Browse > Article
http://dx.doi.org/10.4490/algae.2016.31.6.5

A novice’s guide to analyzing NGS-derived organelle and metagenome data  

Song, Hae Jung (Department of Biological Sciences, Sungkyunkwan University)
Lee, JunMo (Department of Biological Sciences, Sungkyunkwan University)
Graf, Louis (Department of Biological Sciences, Sungkyunkwan University)
Rho, Mina (Division of Computer Science & Engineering, Hanyang University)
Qiu, Huan (Department of Ecology, Evolution and Natural Resources, Rutgers University)
Bhattacharya, Debashish (Department of Ecology, Evolution and Natural Resources, Rutgers University)
Yoon, Hwan Su (Department of Biological Sciences, Sungkyunkwan University)
Publication Information
ALGAE / v.31, no.2, 2016 , pp. 137-154 More about this Journal
Abstract
Next generation sequencing (NGS) technologies have revolutionized many areas of biological research due to the sharp reduction in costs that has led to the generation of massive amounts of sequence information. Analysis of large genome data sets is however still a challenging task because it often requires significant computer resources and knowledge of bioinformatics. Here, we provide a guide for an uninitiated who wish to analyze high-throughput NGS data. We focus specifically on the analysis of organelle genome and metagenome data and describe the current bioinformatic pipelines suited for this purpose.
Keywords
bioinformatic; NGS data analysis; organelle genome; metagenome;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Lee, J. -Y., Yoo, C., Jun, S. -Y., Ahn, C. -Y. & Oh, H. -M. 2010. Comparison of several methods for effective lipid extraction from microalgae. Bioresour. Technol. 101(Suppl.):S75-S77.   DOI
2 Li, D., Liu, C. -M., Luo, R., Sadakane, K. & Lam, T. -W. 2015. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31:1674-1676.   DOI
3 Li, H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997.
4 Li, H. & Durbin, R. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754-1760.   DOI
5 Li, R. Q. 2009. Short Oligonucleotide Analysis Package: SOAP-denovo 1.03. Beijing Genomics Institute, Beijing.
6 Liu, C., Shi, L., Zhu, Y., Chen, H., Zhang, J., Lin, X. & Guan, X. 2012. CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genomics 13:715.   DOI
7 Liu, Y., Schmidt, B. & Maskell, D. L. 2011. Parallelized short read assembly of large genomes using de Bruijn graphs. BMC Bioinformatics 12:354.   DOI
8 Lohse, M., Drechsel, O. & Bock, R. 2007. OrganellarGenome-DRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr. Genet. 52:267-274.   DOI
9 Loomis, E. W., Eid, J. S., Peluso, P., Yin, J., Hickey, L., Rank, D., McCalmon, S., Hagerman, R. J., Tassone, F. & Hagerman, P. J. 2013. Sequencing the unsequenceable: expanded CGG-repeat alleles of the fragile X gene. Genome Res. 23:121-128.   DOI
10 Lowe, T. M. & Eddy, S. R. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.   DOI
11 Ludwig, M. & Bryant, D. A. 2011. Transcription profiling of the model cyanobacterium Synechococcus sp. strain PCC 7002 by Next-Gen (SOLiDTM) sequencing of cDNA. Front Microbiol. 2:41.
12 Lunter, G. & Goodson, M. 2011. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 21:936-939.   DOI
13 Maréchal, A. & Brisson, N. 2010. Recombination and the maintenance of plant organelle genome stability. New Phytol. 186:299-317.   DOI
14 Markowitz, V. M., Chen, I. -M. A., Chu, K., Szeto, E., Palaniappan, K., Grechkin, Y., Ratner, A., Jacob, B., Pati, A., Huntemann, M., Liolios, K., Pagani, I., Anderson, I., Mavromatis, K., Ivanova, N. N. & Kyrpides, N. C. 2012. IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res. 40:D123-D129.   DOI
15 Martin, W. & Müller, M. 1998. The hydrogen hypothesis for the first eukaryote. Nature 392:37-41.   DOI
16 McKinnon, A. E., Vaillancourt, R. E., Tilyard, P. A. & Potts, B. M. 2001. Maternal inheritance of the chloroplast genome in Eucalyptus globulus and interspecific hybrids. Genome. 44:831-835.   DOI
17 Meyer, F., Paarmann, D., D’Souza, M., Olson, R., Glass, E. M., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A., Wilkening, J. & Edwards, R. A. 2008. The metagenomics RAST server: a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386.   DOI
18 Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., Mende, D. R., 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, H. B., 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, S. D. & Wang, J. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59-65.   DOI
19 Pruitt, K. D., Tatusova, T. & Maglott, D. R. 2007. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35:D61-D65.   DOI
20 Qiagen. 2015. CLC Genomics Workbench 8.0.3. Available from: https://www.qiagenbioinformatics.com/. Accessed May 2, 2016.
