The mitochondrial genome of Grateloupia taiwanensis (Halymeniaceae, Rhodophyta) and comparative mitochondrial genomics of Red Algae

Biological Bulletin

Volumn 227, Issue 2, 2014, Pages 191-200

  DePriest, Michael S ^a   Bhattacharya, Debashish ^b   López Bautista, Juan M ^a  

^a UNIVERSITY OF ALABAMA   (United States)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BENTHIC ENVIRONMENT; CELL ORGANELLE; GENOME; HABITAT TYPE; MITOCHONDRION; PHYLOGENY; PROTEIN; RED ALGA;

GRATELOUPIA; HALYMENIACEAE; RHODOPHYTA;

CLASSIFICATION; DNA BASE COMPOSITION; GENETICS; GENOMICS; MITOCHONDRIAL GENOME; PHYLOGENY; RED ALGA; SPECIES DIFFERENCE;

BASE COMPOSITION; GENOME, MITOCHONDRIAL; GENOMICS; PHYLOGENY; RHODOPHYTA; SPECIES SPECIFICITY;

EID: 84911426956     PISSN: 00063185     EISSN: None     Source Type: Journal    
DOI: 10.1086/BBLv227n2p191     Document Type: Article

References (41)

1. Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, and Z. Zhang. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
2. Baurain, D., H. Brinkmann, J. Petersen, N. Rodríguez-Ezpeleta, A. Stechmann, V. Demoulin, A. J. Roger, G. Burger, B. F. Lang, and H. Philippe. 2010. Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles. Mol. Biol. Evol. 27: 1698-1709.
3. Bhattacharya, D., D. C. Price, C. X. Chan, H. Qiu, N. Rose, S. Ball, A. P. M. Weber, M. C. Arias, B. Henrissat, P. M. Coutinho et al. 2013. Genome of the red alga Porphyridium purpureum. Nat. Commun. 4: 1941.
4. Bixler, H. J., and H. Porse. 2011. A decade of change in the seaweed hydrocolloids industry. J. Appl. Phycol. 23: 321-335.
5. Bock, R., M. Lohse, and O. Drechsel. 2007. OrganellarGenomeDraw (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr. Genet. 52: 267-274.
6. Boyen, C., C. Leblanc, G. Bonnard, J. M. Grienenberger, and B. Kloareg. 1994. Nucleotide sequence of the cox3 gene from Chondrus crispus: evidence that UGA encodes tryptophan and evolutionary implications. Nucleic Acids Res. 22: 1400-1403.
7. Burger, G., D. Saint-Louis, M. W. Gray, and B. F. Lang. 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: 1675-1694.
8. Burki, F., N. Okamoto, J.-F. Pombert, and P. J. Keeling. 2012. The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins. Proc. R. Soc. B 279: 2246-2254.
9. Campbell, M. A., G. Presting, M. S. Bennett, and A. R. Sherwood. 2014. Highly conserved organellar genomes in the Gracilariales as inferred using new data from the Hawaiian invasive alga Gracilaria salicornia (Rhodophyta). Phycologia 53: 109-116.
10. Collén, J., B. Porcel, W. Carré, S. G. Ball, C. Chaparro, T. Tonon, T. Barbeyron, G. Michel, B. Noel, K. Velentin et al. 2013. Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida. Proc. Natl. Acad. Sci. USA 13: 5247-5252.
11. Darling, A. E., B. Mau, F. R. Blatter, and N. T. Perna. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14: 1394-1403.
12. Darling, A. E., B. Mau, and N. T. Perna. 2010. progressiveMauve: multiple genome alignment with gene gain, loss, and rearrangement. PLoS One 5: e11147.
13. DePriest, M. S., and J. M. López-Bautista. 2012. Sequencing of the rbcL marker reveals the nonnative red alga Grateloupia taiwanensis (Halymeniaceae, Rhodophyta) in Alabama. Gulf Mex. Sci. 2012: 8-13.
14. DePriest, M. S., D. Bhattacharya, and J. M. López-Bautista. 2013. The plastid genome of the red macroalga Grateloupia taiwanensis (Halymeniaceae). PLoS One 8: e68246.
15. Freshwater, D. W., S. Fredericq, B. S. Butler, M. H. Hommersand, and M. W. Chase. 1994. A gene phylogeny of the red algae (Rhodophyta) based on plastid rbcL. Proc. Natl. Acad. Sci. USA 91: 7281-7285.
16. Garbary, D. J., and Z. Pei. 2006. Mitochondrial dynamics in red algae. 3. Filament apices in Colaconema caespitosum (Acrochaetales) and Antithamnion cruciatum (Ceramiales). Algae 23: 323-332.
17. Gargiulo, G. M., M. Morabito, and A. Manghisi. 2013. A re-assessment of reproductive anatomy and postfertilization development in the systematics of Grateloupia (Halymeniales, Rhodophyta). Cryptogam. Algol. 34: 3-35.
18. Geneious. 2014. Bioinformatics software platform. [Online]. Available: http://www. geneious. com/[2014, October 7].
19. Guiry, M. D. 2012. How many species of algae are there? J. Phycol. 48: 1057-1063.
