The mitochondrial genome of the red alga Kappaphycus striatus (“Green Sacol” variety): Complete nucleotide sequence, genome structure and organization, and comparative analysis

Marine Genomics - Tập 18 - Trang 155-161 - 2014
Francis A. Tablizo1,2,3, Arturo O. Lluisma1,2
1Marine Genomics and Molecular Genetics Laboratory, Marine Science Institute, University of the Philippines, Diliman, Quezon City, 1101 Philippines
2Core Facility for Bioinformatics, Philippine Genome Center, University of the Philippines, Philippines
3National Institute of Molecular Biology and Biotechnology, University of the Philippines, Diliman, Quezon City, 1101 Philippines

Tài liệu tham khảo

Alikhan, 2011, BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, 12, 402, 10.1186/1471-2164-12-402 Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2 Burger, 1999, Complete sequence of the mitochondrial DNA of the red alga Porphyra purpurea: cyanobacterial introns and shared ancestry of red and green algae, Plant Cell, 11, 1675, 10.1105/tpc.11.9.1675 Burger, 2003, The enigmatic mitochondrial ORF ymf39 codes for ATP synthase chain B, Nucleic Acids Res., 31, 2353, 10.1093/nar/gkg326 Darling, 2004, Mauve: multiple alignment of conserved genomic sequence with rearrangements, Genome Res., 14, 1394, 10.1101/gr.2289704 Gray, 2012, Mitochondrial evolution, Cold Spring Harb. Perspect. Biol., 4, a011403, 10.1101/cshperspect.a011403 Gruber, 2008, The Vienna RNA Websuite, Nucleic Acids Res., 36, W70, 10.1093/nar/gkn188 Hancock, 2010, Red algae lose key mitochondrial genes in response to becoming parasitic, Genome Biol. Evol., 2, 897, 10.1093/gbe/evq075 Hwang, 2013, Complete sequence and genetic features of the mitochondrial genome of Pyropia tenera (Rhodophyta), Plant Biotechnol. Rep., 7, 435, 10.1007/s11816-013-0281-4 Kim, 2013, Complete mitochondrial genome of a rhodolith, Sporolithon durum (Sporolithales, Rhodophyta), Mitochondrial DNA, 10.3109/19401736.2013.819500 Kim, 2013, Complete mitochondrial genome of the marine red alga Grateloupia angusta (Halymeniales), Mitochondrial DNA Kong, 2013, Complete mitochondrial genome of Pyropia yezoensis: reasserting the revision of genus Porphyra, Mitochondrial DNA Leblanc, 1995, Complete sequence of the mitochondrial DNA of the rhodophyte Chondrus crispus (Gigartinales). Gene content and genome organization, J. Mol. Biol., 250, 484, 10.1006/jmbi.1995.0392 Lowe, 1997, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res., 25, 955, 10.1093/nar/25.5.0955 Mao, 2012, The complete mitochondrial genome of Pyropia haitanensis Chang et Zheng, Mitochondrial DNA, 23, 344, 10.3109/19401736.2012.690751 Nozaki, 2003, The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids, J. Mol. Evol., 56, 485, 10.1007/s00239-002-2419-9 Ohta, 1998, Structure and organization of the mitochondrial genome of the unicellular red alga Cyanidioschyzon merolae deduced from the complete nucleotide sequence, Nucleic Acids Res., 26, 5190, 10.1093/nar/26.22.5190 Smith, 2012, Relative rates of evolution among the three genetic compartments of the red alga Porphyra differ from those of green plants and do not correlate with genome architecture, Mol. Phylogenet. Evol., 65, 339, 10.1016/j.ympev.2012.06.017 Stothart, 2005, Circular genome visualization and exploration using CGView, Bioinformatics, 21, 537, 10.1093/bioinformatics/bti054 Tamura, 2011, MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol. Biol. Evol., 28, 2731, 10.1093/molbev/msr121 Yang, 2013, Complete mitochondrial genome of agar-producing red alga Gracilriopsis chorda (Gracilariales), Mitochondrial DNA Yang, 2013, Complete mitochondrial genome of the agarophyte red alaga Gelidium vagum (Gelidiales), Mitochondrial DNA Zhang, 2012, Complete sequences of the mitochondrial DNA of the wild Gracilariopsis lemaneiformis and two mutagenic cultivated breeds (Gracilariaceae, Rhodophyta), PLoS One, 7, E40241, 10.1371/journal.pone.0040241 Zuker, 2003, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Res., 31, 3406, 10.1093/nar/gkg595