21 Qiu, H., Price, D. C., Weber, A. P. M., Reeb, V., Yang, E. C., Lee, J. M., Kim, S. Y., Yoon, H. S. & Bhattacharya, D. 2013. Adaptation through horizontal gene transfer in the cryptoendolithic red alga Galdieria phlegrea. Curr. Biol. 23:R865-R866.   DOI
22 Qiu, H., Price, D. C., Yang, E. C., Yoon, H. S. & Bhattacharya, D. 2015. Evidence of ancient genome reduction in red algae (Rhodophyta). J. Phycol. 51:624-636.   DOI
23 Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J. & Glöckner, F. O. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41:D590-D596.   DOI
24 Warinner, C., Speller, C., Collins, M. J. & Lewis, C. M. Jr. 2015. Ancient human microbiomes. J. Hum. Evol. 79:125-136.   DOI
25 UniProt Consortium. 2015. UniProt: a hub for protein information. Nucleic Acids Res. 43:D204-D212.   DOI
26 Vellai, T., Takács, K. & Vida, G. 1998. A new aspect to the origin and evolution of eukaryotes. J. Mol. Evol. 46:499-507.   DOI
27 Walsh, P. S., Metzger, D. A. & Higuchi, R. 1991. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10:506-513.
28 Weinstock, G. M. 2012. Genomic approaches to studying the human microbiota. Nature 489:250-256.   DOI
29 Wyman, S. K., Jansen, R. K. & Boore, J. L. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252-3255.   DOI
30 Yang, E. C., Kim, K. M., Kim, S. Y., Lee, J., Boo, G. H., Lee, J.-H., Nelson, W. A., Yi, G., Schmidt, W. E., Fredericq, S., Boo, S. M., Bhattacharya, D. & Yoon, H. S. 2015. Highly conserved mitochondrial genomes among multicellular red algae of the Florideophyceae. Genome Biol. Evol. 7:2394-2406.   DOI
31 Zerbino, D. R. & Birney, E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-829.
32 Zeugin, J. A. & Hartley, J. L. 1985. Ethanol precipitation of DNA. Focus 7:1-2.
33 Zhao, Y., Tang, H. & Ye, Y. 2012. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics 28:125-126.   DOI
34 Nguyen, L. -T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32:268-274.   DOI
35 Mitra, S., Rupek, P., Richter, D. C., Urich, T., Gilbert, J. A., Meyer, F., Wilke, A. & Huson, D. H. 2011. Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. BMC Bioinformatics 12(Suppl. 1):S21.
36 Mocali, S. & Benedetti, A. 2010. Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology. Res. Microbiol. 161:497-505.   DOI
37 Namiki, T., Hachiya, T., Tanaka, H. & Sakakibara, Y. 2012. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res. 40:e155.   DOI
38 Partek Inc. 1998. Partek software, version 2.0B7. Partek Inc., St. Peters, MO.
39 Paszkiewicz, K. & Studholme, D. J. 2010. De novo assembly of short sequence reads. Brief Bioinform. 11:457-472.   DOI
40 Peng, Y., Leung, H. C. M., Yiu, S. M. & Chin, F. Y. L. 2010. IDBA: a practical iterative de Bruijn graph de novo assembler. In Berger, B. (Ed.) Research in Computational Molecular Biology. Springer Berlin, Heidelberg, pp. 426-440.