20. Hwang, M. S., S.-O. Kim, D.-S. Ha, J. E. Lee, and S.-R. Lee. 2013. Complete sequence and genetic features of the mitochondrial genome of Pyropia tenera. Plant Biotechnol. Rep. 7: 435-443.
21. Keeling, P. J. 2013. The number, speed, and impact of plastid endosymbioses in eukaryotic evolution. Annu. Rev. Plant Biol. 64: 583-607.
22. Kim, K. M., E. C. Yang, J. H. Kim, W. A. Nelson, and H. S. Yoon. 2013. Complete mitochondrial genome of a rhodolith, Sporolithon durum (Sporolithales, Rhodophyta). Mitochondrial DNA. [Online]. Available: http://informahealthcare. com/doi/abs/10. 3109/19401736. 2013. 819500 [2014, October 7].
23. Kim, K. M., E. C. Yang, G. Yi, and H. S. Yoon. 2014. Complete mitochondrial genome of sublittoral macroalga Rhodymenia pseudopalmata (Rhodymeniales, Rhodophyta). Mitochondrial DNA 25: 273-274.
24. Kim, S. Y., E. C. Yang, S. M. Boo, and H. S. Yoon. 2014. Complete mitochondrial genome of the marine red alga Grateloupia angusta (Halymeniales). Mitochondrial DNA 25: 269-270.
25. Leblanc, C., C. Boyen, O. Richard, G. Bonnard, J. M. Grienenberger, and B. Kloareg. 1995. Complete sequence of the mitochondrial DNA of the rhodophyte Chondrus crispus (Gigartinales). Gene content and genome organization. J. Mol. Biol. 250: 484-495.
26. Le Gall, L., and G. W. Saunders. 2007. A nuclear phylogeny of the Florideophyceae (Rhodophyta) inferred from combined EF2, small subunit and large subunit ribosomal DNA: establishing the new algal subclass Corallinophycidae. Mol. Phylogenet. Evol. 43: 1118-1130.
27. Lin, S.-M., H.-Y. Liang, and M. H. Hommersand. 2008. Two types of auxiliary cell ampullae in Grateloupia (Halymeniaceae, Rhodophyta), including G. taiwanensis sp. nov. and G. orientalis sp. nov. from Taiwan based on rbcL gene sequence analysis and cystocarp development. J. Phycol. 44: 196-214.
28. Lowe, T. M., and S. R. Eddy. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.
29. Mao, Y., B. Zhang, F. Kong, and L. Wang. 2012. The complete mitochondrial genome of Pyropia haitanensis Chang et Zheng. Mitochondrial DNA 23: 344-346.
30. Matsuzaki, M., O. Misumi, T. Shin-i, S. Maruyama, M. Takahara, S.-y Miyagishima, T. Mori, K. Nishida, F. Yagisawa, K. Nishida et al. 2004. Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428: 653-657.
31. Nakamura, Y., N. Sasaki, M. Kobayashi, N. Ojima, M. Yasuike, Y. Shigenobu, M. Satomi, Y. Fukuma, K. Shiwaku, A. Tsujimoto et al. 2013. The first symbiont-free genome sequence of the marine red alga, susabi-nori (Pyropia yezoensis). PLoS One 8(3): e57122.
32. Ohta, N., N. Sato, and T. Kuroiwa. 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: 5190-5198.
33. Oliveira, M. C., and D. Bhattacharya. 2000. Phylogeny of the Bangiophyceae (Rhodophyta) and the secondary endosymbiotic origin of algal plastids. Am. J. Bot. 87: 482-492.
34. Qiu, H., H. S. Yoon, and D. Bhattacharya. 2013. Algal endosymbionts as vectors of horizontal gene transfer in photosynthetic eukaryotes. Front. Plant Sci. 4: 366.
35. Ragan, M. A., C. J. Bird, E. L. Rice, R. R. Gutell, C. A. Murphy, and R. K. Singh. 1994. A molecular phylogeny of the marine red algae (Rhodophyta) based on the nuclear small-subunit rRNA gene. Proc. Natl. Acad. Sci. USA 91: 7276-7280.
36. Saunders, G. W., and M. H. Hommersand. 2004. Assessing red algal supraordinal diversity and taxonomy in the context of contemporary systematic data. Am. J. Bot. 91: 1494-1507.
37. Schattner, P., A. N. Brooks, and T. M. Lowe. 2005. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33: W686-W689.
38. Timmis, J. N., M. A. Ayliffe, C. Y. Huang, and W. Martin. 2004. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat. Rev. Genet. 5: 123-136.
39. UniProt. 2014. UniProtKB sequence database. [Online]. Available: http://www. uniprot. org [2014, October 7].
40. Yang, E. C., K. M. Kim, G. H. Boo, J.-H. Lee, S. M. Boo, and H. S. Yoon. 2014. Complete mitochondrial genome of the agarophyte red alga Gelidium vagum (Gelidiales). Mitochondrial DNA 25: 267-268.
41. Yoon, H. S., K. M. Mü ller, R. G. Sheath, F. D. Ott, and D. Bhattacharya. 2006. Defining the major lineages of red algae (Rhodophyta). J. Phycol. 42: 482-492.