scholarly journals Under-representation of repetitive sequences in whole-genome shotgun sequence databases: an illustration using a recently acquired transposable element

Genome ◽  
2012 ◽  
Vol 55 (2) ◽  
pp. 172-175 ◽  
Author(s):  
Akihiko Koga
Keyword(s):  
Southern Blot Analysis ◽  
Repetitive Sequences ◽  
Whole Genome Shotgun ◽  
Whole Genome ◽  
Sequence Database ◽  
Shotgun Sequence ◽  
Whole Genome Shotgun Sequence ◽  
A Genome ◽  
Genome Shotgun Sequence ◽  
Sequence Databases

It is widely accepted in a conceptual framework that repetitive sequences, especially those with high sequence homogeneity among copies, tend to be under-represented in whole-genome shotgun sequence databases, because of the difficulty of assembling sequence reads into contigs. Although this is easily inferred, there is no quantitative illsutration of this phenomenon. An example using a currently used database is expected to contribute to the intuitive understanding of how serious the under-representation is. The present study provides the first quantitative example (in the case of 16 copies of virtually identical, 4.7-kb sequences in a genome of 7 × 10 8 bp) by comparing the results of BLAST searches of a sequence database (contig N50; 9.8 kb) with those of Southern blot analysis of genomic DNA. This has revealed that the internal regions of the repetitive sequences are under-represented to a striking extent.

scholarly journals Whole-Genome Shotgun Sequence of Halomonas sp. Strain SBS 10, Isolated from a Hypersaline Lake in India

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Bijayendra Kushwaha ◽  
Guru Prasad Sharma ◽  
Anshul Sharma ◽  
Prem Shankar ◽  
Anjali Geethadevi ◽  
...  
Keyword(s):  
Genome Size ◽  
Gene Clusters ◽  
Halophilic Bacterium ◽  
Whole Genome Shotgun ◽  
Hypersaline Lake ◽  
Whole Genome ◽  
Shotgun Sequence ◽  
Whole Genome Shotgun Sequence ◽  
Moderately Halophilic Bacterium ◽  
Genome Shotgun Sequence

The whole-genome shotgun sequence of a moderately halophilic bacterium, Halomonas sp. strain SBS 10, was assembled and studied. The assembled genome size was 1.5 Mb, with a G+C content of 63.6%. The genome sequence of this Halomonas sp. SBS 10 isolate will be valuable in understanding gene clusters and functions involved in the adaptability of this bacterium to hypersaline conditions.

scholarly journals Whole-Genome Shotgun Sequence of Salmonella bongori, First Isolated in Northwestern Italy

2017 ◽  
Vol 5 (27) ◽  
Author(s):  
Angelo Romano ◽  
Alberto Bellio ◽  
Guerrino Macori ◽  
Paul D. Cotter ◽  
Daniela Manila Bianchi ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Symptomatic Patient ◽  
Whole Genome Shotgun ◽  
Draft Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Shotgun Sequence ◽  
Whole Genome Shotgun Sequence ◽  
Genome Shotgun Sequence

ABSTRACT This study describes the whole-genome shotgun sequence of Salmonella bongori 48:z35:–, originally isolated from a 1-year-old symptomatic patient in northwest Italy, a typically nonendemic area. The draft genome sequence contained 4.56 Mbp and the G+C content was 51.27%.

scholarly journals Long-read, whole-genome shotgun sequence data for five model organisms

2014 ◽  
Vol 1 (1) ◽  
Author(s):  
Kristi E Kim ◽  
Paul Peluso ◽  
Primo Babayan ◽  
P. Jane Yeadon ◽  
Charles Yu ◽  
...  
Keyword(s):  
Sequence Data ◽  
Whole Genome Shotgun ◽  
Model Organisms ◽  
Whole Genome ◽  
Shotgun Sequence ◽  
Whole Genome Shotgun Sequence ◽  
Long Read ◽  
Genome Shotgun Sequence

scholarly journals Annotated Whole-Genome Shotgun Sequence of Multidrug-Resistant Mycobacterium tuberculosis MTB13_M Isolated from Morocco

2017 ◽  
Vol 5 (9) ◽  
Author(s):  
L. Lahlou ◽  
N. El Mrimar ◽  
T. Alouane ◽  
M. Laamarti ◽  
S. Karti ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Genome Sequence ◽  
Sputum Sample ◽  
Multidrug Resistant ◽  
Whole Genome Shotgun ◽  
Whole Genome ◽  
Content Type ◽  
Shotgun Sequence ◽  
Whole Genome Shotgun Sequence ◽  
Genome Shotgun Sequence

ABSTRACT Here, we describe the annotated genome sequence of Mycobacterium tuberculosis MTB13_M. The organism was isolated from a sputum sample in Morocco.

scholarly journals Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data

2007 ◽  
Vol 3 (9) ◽  
pp. e181 ◽  
Author(s):  
Can Alkan ◽  
Mario Ventura ◽  
Nicoletta Archidiacono ◽  
Mariano Rocchi ◽  
S. Cenk Sahinalp ◽  
...  
Keyword(s):  
Sequence Data ◽  
Whole Genome Shotgun ◽  
Whole Genome ◽  
Centromeric Dna ◽  
Shotgun Sequence ◽  
Whole Genome Shotgun Sequence ◽  
Genome Shotgun Sequence

scholarly journals First Whole-Genome Shotgun Sequence of a Promising Cellulase Secretor, Trichoderma koningiopsis Strain POS7

2017 ◽  
Vol 5 (37) ◽  
Author(s):  
María Lorena Castrillo ◽  
Gustavo Ángel Bich ◽  
Carlos Modenutti ◽  
Adrián Turjanski ◽  
Pedro Darío Zapata ◽  
...  
Keyword(s):  
Solid State ◽  
Sequence Analysis ◽  
Ab Initio ◽  
Genome Size ◽  
Solid State Fermentation ◽  
Whole Genome Shotgun ◽  
Whole Genome ◽  
Shotgun Sequence ◽  
Whole Genome Shotgun Sequence ◽  
Genome Shotgun Sequence

ABSTRACT Trichoderma koningiopsis strain POS7 produces significantly large amounts of cellulase enzymes in solid-state fermentation. The Illumina-based sequence analysis reveals an approximate genome size of 36.6 Mbp, with a G+C content of 48.82% for T. koningiopsis POS7. Based on ab initio prediction, 12,661 coding genes were annotated.

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