41 Peng, Y., Leung, H. C., Yiu, S. M. & Chin, F. Y. 2011. Meta-IDBA: a de novo assembler for metagenomic data. Bioinformatics 27:i94-i101.   DOI
42 Peng, Y., Leung, H. C., Yiu, S. M. & Chin, F. Y. 2012. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28:1420-1428.   DOI
43 Rothberg, J. M. & Leamon, J. H. 2008. The development and impact of 454 sequencing. Nat. Biotechnol. 26:1117-1124.   DOI
44 Redfern, O., Grant, A., Maibaum, M. & Orengo, C. 2005. Survey of current protein family databases and their application in comparative, structural and functional genomics. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 815:97-107.   DOI
45 Rombel, I. T., Sykes, K. F., Rayner, S. & Johnston, S. A. 2002. ORF-FINDER: a vector for high-throughput gene identification. Gene 282:33-41.   DOI
46 Ronaghi, M., Karamohamed, S., Pettersson, B., Uhlén, M. & Nyrén, P. 1996. Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem. 242:84-89.   DOI
47 Samarasinghe, N., Fernando, S., Lacey, R. & Faulkner, W. B. 2012. Algal cell rupture using high pressure homogenization as a prelude to oil extraction. Renew. Energy 48:300-308.   DOI
48 Sanger, F., Nicklen, S. & Coulson, A. R. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. U. S. A. 74:5463-5467.   DOI
49 Schmidt, B., Sinha, R., Beresford-Smith, B. & Puglisi, S. J. 2009. A fast hybrid short read fragment assembly algorithm. Bioinformatics 25:2279-2280.   DOI
50 Scholz, M. B., Lo, C. -C. & Chain, P. S. G. 2012. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr. Opin. Biotechnol. 23:9-15.   DOI
51 Sharon, D., Tilgner, H., Grubert, F. & Snyder, M. 2013. A single-molecule long-read survey of the human transcriptome. Nat. Biotechnol. 31:1009-1014.   DOI
52 Swindell, S. R. & Plasterer, T. N. 1997. SEQMAN. Contig assembly. In Swindell, S. R. (Ed.) Sequence Data Analysis Guidebook. Springer, New York, pp. 75-89.
53 Simpson, J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones, S. J. M. & Birol, I. 2009. ABySS: a parallel assembler for short read sequence data. Genome Res. 19:1117-1123.   DOI
54 Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.   DOI
55 Sunagawa, S., Coelho, L. P., Chaffron, S., Kultima, J. R., Labadie, K., Salazar, G., Djahanschiri, B., Zeller, G., Mende, D. R., Alberti, A., Cornejo-Castillo, F. M., Costea, P. I., Cruaud, C., d’Ovidio, F., Engelen, S., Ferrera, I., Gasol, J. M., Guidi, L., Hildebrand, F., Kokoszka, F., Lepoivre, C., Lima-Mendez, G., Poulain, J., Poulos, B. T., Royo-Llonch, M., Sarmento, H., Vieira-Silva, S., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Tara Oceans Coordinators, Bowler, C., de Vargas, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Jaillon, O., Not, F., Ogata, H., Pesant, S., Speich, S., Stemmann, L., Sullivan, M. B., Weissenbach, J., Wincker, P., Karsenti, E., Raes, J., Acinas, S. G. & Bork, P. 2015. Structure and function of the global ocean microbiome. Science 348:1261359.   DOI
56 Thomas, T., Gilbert, J. & Meyer, F. 2012. Metagenomics: a guide from sampling to data analysis. Microb. Inform. Exp. 2:3.   DOI
57 Tombácz, D., Sharon, D., Oláh, P., Csabai, Z., Snyder, M. & Boldogkői, Z. 2014. Strain kaplan of pseudorabies virus genome sequenced by PacBio single-molecule real-time sequencing technology. Genome Announc. 2:e00628-14.
58 Trapnell, C., Pachter, L. & Salzberg, S. L. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105-1111.   DOI
59 Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.   DOI
60 Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.   DOI
61 Biers, E. J., Sun, S. & Howard, E. C. 2009. Prokaryotic genomes and diversity in surface ocean waters: interrogating the global ocean sampling metagenome. Appl. Environ. Microbiol. 75:2221-2229.   DOI
62 Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev, M. A. & Pevzner, P. A. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19:455-477.   DOI
63 Beck, N. & Lang, B. F. 2010. MFannot, organelle genome annotation websever. Available from: http://megasun.bch.umontreal.ca. Accessed May 2, 2016.
64 Bernt, M., Donath, A., Jühling, F., Externbrink, F., Florentz, C., Fritzsch, G., Pütz, J., Middendorf, M. & Stadler, P. F. 2013. MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol. 69:313-319.   DOI
65 Biosoft, H. 2012. DNA Baser Sequence Assembler v3x. Heracle BioSoft SRL Romania, Pitesti.
66 Boisvert, S., Laviolette, F. & Corbeil, J. 2010. Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J. Comput. Biol. 17:1519-1533.   DOI
67 Boisvert, S., Raymond, F., Godzaridis, É., Laviolette, F. & Corbeil, J. 2012. Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol. 13:R122.   DOI
68 Boom, R., Sol, C. J. A., Salimans, M. M. M., Jansen, C. L., Wertheim-van Dillen, P. M. E. & Van der Noordaa, J. 1990. Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28:495-503.
