scholarly journals A haplotype method detects diverse scenarios of local adaptation from genomic sequence variation

2016 ◽  
Vol 25 (13) ◽  
pp. 3081-3100 ◽  
Author(s):  
Jeremy D. Lange ◽  
John E. Pool
Keyword(s):  
Local Adaptation ◽  
Sequence Variation ◽  
Genomic Sequence

scholarly journals Exploring neighborhoods in large metagenome assembly graphs reveals hidden sequence diversity

2018 ◽  
Author(s):  
C. Titus Brown ◽  
Dominik Moritz ◽  
Michael P. O’Brien ◽  
Felix Reidl ◽  
Taylor Reiter ◽  
...  
Keyword(s):  
Sequence Variation ◽  
Retrieval System ◽  
Genomic Sequence ◽  
Information Retrieval System ◽  
Software Implementation ◽  
Metagenomic Data ◽  
Data Sets ◽  
Dna Assembly ◽  
Strain Variation ◽  
Metagenome Assembly

Genomes computationally inferred from large metagenomic data sets are often incomplete and may be missing functionally important content and strain variation. We introduce an information retrieval system for large metagenomic data sets that exploits the sparsity of DNA assembly graphs to efficiently extract subgraphs surrounding an inferred genome. We apply this system to recover missing content from genome bins and show that substantial genomic sequence variation is present in a real metagenome. Our software implementation is available at https://github.com/spacegraphcats/ spacegraphcats under the 3-Clause BSD License.

scholarly journals Sequence Variation among Group III F-Specific RNA Coliphages from Water Samples and Swine Lagoons

2006 ◽  
Vol 72 (2) ◽  
pp. 1226-1230 ◽  
Author(s):  
Jill R. Stewart ◽  
Jan Vinjé ◽  
Sjon J. G. Oudejans ◽  
Geoff I. Scott ◽  
Mark D. Sobsey
Keyword(s):  
South Carolina ◽  
Surface Waters ◽  
Sequence Variation ◽  
Genomic Sequence ◽  
Nucleic Acid Hybridization ◽  
Nucleotide Sequencing ◽  
Sequence Information ◽  
Group Iii ◽  
Swine Lagoons ◽  
Prototype Virus

ABSTRACT Typing of F-specific RNA (FRNA) coliphages has been proposed as a useful method for distinguishing human from animal fecal contamination in environmental samples. Group II and III FRNA coliphages are generally associated with human wastes, but several exceptions have been noted. In the present study, we have genotyped and partially sequenced group III FRNA coliphage field isolates from swine lagoons in North Carolina (NC) and South Carolina (SC), along with isolates from surface waters and municipal wastewaters. Phylogenetic analysis of a region of the 5′ end of the maturation protein gene revealed two genetically different group III FRNA subclusters with 36.6% sequence variation. The SC swine lagoon isolates were more closely related to group III prototype virus M11, whereas the isolates from a swine lagoon in NC, surface waters, and wastewaters grouped with prototype virus Q-beta. These results suggest that refining phage genotyping systems to discriminate M11-like phages from Q-beta-like phages would not necessarily provide greater discriminatory power in distinguishing human from animal sources of pollution. Within the group III subclusters, nucleotide sequence diversity ranged from 0% to 6.9% for M11-like strains and from 0% to 8.7% for Q-beta-like strains. It is demonstrated here that nucleotide sequencing of closely related FRNA strains can be used to help track sources of contamination in surface waters. A similar use of phage genomic sequence information to track fecal pollution promises more reliable results than phage typing by nucleic acid hybridization and may hold more potential for field applications.

Timing and rate of genome variation in triticale following allopolyploidization

Genome ◽  
2006 ◽  
Vol 49 (8) ◽  
pp. 950-958 ◽  
Author(s):  
Xue-Feng Ma ◽  
J Perry Gustafson
Keyword(s):  
Sequence Variation ◽  
Genomic Sequence ◽  
Chromosome Doubling ◽  
Genomic Variation ◽  
Key Factors ◽  
Genome Variation ◽  
Triticum Spp ◽  
Secale Cereale L ◽  
Triticosecale Wittmack ◽  
The Relationship

The timing and rate of genomic variation induced by allopolyploidization in the intergeneric wheat-rye (Triticum spp. – Secale cereale L.) hybrid triticale (× Triticosecale Wittmack) was studied using amplified fragment length polymorphism (AFLP) analyses with 2 sets of primers, EcoRI–MseI (E–M) and PstI–MseI (P–M), which primarily amplify repetitive and low-copy sequences, respectively. The results showed that allopolyploidization induced genome sequence variation in triticale and that a great degree of the genome variation occurred immediately following wide hybridization. Specifically, about 46.3% and 36.2% of the wheat parental band loss and 74.5% and 68.4% of the rye parental band loss occurred in the F1 hybrids (before chromosome doubling) for E–M and P–M primers, respectively. The sequence variation events that followed chromosome doubling consisted of continuous modifications that occurred at a very small rate compared with the rate of variation before chromosome doubling. However, the rate of sequence variation involving the rye parental genome was much higher in the first 5 generations following chromosome doubling than in any subsequent generation. Surprisingly, the highest rate of rye genomic variation occurring after chromosome doubling was in C3 or later, but not in C1. The data suggested that the cytoplasm and the degree of the relationship between the parental genomes were the key factors in determining the direction, amount, timing, and rate of genomic sequence variation occurring during intergeneric allopolyploidization.Key words: genome evolution, sequence variation, allopolyploid, triticale, AFLP.

scholarly journals Whole-Genome Sequence Variation among Multiple Isolates of Pseudomonas aeruginosa

2003 ◽  
Vol 185 (4) ◽  
pp. 1316-1325 ◽  
Author(s):  
David H. Spencer ◽  
Arnold Kas ◽  
Eric E. Smith ◽  
Christopher K. Raymond ◽  
Elizabeth H. Sims ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Nucleotide Diversity ◽  
Sequence Variation ◽  
Genomic Sequence ◽  
Genetic Material ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Specific Sequence ◽  
O Antigen

ABSTRACT Whole-genome shotgun sequencing was used to study the sequence variation of three Pseudomonas aeruginosa isolates, two from clonal infections of cystic fibrosis patients and one from an aquatic environment, relative to the genomic sequence of reference strain PAO1. The majority of the PAO1 genome is represented in these strains; however, at least three prominent islands of PAO1-specific sequence are apparent. Conversely, ∼10% of the sequencing reads derived from each isolate fail to align with the PAO1 backbone. While average sequence variation among all strains is roughly 0.5%, regions of pronounced differences were evident in whole-genome scans of nucleotide diversity. We analyzed two such divergent loci, the pyoverdine and O-antigen biosynthesis regions, by complete resequencing. A thorough analysis of isolates collected over time from one of the cystic fibrosis patients revealed independent mutations resulting in the loss of O-antigen synthesis alternating with a mucoid phenotype. Overall, we conclude that most of the PAO1 genome represents a core P. aeruginosa backbone sequence while the strains addressed in this study possess additional genetic material that accounts for at least 10% of their genomes. Approximately half of these additional sequences are novel.

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