NOVOPlasty: De novo assembly of organelle genomes from whole genome data

Nucleic Acids Research

Volumn 45, Issue 4, 2017, Pages

  Dierckxsens, Nicolas ^a   Mardulyn, Patrick ^a,b   Smits, Guillaume ^a,c,d  

^a Interuniversity Institute of Bioinformatics in Brussels (IB)2   (Belgium)

^b UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^c HOP UNIV DES ENFANTS REINE FABIOLA   (Belgium)

^d ERASME HOSPITAL   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARABIDOPSIS THALIANA; ARTICLE; AVICENNIA MARINA; CELL ORGANELLE; CHLOROPLAST; CHLOROPLAST GENE; CONTIG MAPPING; CONTROLLED STUDY; GENETIC COMPATIBILITY; GENOME ANALYSIS; HUMAN; MEASUREMENT ACCURACY; MITOCHONDRION; NEXT GENERATION SEQUENCING; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; RICE; SEQUENCE ALIGNMENT; WHOLE GENOME SEQUENCING; ANIMAL; AVICENNIA; BEETLE; CHLOROPLAST GENOME; GENETICS; MITOCHONDRIAL GENOME; PROCEDURES; SOFTWARE;

ALGORITHMS; ANIMALS; AVICENNIA; COLEOPTERA; GENOME, CHLOROPLAST; GENOME, MITOCHONDRIAL; SOFTWARE; WHOLE GENOME SEQUENCING;

EID: 85007311154     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw955     Document Type: Article

References (24)

1. Brozynska,M., Furtado,A. and Henry,R.J. (2014) Direct chloroplast sequencing: Comparison of sequencing platforms and analysis tools for whole chloroplast barcoding. PLoS One, 9, e110387.
2. Bignell,G.R., Miller,A.R. and Evans,I.H. (1996) Isolation of mitochondrial DNA. Methods Mol. Biol., 53, 109-106.
3. Jansen,R.K., Raubeson,L.A., Boore,J.L., dePamphilis,C.W., Chumley,T.W., Haberle,R.C., Wyman,S.K., Alverson,A.J., Peery,R., Herman,S.J. et al. (2005) Methods for obtaining and analyzing whole chloroplast genome sequences. In: Elizabeth,AZ and Eric,HR (eds). Methods in Enzymology. Academic Press, pp. 348-384.
4. Khan,A., Khan,I.A, Asif,H. and Azim,M.K. (2010) Current trends in chloroplast genome research. Afr. J. Biotechnol., 9, 3494-3500.
5. Wu,J., Liu,B., Cheng,F., Ramchiary,N., Choi,S.R., Lim,Y.P. and Wang,X-W. (2012) Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology. Front. Plant Sci., 3, 243.
6. Ahmed,I. (2015) Chloroplast genome sequencing: some reflections. Next Gen. Seq. Appl., 2, 2.
7. Ekblom,R., Smeds,L. and Ellegren,H. (2014) Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria. BMC Genomics, 15, 1-9.
8. McPherson,H., van der Merwe,M., Delaney,S.K., Edwards,M.A. and Henry,R.J. (2013) Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree. BMC Ecol., 13, 8.
9. Hahn,C., Bachmann,L. and Chevreux,B. (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads-a baiting and iterative mapping approach. Nucleic Acids Res., 41, e129.
10. Chevreux,B., Wetter,T. and Suhai,S. (1999) Genome sequence assembly using trace signals and additional sequence information. Comput. Sci. Biol., 99, 45-56.
11. Luo,R., Liu,B., Xie,Y., Li,Z., Huang,W., Yuan,J., He,G., Chen,Y., Pan,Q., Liu,Y. et al. (2012) SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler. GigaScience, 1, 18.
12. Langmead,B. and Salzberg,S. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
13. Milne,I., Bayer,M., Stephen,G., Cardle,L. and Marshall,D. (2016) Tablet: visualizing next-generation sequence assemblies and mappings. Methods Mol. Biol., 1374, 253-268.
14. Warren,R.L., Sutton,G.G., Jones,S.J. and Holt,R.A. (2007) Assembling millions of short DNA sequences using SSAKE. Bioinformatics, 23, 500-501.
15. Jeck,W.R., Reinhardt,J.A., Baltrus,D.A., Hickenbotham,M.T., Magrini,V., Mardis,E.R., Dangl,J.L. and Jones,C.D. (2007) Extending assembly of short DNA sequences to handle error. Bioinformatics, 23, 2942-2944.
16. Ross,M.G., Ross,M.G., Russ,C., Costello,M., Hollinger,A., Lennon,N.J., Hegarty,R., Nusbaum,C. and Jaffe,D.B. (2013) Characterizing and measuring bias in sequence data. Genome Biol., 14, R51.
17. Mardulyn,P., Termonia,A. and Milinkovitch,M.C. (2003) Structure and evolution of the mitochondrial control region of leaf beetles (Coleoptera: Chrysomelidae): a hierarchical analysis of nucleotide sequence variation. J. Mol. Evol., 56, 38-45.
18. Tsai,C.H. and Strauss,S.H. (1989) Dispersed repetitive sequences in the chloroplast genome of Douglas-fir. Curr. Genet., 16, 211-218.
19. Alverson,A.J., Wei,X.X., Rice,D.W., Stern,D.B., Barry,K. and Palmer,J.D. (2010) Insights into the evolution of mitochondrial genome size from complete sequences of citrullus lanatus and cucurbita pepo (Cucurbitaceae). Mol. Biol. Evol., 27, 1436-1448.
20. Federhen,S. (2012) The NCBI taxonomy database. Nucleic Acids Res., 40, D136-D143.
21. Benson,D.A., Cavanaugh,M., Clark,K., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J. and Sayers,E.W. (2013) GenBank. Nucleic Acids Res., 41, D36-D42.
22. Smith,D.R. (2015) The past, present and future of mitochondrial genomics: have we sequenced enough mtDNAs? Brief. Funct. Genomics, 15, 47-54.
23. Naito,K., Kaga,A., Tomooka,N. and Kawase,M. (2013) De novo assembly of the complete organelle genome sequences of azuki bean (Vigna angularis) using next-generation sequencers. Breed. Sci., 63, 176-182.
24. Ye,C.-Y., Lin,Z., Li,G., Wang,Y.-Y., Qiu,J., Fu,F., Zhang,H., Chen,L., Ye,S., Song,W. et al. (2014) Echinochloa chloroplast genomes: insights into the evolution and taxonomic identification of two weedy species. PLoS One, 9, e113657.