69 Chaisson, M. J. & Pevzner, P. A. 2008. Short read fragment assembly of bacterial genomes. Genome Res. 18:324-330.   DOI
70 Chevreux, B., Wetter, T. & Suhai, S. 1999. Genome sequence assembly using trace signals and additional sequence information. In Beyer, A. & Schroeder, M. (Eds.) German Conference on Bioinformatics, Dresden, Germany, Vol. 99, pp. 45-56.
71 Conant, G. C. & Wolfe, K. H. 2008. GenomeVx: simple web-based creation of editable circular chromosome maps. Bioinformatics 24:861-862.   DOI
72 Conklin, K. Y., Kurihara, A. & Sherwood, A. R. 2009. A molecular method for identification of the morphologically plastic invasive algal genera Eucheuma and Kappaphycus (Rhodophyta, Gigartinales) in Hawaii. J. Appl. Phycol. 21:691-699.   DOI
73 Csaikl, U. M., Bastian, H., Brettschneider, R., Gauch, S., Meir, A., Schauerte, M., Scholz, F., Sperisen, C., Vornam, B. & Ziegenhagen, B. 1998. Comparative analysis of different DNA extraction protocols: a fast, universal maxi-preparation of high quality plant DNA for genetic evaluation and phylogenetic studies. Plant Mol. Biol. Rep. 16:69-86.   DOI
74 Darling, A. C. E., Mau, B., Blattner, F. R. & Perna, N. T. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14:1394-1403.   DOI
75 David, M., Dzamba, M., Lister, D., Ilie, L. & Brudno, M. 2011. SHRiMP2: sensitive yet practical short read mapping. Bioinformatics 27:1011-1012.   DOI
76 Debroas, D., Humbert, J. -F., Enault, F., Bronner, G., Faubladier, M. & Cornillot, E. 2009. Metagenomic approach studying the taxonomic and functional diversity of the bacterial community in a mesotrophic lake (Lac du Bourget–France). Environ. Microbiol. 11:2412-2424.   DOI
77 Delcher, A. L., Kasif, S., Fleischmann, R. D., Peterson, J., White, O. & Salzberg, S. L. 1999. Alignment of whole genomes. Nucleic Acids Res. 27:2369-2376.   DOI
78 Drummond, A., Ashton, B., Buxton, S., Cheung, M., Cooper, A., Duran, C., Field, M., Heled, J., Kearse, M. & Markowitz, S. 2011. Geneious v5. 4. Biomatters Limited., Auckland.
79 Disz, T., Akhter, S., Cuevas, D., Olson, R., Overbeek, R., Vonstein, V., Stevens, R. & Edwards, R. A. 2010. Accessing the SEED genome databases via Web services API: tools for programmers. BMC Bioinformatics 11:319.   DOI
80 Doorduin, L., Gravendeel, B., Lammers, Y., Ariyurek, Y., Chin-A-Woeng, T. & Vrieling, K. 2011. The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, microsatellites and barcoding markers for population and phylogenetic studies. DNA Res. 18:93-105.   DOI
81 Edgar, R. C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460-2461.   DOI
82 Ferrarini, M., Moretto, M., Ward, J. A., Šurbanovski, N., Stevanović, V., Giongo, L., Viola, R., Cavalieri, D., Velasco, R., Cestaro, A. & Sargent, D. J. 2013. An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome. BMC Genomics 14:670.   DOI
83 Glass, E. M., Wilkening, J., Wilke, A., Antonopoulos, D. & Meyer, F. 2010. Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb. Protoc. 2010:pdb.prot5368.
84 Gordon, D., Abajian, C. & Green, P. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202.   DOI
85 Griffiths-Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S. R. & Bateman, A. 2005. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33(Suppl. 1):D121-D124.
86 Huang, Y., Gilna, P. & Li, W. 2009. Identification of ribosomal RNA genes in metagenomic fragments. Bioinformatics 25:1338-1340.   DOI
87 Haider, B., Ahn, T. -H., Bushnell, B., Chai, J., Copeland, A. & Pan, C. 2014. Omega: an Overlap-graph de novo Assembler for Metagenomics. Bioinformatics 30:2717-2722.   DOI
88 Handelsman, J., Rondon, M. R., Brady, S. F., Clardy, J. & Goodman, R. M. 1998. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5:R245-R249.   DOI
89 Hernandez, D., François, P., Farinelli, L., Østerås, M. & Schrenzel, J. 2008. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res. 18:802-809.   DOI
90 Huddleston, J., Ranade, S., Malig, M., Antonacci, F., Chaisson, M., Hon, L., Sudmant, P. H., Graves, T. A., Alkan, C., Dennis, M. Y., Wilson, R. K., Turner, S. W., Korlach, J. & Eichler, E. E. 2014. Reconstructing complex regions of genomes using long-read sequencing technology. Genome Res. 24:688-696.   DOI
91 Huerta-Cepas, J., Szklarczyk, D., Forslund, K., Cook, H., Heller, D., Walter, M. C., Rattei, T., Mende, D. R., Sunagawa, S., Kuhn, M., Jensen, L. J., von Mering, C. & Bork, P. 2015. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44:D286-D293.
