Genome rearrangement

1984 ◽  
Vol 26 (S8B) ◽  
pp. 119-164
Keyword(s):  
Genome Rearrangement

scholarly journals Comparative insights into genome signatures of ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yong Guo ◽  
Tomo Aoyagi ◽  
Tomoyuki Hori
Keyword(s):  
Iron Oxide ◽  
Genome Rearrangement ◽  
Ferric Iron ◽  
Electron Acceptors ◽  
Extracellular Electron Transfer ◽  
Redox Potentials ◽  
Bacterial Strains ◽  
Biosynthesis Gene Cluster ◽  
Genomic Signatures ◽  
Flagellar Biosynthesis

Abstract Background Halotolerant Fe (III) oxide reducers affiliated in the family Desulfuromonadaceae are ubiquitous and drive the carbon, nitrogen, sulfur and metal cycles in marine subsurface sediment. Due to their possible application in bioremediation and bioelectrochemical engineering, some of phylogenetically close Desulfuromonas spp. strains have been isolated through enrichment with crystalline Fe (III) oxide and anode. The strains isolated using electron acceptors with distinct redox potentials may have different abilities, for instance, of extracellular electron transport, surface recognition and colonization. The objective of this study was to identify the different genomic signatures between the crystalline Fe (III) oxide-stimulated strain AOP6 and the anode-stimulated strains WTL and DDH964 by comparative genome analysis. Results The AOP6 genome possessed the flagellar biosynthesis gene cluster, as well as diverse and abundant genes involved in chemotaxis sensory systems and c-type cytochromes capable of reduction of electron acceptors with low redox potentials. The WTL and DDH964 genomes lacked the flagellar biosynthesis cluster and exhibited a massive expansion of transposable gene elements that might mediate genome rearrangement, while they were deficient in some of the chemotaxis and cytochrome genes and included the genes for oxygen resistance. Conclusions Our results revealed the genomic signatures distinctive for the ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains. These findings highlighted the different metabolic abilities, such as extracellular electron transfer and environmental stress resistance, of these phylogenetically close bacterial strains, casting light on genome evolution of the subsurface Fe (III) oxide reducers.

Analysis of Genome Rearrangement by Block-Interchanges

2007 ◽  
pp. 121-134 ◽  
Author(s):  
Lung Lu Chin ◽  
Chih Lin Ying ◽  
Lin Huang Yen ◽  
Yi Tang Chuan
Keyword(s):  
Genome Rearrangement

scholarly journals Circularization restores signal recognition particle RNA functionality in Thermoproteus

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
André Plagens ◽  
Michael Daume ◽  
Julia Wiegel ◽  
Lennart Randau
Keyword(s):  
Genome Rearrangement ◽  
Signal Recognition Particle ◽  
Circular Rna ◽  
Signal Recognition ◽  
Rna Molecules ◽  
Trna Splicing ◽  
Ribonucleoprotein Complexes ◽  
Domains Of Life ◽  
Thermoproteus Tenax ◽  
Srp Rna

Signal recognition particles (SRPs) are universal ribonucleoprotein complexes found in all three domains of life that direct the cellular traffic and secretion of proteins. These complexes consist of SRP proteins and a single, highly structured SRP RNA. Canonical SRP RNA genes have not been identified for some Thermoproteus species even though they contain SRP19 and SRP54 proteins. Here, we show that genome rearrangement events in Thermoproteus tenax created a permuted SRP RNA gene. The 5'- and 3'-termini of this SRP RNA are located close to a functionally important loop present in all known SRP RNAs. RNA-Seq analyses revealed that these termini are ligated together to generate circular SRP RNA molecules that can bind to SRP19 and SRP54. The circularization site is processed by the tRNA splicing endonuclease. This moonlighting activity of the tRNA splicing machinery permits the permutation of the SRP RNA and creates highly stable and functional circular RNA molecules.

scholarly journals Minimum Common String Partition Problem: Hardness and Approximations

