research. The availability of multiple complete genome sequences from different fungal groups—currently 18 hemiascomycetes, 8 euascomycetes and 4 basidiomycetes—enables us to gain a broad perspective on genome evolution. The sequenced genomes span a continuum of divergence levels ranging from multiple individuals within a species to species pairs with low levels of protein sequence identity and no conservation of gene order. One of the most interesting emerging areas is the growing number of events such as gene losses, gene displacements and gene relocations that can be attributed to the action of natural selection.

scholarly journals Genome evolution in trypanosomatid parasites

Parasitology ◽  
2014 ◽  
Vol 142 (S1) ◽  
pp. S40-S56 ◽  
Author(s):  
ANDREW P. JACKSON
Keyword(s):  
Comparative Genomics ◽  
Genome Evolution ◽  
Genome Sequencing ◽  
Molecular Mechanisms ◽  
Genome Sequences ◽  
Parasitic Lifestyle ◽  
Trypanosomatid Parasites ◽  
The Many ◽  
Species Specific ◽  
Fresh Impetus

SUMMARYA decade of genome sequencing has transformed our understanding of how trypanosomatid parasites have evolved and provided fresh impetus to explaining the origins of parasitism in the Kinetoplastida. In this review, I will consider the many ways in which genome sequences have influenced our view of genomic reduction in trypanosomatids; how species-specific genes, and the genomic domains they occupy, have illuminated the innovations in trypanosomatid genomes; and how comparative genomics has exposed the molecular mechanisms responsible for innovation and adaptation to a parasitic lifestyle.

scholarly journals Comparative Genomics of the T4-Like Escherichia coli Phage JS98: Implications for the Evolution of T4 Phages

2004 ◽  
Vol 186 (24) ◽  
pp. 8276-8286 ◽  
Author(s):  
Sandra Chibani-Chennoufi ◽  
Carlos Canchaya ◽  
Anne Bruttin ◽  
Harald Brüssow
Keyword(s):  
Dna Replication ◽  
Comparative Genomics ◽  
Protein Sequence ◽  
Point Mutations ◽  
Sequence Information ◽  
Tail Fiber ◽  
Mobile Dna ◽  
Putative Gene ◽  
Sequence Identity ◽  
Protein Sequence Identity

ABSTRACT About 130 kb of sequence information was obtained from the coliphage JS98 isolated from the stool of a pediatric diarrhea patient in Bangladesh. The DNA shared up to 81% base pair identity with phage T4. The most conserved regions between JS98 and T4 were the structural genes, but their degree of conservation was not uniform. The head genes showed the highest sequence conservation, followed by the tail, baseplate, and tail fiber genes. Many tail fiber genes shared only protein sequence identity. Except for the insertion of endonuclease genes in T4 and gene 24 duplication in JS98, the structural gene maps of the two phages were colinear. The receptor-recognizing tail fiber proteins gp37 and gp38 were only distantly related to T4, but shared up to 83% amino acid identity to other T6-like phages, suggesting lateral gene transfer. A greater degree of variability was seen between JS98 and T4 over DNA replication and DNA transaction genes. While most of these genes came in the same order and shared up to 76% protein sequence identity, a few rearrangements, insertions, and replacements of genes were observed. Many putative gene insertions in the DNA replication module of T4 were flanked by intron-related endonuclease genes, suggesting mobile DNA elements. A hotspot of genome diversification was located downstream of the DNA polymerase gene 43 and the DNA binding gene 32. Comparative genomics of 100-kb genome sequence revealed that T4-like phages diversify more by the accumulation of point mutations and occasional gene duplication events than by modular exchanges.

scholarly journals Four Novel Mycoviruses from the Hypovirulent Botrytis cinerea SZ-2-3y Isolate from Paris polyphylla: Molecular Characterisation and Mitoviral Sequence Transboundary Entry into Plants

Viruses ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 151
Author(s):  
Qiong Wang ◽  
Qi Zou ◽  
Zhaoji Dai ◽  
Ni Hong ◽  
Guoping Wang ◽  
...  
Keyword(s):  
Botrytis Cinerea ◽  
Amino Acid Sequence Identity ◽  
Horizontal Transmission ◽  
Plant Mitochondria ◽  
Full Length ◽  
Genome Sequences ◽  
Rna Dependent Rna Polymerase ◽  
New Members ◽  
Sequence Identity ◽  
Paris Polyphylla

