Genome Sequencing of Chlamydia pecorum Strains

Genome sequencing was performed by The Gene Pool genomic facility in The University of Edinburgh using Roche 454 GS-FLX and Solexa/Illumina 35-bp paired-end sequencing on standard libraries constructed according to the manufacturers instructions. Reads were assembled using Newbler v2 (Roche) and Velvet v.0.7 [52 (link)], combined using minimus2 and mapped to the reference genome of C. pecorum E58 [24 (link)] to generate 13, 10 and 9 contigs for P787, W73 and PV3056/3 respectively. In total, 12,926,259 (PV3056/3), 8,169,259 (W73) and 10,039,539 (P787) reads obtained from Solexa/Illumina sequencing and 95,683 (PV3056/3), 101,405 (W73) and 65,050 (P787) reads from Roche 454 GS-FLX sequencing were obtained. Following quality filtering, sequencing reads were mapped to the reference genome providing approximately 253× (PV3056/3), 136× (W73) and 59.4× (P787) sequencing coverage. Regions spanning the contig ends were PCR-amplified using Phusion High-fidelity DNA polymerase (NEB) and the sequence determined ensuring that each base was covered by sequence in each direction.

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Sait M., Livingstone M., Clark E.M., Wheelhouse N., Spalding L., Markey B., Magnino S., Lainson F.A., Myers G.S, & Longbottom D. (2014). Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes. BMC Genomics, 15(1), 23.

Publication 2014

Roche 454 GS-FLX

Dna polymerase Genomic Quality

Corresponding Organization :

Other organizations : University of Melbourne, Moredun Research Institute, University College Dublin, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", University of Maryland, Baltimore

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Variable analysis

independent variables

Genome sequencing performed by The Gene Pool genomic facility in The University of Edinburgh
Using Roche 454 GS-FLX and Solexa/Illumina 35-bp paired-end sequencing
Standard libraries constructed according to the manufacturers instructions
Reads assembled using Newbler v2 (Roche) and Velvet v.0.7
Contigs combined using minimus2 and mapped to the reference genome of C. pecorum E58

dependent variables

Number of contigs generated for P787, W73 and PV3056/3
Number of reads obtained from Solexa/Illumina and Roche 454 GS-FLX sequencing for P787, W73 and PV3056/3
Sequencing coverage for P787, W73 and PV3056/3

control variables

Regions spanning the contig ends were PCR-amplified using Phusion High-fidelity DNA polymerase (NEB) and the sequence determined ensuring that each base was covered by sequence in each direction

controls

No positive or negative controls explicitly mentioned

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