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- W2783825348 abstract "Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, an incompleteness that causes numerous problems and constitutes a major obstacle to genotypic and phenotypic interpretation. In this work, we began with an example from the class Bacteroidia in the phylum Bacteroidetes, which is preponderant among human orodigestive microbiota. We successfully identify the genetic loci responsible for assembly breaks and misassemblies and demonstrate the importance and usefulness of long-read sequencing and curated reannotation. We showed that the fragmentation in Bacteroidia draft genomes assembled from massively parallel sequencing linearly correlates with genomic repeats of the same or greater size than the reads. We also demonstrated that some of these repeats, especially the long ones, correspond to misassembled loci in three reference Porphyromonas gingivalis genomes marked as circularized (thus complete or finished). We prove that even at modest coverage (30X), long-read resequencing together with PCR contiguity verification (rrn operons and an integrative and conjugative element or ICE) can be used to identify and correct the wrongly combined or assembled regions. Finally, although time-consuming and labor-intensive, consistent manual biocuration of three P. gingivalis strains allowed us to compare and correct the existing genomic annotations, resulting in a more accurate interpretation of the genomic differences among these strains. In this study, we demonstrate the usefulness and importance of long-read sequencing in verifying published genomes (even when complete) and generating assemblies for new bacterial strains/species with high genomic plasticity. We also show that when combined with biological validation processes and diligent biocurated annotation, this strategy helps reduce the propagation of errors in shared databases, thus limiting false conclusions based on incomplete or misleading information." @default.
- W2783825348 created "2018-01-26" @default.
- W2783825348 creator A5011589051 @default.
- W2783825348 creator A5011594490 @default.
- W2783825348 creator A5045037534 @default.
- W2783825348 creator A5065390624 @default.
- W2783825348 creator A5066876231 @default.
- W2783825348 date "2018-01-16" @default.
- W2783825348 modified "2023-10-17" @default.
- W2783825348 title "Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains" @default.
- W2783825348 cites W1255716819 @default.
- W2783825348 cites W1506991196 @default.
- W2783825348 cites W1511583500 @default.
- W2783825348 cites W1553112231 @default.
- W2783825348 cites W1558097999 @default.
- W2783825348 cites W1562379515 @default.
- W2783825348 cites W1577822803 @default.
- W2783825348 cites W1810384854 @default.
- W2783825348 cites W1906262170 @default.
- W2783825348 cites W1906470927 @default.
- W2783825348 cites W1966336245 @default.
- W2783825348 cites W1969326676 @default.
- W2783825348 cites W1970995855 @default.
- W2783825348 cites W1972755256 @default.
- W2783825348 cites W1972936428 @default.
- W2783825348 cites W1974383394 @default.
- W2783825348 cites W1974640383 @default.
- W2783825348 cites W1977730635 @default.
- W2783825348 cites W1982579644 @default.
- W2783825348 cites W1985491754 @default.
- W2783825348 cites W1989895641 @default.
- W2783825348 cites W1990814944 @default.
- W2783825348 cites W1991608395 @default.
- W2783825348 cites W1997246534 @default.
- W2783825348 cites W2001660787 @default.
- W2783825348 cites W2002955517 @default.
- W2783825348 cites W2004589024 @default.
- W2783825348 cites W2005077092 @default.
- W2783825348 cites W2009596137 @default.
- W2783825348 cites W2013219901 @default.
- W2783825348 cites W2014564174 @default.
- W2783825348 cites W2026294678 @default.
- W2783825348 cites W2026347365 @default.
- W2783825348 cites W2032230795 @default.
- W2783825348 cites W2036274080 @default.
- W2783825348 cites W2037069087 @default.
- W2783825348 cites W2041257508 @default.
- W2783825348 cites W2046137036 @default.
- W2783825348 cites W2048565041 @default.
- W2783825348 cites W2051824825 @default.
- W2783825348 cites W2054605909 @default.
- W2783825348 cites W2055043387 @default.
- W2783825348 cites W2061379404 @default.
- W2783825348 cites W2061657565 @default.
- W2783825348 cites W2063756105 @default.
- W2783825348 cites W2063892792 @default.
- W2783825348 cites W2067865784 @default.
- W2783825348 cites W2072534996 @default.
- W2783825348 cites W2074800586 @default.
- W2783825348 cites W2078859666 @default.
- W2783825348 cites W2079899518 @default.
- W2783825348 cites W2083962492 @default.
- W2783825348 cites W2091232725 @default.
- W2783825348 cites W2091328482 @default.
- W2783825348 cites W2094201044 @default.
- W2783825348 cites W2096093282 @default.
- W2783825348 cites W2096143955 @default.
- W2783825348 cites W2098172271 @default.
- W2783825348 cites W2101330256 @default.
- W2783825348 cites W2103546861 @default.
- W2783825348 cites W2104046507 @default.
- W2783825348 cites W2104677379 @default.
- W2783825348 cites W2105656684 @default.
- W2783825348 cites W2105708056 @default.
- W2783825348 cites W2105831375 @default.
- W2783825348 cites W2106056635 @default.
- W2783825348 cites W2106203512 @default.
- W2783825348 cites W2107247090 @default.
- W2783825348 cites W2107772251 @default.
- W2783825348 cites W2108228587 @default.
- W2783825348 cites W2108528950 @default.
- W2783825348 cites W2116846792 @default.
- W2783825348 cites W2119121014 @default.
- W2783825348 cites W2119284644 @default.
- W2783825348 cites W2120172561 @default.
- W2783825348 cites W2120457919 @default.
- W2783825348 cites W2120721793 @default.
- W2783825348 cites W2120902911 @default.
- W2783825348 cites W2121364424 @default.
- W2783825348 cites W2121621283 @default.
- W2783825348 cites W2122701921 @default.
- W2783825348 cites W2125591244 @default.
- W2783825348 cites W2125826054 @default.
- W2783825348 cites W2125978670 @default.
- W2783825348 cites W2126098996 @default.
- W2783825348 cites W2127391962 @default.
- W2783825348 cites W2127774996 @default.
- W2783825348 cites W2127781493 @default.
- W2783825348 cites W2128711701 @default.
- W2783825348 cites W2128769815 @default.