Improved hybrid genome assemblies of two strains of Bacteroides xylanisolvens, SD_CC_1b and SD_CC_2a, obtained using Illumina and 454 sequencing technologies

Genome Announcements

Volumn 2, Issue 2, 2014, Pages

  Ramaraj, Thiruvarangan ^a   Sundararajan, Anitha ^a   Schilkey, Faye D ^a   DelVecchio, Vito G ^b   Donlon, Mildred ^c   Ziemer, Cherie ^d   Mudge, Joann ^a  

^a NATIONAL CENTER FOR GENOME RESOURCES   (United States)

^b Vital Probes   (United States)

^c DEFENSE ADVANCED RESEARCH PROJECTS AGENCY   (United States)

^d U S DEPARTMENT OF AGRICULTURE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84998704895     PISSN: None     EISSN: 21698287     Source Type: Journal    
DOI: 10.1128/genomeA.00237-14     Document Type: Article

References (10)

1. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto J-M, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, MetaHIT Consortium, Bork P, Ehrlich SD, Wang J. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59. http://dx.doi.org/10.1038/nature08821.
2. Mirande C, Kadlecikova E, Matulova M, Capek P, Bernalier-Donadille A, Forano E, Béra-Maillet C. 2010. Dietary fibre degradation and fermentation by two xylanolytic bacteria Bacteroides xylanisolvens XB1A and Roseburia intestinalis XB6B4 from the human intestine. J. Appl. Microbiol. 109:451-460. http://dx.doi.org/10.1111/j.1365-2672.2010.04671.x.
3. Allison MJ, Robinson IM, Bucklin JA, Booth GD. 1979. Comparison of bacterial populations of the pig cecum and colon based upon enumeration with specific energy sources. Appl. Environ. Microbiol. 37:1142-1151.
4. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. 2005 Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380. http://dx.doi.org/10.1038/nature03959.
5. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. 2009. ABySS: a parallel assembler for short read sequence data. Genome Res. 19:1117-1123. http://dx.doi.org/10.1101/gr.089532.108.
6. Ewing B, Hillier L, Wendl MC, Green P. 1998. Base calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res. 8:175-185.
7. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760. http://dx.doi.org/10.1093/bioinformatics/btp324.
8. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. http://dx.doi.org/10.1186/1471-2164-9-75.
9. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673-679. http://dx.doi.org/10.1093/bioinformatics/btm009.
10. Salzberg SL, Delcher AL, Kasif S, White O. 1998. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 26: 544-548. http://dx.doi.org/10.1093/nar/26.2.544.