A hypovirulent SZ-2-3y strain isolated from diseased Paris polyphylla was identified as Botrytis cinerea. Interestingly, SZ-2-3y was coinfected with a mitovirus, two botouliviruses, and a 3074 nt fusarivirus, designated Botrytis cinerea fusarivirus 8 (BcFV8); it shares an 87.2% sequence identity with the previously identified Botrytis cinerea fusarivirus 6 (BcFV6). The full-length 2945 nt genome sequence of the mitovirus, termed Botrytis cinerea mitovirus 10 (BcMV10), shares a 54% sequence identity with Fusarium boothii mitovirus 1 (FbMV1), and clusters with fungus mitoviruses, plant mitoviruses and plant mitochondria; hence BcMV10 is a new Mitoviridae member. The full-length 2759 nt and 2812 nt genome sequences of the other two botouliviruses, named Botrytis cinerea botoulivirus 18 and 19 (BcBoV18 and 19), share a 40% amino acid sequence identity with RNA-dependent RNA polymerase protein (RdRp), and these are new members of the Botoulivirus genus of Botourmiaviridae. Horizontal transmission analysis showed that BcBoV18, BcBoV19 and BcFV8 are not related to hypovirulence, suggesting that BcMV10 may induce hypovirulence. Intriguingly, a partial BcMV10 sequence was detected in cucumber plants inoculated with SZ-2-3y mycelium or pXT1/BcMV10 agrobacterium. In conclusion, we identified a hypovirulent SZ-2-3y fungal strain from P. polyphylla, coinfected with four novel mycoviruses that could serve as potential biocontrol agents. Our findings provide evidence of cross-kingdom mycoviral sequence transmission.

scholarly journals Genome evolution of SARS-CoV-2 and its virological characteristics

2020 ◽  
Vol 40 (1) ◽  
Author(s):  
So Nakagawa ◽  
Takayuki Miyazawa
Keyword(s):  
Genome Evolution ◽  
Genome Sequence ◽  
Causative Agent ◽  
Sequence Data ◽  
Genome Sequences ◽  
Genome Sequence Data ◽  
Global Prevalence ◽  
Horseshoe Bats

AbstractCoronavirus disease of 2019 (COVID-19), which originated in China in 2019, shows mild cold and pneumonia symptoms that can occasionally worsen and result in deaths. SARS-CoV-2 was reported to be the causative agent of the disease and was identified as being similar to SARS-CoV, a causative agent of SARS in 2003. In this review, we described the phylogeny of SARS-CoV-2, covering various related studies, in particular, focusing on viruses obtained from horseshoe bats and pangolins that belong to Sarbecovirus, a subgenus of Betacoronavirus. We also describe the virological characteristics of SARS-CoV-2 and compare them with other coronaviruses. More than 30,000 genome sequences of SARS-CoV-2 are available in the GISAID database as of May 28, 2020. Using the genome sequence data of closely related viruses, the genomic characteristics and evolution of SARS-CoV-2 were extensively studied. However, given the global prevalence of COVID-19 and the large number of associated deaths, further computational and experimental virological analyses are required to fully characterize SARS-CoV-2.

Relationships of tailed phages: a survey of protein sequence identity

1995 ◽  
Vol 140 (10) ◽  
pp. 1871-1884 ◽  
Author(s):  
H. -W. Ackermann ◽  
A. Elzanowski ◽  
G. Fobo ◽  
G. Stewart
Keyword(s):  
Protein Sequence ◽  
Sequence Identity ◽  
Protein Sequence Identity

Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi

2020 ◽  
Author(s):  
Lotus A. Lofgren ◽  
Nhu H. Nguyen ◽  
Rytas Vilgalys ◽  
Joske Ruytinx ◽  
Hui‐Ling Liao ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Genome Evolution ◽  
Ectomycorrhizal Fungi ◽  
Dynamic Genome

scholarly journals Two Metagenome-Assembled Genome Sequences of Magnetotactic Bacteria in the Order Magnetococcales

2020 ◽  
Vol 9 (35) ◽  
Author(s):  
Wensi Zhang ◽  
Runjia Ji ◽  
Jia Liu ◽  
Yongxin Pan ◽  
Long-Fei Wu ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Magnetotactic Bacteria ◽  
Model System ◽  
Genome Sequences

ABSTRACT Magnetotactic bacteria represent a valuable model system for the study of microbial biomineralization and magnetotaxis. Here, we report two metagenome-assembled genome sequences of uncultivated magnetotactic bacteria belonging to the order Magnetococcales. These genomes contain nearly complete magnetosome gene clusters responsible for magnetosome biomineralization.

scholarly journals Complete Genome Sequences of Six Legionella pneumophila Isolates from Two Collocated Outbreaks of Legionnaires’ Disease in 2005 and 2008 in Sarpsborg/Fredrikstad, Norway

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Marius Dybwad ◽  
Tone Aarskaug ◽  
Else-Marie Fykse ◽  
Elisabeth Henie Madslien ◽  
Janet Martha Blatny
Keyword(s):  
Comparative Genomics ◽  
Genetic Relationship ◽  
Legionella Pneumophila ◽  
Complete Genome ◽  
Sequence Similarity ◽  
Secretion Systems ◽  
Environmental Isolates ◽  
Genome Sequences ◽  
High Sequence Similarity ◽  
Legionnaires Disease

Here, we report the complete genome sequences of Legionella pneumophila isolates from two collocated outbreaks of Legionnaires’ disease in 2005 and 2008 in Sarpsborg/Fredrikstad, Norway. One clinical and two environmental isolates were sequenced from each outbreak. The genome of all six isolates consisted of a 3.36 Mb-chromosome, while the 2005 genomes featured an additional 68 kb-episome sharing high sequence similarity with the L. pneumophila Lens plasmid. All six genomes contained multiple mobile genetic elements including novel combinations of type-IVA secretion systems. A comparative genomics study will be launched to resolve the genetic relationship between the L. pneumophila isolates.

Sign in / Sign up

Export Citation Format

Share Document