10.37236/1947 ◽  
2005 ◽  
Vol 12 (1) ◽  
Author(s):  
Avraham Goldstein ◽  
Petr Kolman ◽  
Jie Zheng
Keyword(s):  
Genome Rearrangement ◽  
Linear Time ◽  
Fundamental Problem ◽  
Text Processing ◽  
Partition Problem ◽  
Sorting By Reversals ◽  
String Comparison ◽  
Minimum Number ◽  
Tight Connection ◽  
Minimum Common String Partition

String comparison is a fundamental problem in computer science, with applications in areas such as computational biology, text processing and compression. In this paper we address the minimum common string partition problem, a string comparison problem with tight connection to the problem of sorting by reversals with duplicates, a key problem in genome rearrangement. A partition of a string $A$ is a sequence ${\cal P} = (P_1,P_2,\dots,P_m)$ of strings, called the blocks, whose concatenation is equal to $A$. Given a partition ${\cal P}$ of a string $A$ and a partition ${\cal Q}$ of a string $B$, we say that the pair $\langle{{\cal P},{\cal Q}}\rangle$ is a common partition of $A$ and $B$ if ${\cal Q}$ is a permutation of ${\cal P}$. The minimum common string partition problem (MCSP) is to find a common partition of two strings $A$ and $B$ with the minimum number of blocks. The restricted version of MCSP where each letter occurs at most $k$ times in each input string, is denoted by $k$-MCSP. In this paper, we show that $2$-MCSP (and therefore MCSP) is NP-hard and, moreover, even APX-hard. We describe a $1.1037$-approximation for $2$-MCSP and a linear time $4$-approximation algorithm for $3$-MCSP. We are not aware of any better approximations.

scholarly journals Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura

2002 ◽  
Vol 80 (3) ◽  
pp. 163-175 ◽  
Author(s):  
STEPHEN W. SCHAEFFER
Keyword(s):  
Negative Selection ◽  
Genome Rearrangement ◽  
Rare Variants ◽  
Natural Populations ◽  
Population Expansion ◽  
Purifying Selection ◽  
Sequence Length ◽  
Nucleotide Sequence Analysis ◽  
Drosophila Pseudoobscura ◽  
Indel Variation

Positive and negative selection on indel variation may explain the correlation between intron length and recombination levels in natural populations of Drosophila. A nucleotide sequence analysis of the 3·5 kilobase sequence of the alcohol dehydrogenase (Adh) region from 139 Drosophila pseudoobscura strains and one D. miranda strain was used to determine whether positive or negative selection acts on indel variation in a gene that experiences high levels of recombination. A total of 30 deletion and 36 insertion polymorphisms were segregating within D. pseudoobscura populations and no indels were fixed between D. pseudoobscura and its two sibling species D. miranda and D. persimilis. The ratio of Tajima's D to its theoretical minimum value (Dmin) was proposed as a metric to assess the heterogeneity in D among D. pseudoobscura loci when the number of segregating sites differs among loci. The magnitude of the D/Dmin ratio was found to increase as the rate of population expansion increases, allowing one to assess which loci have an excess of rare variants due to population expansion versus purifying selection. D. pseudoobscura populations appear to have had modest increases in size accounting for some of the observed excess of rare variants. The D/Dmin ratio rejected a neutral model for deletion polymorphisms. Linkage disequilibrium among pairs of indels was greater than between pairs of segregating nucleotides. These results suggest that purifying selection removes deletion variation from intron sequences, but not insertion polymorphisms. Genome rearrangement and size-dependent intron evolution are proposed as mechanisms that limit runaway intron expansion.

scholarly journals Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution

2018 ◽  
Vol 50 (11) ◽  
pp. 1617-1617
Author(s):  
Jeramiah J. Smith ◽  
Nataliya Timoshevskaya ◽  
Chengxi Ye ◽  
Carson Holt ◽  
Melissa C. Keinath ◽  
...  
Keyword(s):  
Genome Rearrangement ◽  
Sea Lamprey ◽  
Vertebrate Evolution
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