92 Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207-214.   DOI
93 Huson, D. H., Auch, A. F., Qi, J. & Schuster, S. C. 2007. MEGAN analysis of metagenomic data. Genome Res. 17:377-386.   DOI
94 Janouškovec, J., Liu, S. L., Martone, P. T., Carré, W., Leblanc, C., Collén, J. & Keeling, P. J. 2013. Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers. PLoS One 8:e59001.   DOI
95 Huson, D. H. & Weber, N. 2013. Microbial community analysis using MEGAN. Methods Enzymol. 531:465-485.   DOI
96 Huson, D. H. & Xie, C. 2014. A poor man's BLASTX: high-throughput metagenomic protein database search using PAUDA. Bioinformatics 30:38-39.   DOI
97 Ingman, M., Kaessmann, H., Pääbo, S. & Gyllensten, U. 2000. Mitochondrial genome variation and the origin of modern humans. Nature 408:708-713.   DOI
98 Jeck, W. R., Reinhardt, J. A., Baltrus, D. A., Hickenbotham, M. T., Magrini, V., Mardis, E. R., Dangl, J. L. & Jones, C. D. 2007. Extending assembly of short DNA sequences to handle error. Bioinformatics 23:2942-2944.   DOI
99 Jung, J. Y., Lee, S. H., Kim, J. M., Park, M. S., Bae, J. -W., Hahn, Y., Madsen, E. L. & Jeon, C. O. 2011. Metagenomic analysis of kimchi, a traditional Korean fermented food. Appl. Environ. Microbiol. 77:2264-2274.   DOI
100 Kanehisa, M. & Goto, S. 2000. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28:27-30.   DOI
101 Kim, K. M., Park, J. -H., Bhattacharya, D. & Yoon, H. S. 2014a. Applications of next-generation sequencing to unravelling the evolutionary history of algae. Int. J. Syst. Evol. Microbiol. 64(Pt. 2):333-345.   DOI
102 Kim, S. Y., Yang, E. C., Boo, S. M. & Yoon, H. S. 2014b. Complete mitochondrial genome of the marine red alga Grateloupia angusta (Halymeniales). Mitochondrial DNA 25:269-270.   DOI
103 Langmead, B. & Salzberg, S. L. 2012. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9:357-359.   DOI
104 Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K. & Hugenholtz, P. 2008. A bioinformatician's guide to metagenomics. Microbiol. Mol. Biol. Rev. 72:557-578.   DOI
105 Lagesen, K., Hallin, P., Rødland, E. A., Stærfeldt, H. -H., Rognes, T. & Ussery, D. W. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100-3108.   DOI
106 Lang, B. F., Laforest, M. -J. & Burger, G. 2007. Mitochondrial introns: a critical view. Trends Genet. 23:119-125.   DOI
107 Laslett, D. & Canbäck, B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 32:11-16.   DOI
108 Laslett, D. & Canbäck, B. 2008. ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 24:172-175.   DOI
109 Le Corguillé, G., Pearson, G., Valente, M., Viegas, C., Gschloessl, B., Corre, E., Bailly, X., Peters, A. F., Jubin, C., Vacherie, B., Cock, J. M. & Leblanc, C. 2009. Plastid genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus: further insights on the evolution of red-algal derived plastids. BMC Evol. Biol. 9:253.   DOI
110 Lee, J., Kim, K. M., Yang, E. C., Miller, K. A., Boo, S. M., Bhattacharya, D. & Yoon, H. S. 2016. Reconstructing the complex evolutionary history of mobile plasmids in red algal genomes. Sci. Rep. 6:23744.   DOI
111 Lee, J. -M., Boo, S. M., Mansilla, A. & Yoon, H. S. 2015. Unique repeat and plasmid sequences in the mitochondrial genome of Gracilaria chilensis (Gracilariales, Rhodophyta). Phycologia 54:20-23.   DOI