Highly conserved organellar genomes in the Gracilariales as inferred using new data from the Hawaiian invasive alga Gracilaria salicornia (Rhodophyta)

Phycologia

Volumn 53, Issue 2, 2014, Pages 109-116

  Campbell, Matthew A ^a,c   Presting, Gernot ^a   Bennett, Matthew S ^b   Sherwood, Alison R ^a  

^a UNIVERSITY OF HAWAII   (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

^c UNIVERSITY OF MONTANA   (United States)

Author keywords

Chloroplast genome; Gracilariophila oryzoides; Gracilariopsis andersonii; Hawaii; Horizontal gene transfer; LeuC D; Mitochondrial genome; Synteny

Indexed keywords

EID: 84896961841     PISSN: 00318884     EISSN: None     Source Type: Journal    
DOI: 10.2216/13-222.1     Document Type: Article

References (52)

1. ALTSCHUL S.F., GISH W., MILLER W., MYERS E.W. & LIPMAN D.J. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
2. ALTSCHUL S.F., MADDEN T.L., SCHAFFER A.A., ZHANG J., ZHANG Z., MILLER W. & LIPMAN D.J. 1997. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.
3. ARTIKA I. 2009. Membrane topology of subunit 8 variant of yeast Saccharomyces cerevisiae mitochondrial ATP synthase. Microbiology Indonesia 3: 37-41.
4. BARBROOK A.C., HOWE C.J., KURNIAWAN D.P. & TARR S.J. 2010. Organization and expression of organellar genomes. Philosophical Transactions of the Royal Society B 1541: 785-797.
5. BAUMANN L., BAUMANN P., MORAN N.A., SANDSTROM J. & THAO M.L. 1999. Genetic characterization of plasmids containing genes encoding enzymes of leucine biosynthesis in endosymbionts (Buchnera) of aphids. Journal of Molecular Evolution 48: 77-85.
6. BAYLEY J.P., DEVILEE P. & TASCHNER P.E. 2005. The SDH mutation database: an online resource for succinate dehydrogenase sequence variants involved in pheochromocytoma, paraganglioma and mitochondrial complex II deficiency. BMC Medical Genetics 6: 39.
7. BEZERRA A.F. & MARINHO-SORIANO E. 2010. Cultivation of the red seaweed Gracilaria birdiae (Gracilariales, Rhodophyta) in tropical waters of northeast Brazil. Biomass and Bioenergy 34: 1813-1817.
8. BOUDREAU E. & TURMEL M. 1996. Extensive gene rearrangements in the chloroplast DNAs of Chlamydomonas species featuring multiple dispersed repeats. Molecular Biology and Evolution 13: 233-243.
9. BURGER G., SAING-LOUIS D., GRAY M.W. & LANG G.F. 1999. Complete sequence of the mitochondrial DNA of the red alga Porphyra purpurea: cyanobacterial introns and shared ancestry of red and green algae. The Plant Cell 11: 1675-1694.
10. CAMPBELL M.A., ROKAS A. & SLOT J.C. 2012. Horizontal transfer and death of a fungal secondary metabolic gene cluster. Genome Biology and Evolution 4: 289-293.
11. CAMPBELL M.A., STAATS M., VAN KAN J.L.A., ROKAS A. & SLOT J.C. 2013. Repeated loss of an anciently horizontally transferred gene cluster in Botrytis. Mycologia 105: 1126-1134.
12. CLEGG M.T., GAUT B.S., LEARN G.H. Jr. & MORTON B.R. 1994. Rates and patterns of chloroplast DNA evolution. Proceedings of the National Academy of Sciences 91: 6795-6801.
13. 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. Journal of Applied Phycology 21: 691-699.
14. DARLING A.E., MAU B. & PERNA N.T. 2010. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5: e11147.
15. DE KONING A.P. & KEELING P.J. 2006. The complete plastid genome sequence of the parasitic green alga Helicosporidium sp. is highly reduced and structured. BMC Biology 4: 12.
16. DELUCA T.F., CUI J., JUNG J.Y., ST. GABRIEL K.C. & WALL D.P. 2012. Roundup 2.0: enabling comparative genomics for over 1800 genomes. Bioinformatics 28: 715-716.
17. DEPRIEST M.S., BHATTACHARYA D. & LÓ PEZ-BAUTISTA J.M. 2013. The plastid genome of the red macroalga Grateloupia taiwanensis (Halymeniaceae). PLoS ONE 8: e68246.
18. EGAN S., WIENER P., KALLIFIDAS D. & WELLINGTON E.M.H. 2001. Phylogeny of Streptomyces species and evidence for horizontal transfer of entire and partial antibiotic gene clusters. Antonie van Leeuwenhoek 79: 127-133.
19. FAO. 2003. A guide to the seaweed industry. In: FAO Fisheries Technical Paper (Ed. by D.J. McHugh), p. 105. Food and Agriculture Organization of the United Nations, Rome, Italy.
20. GLOCKNER G., ROSENTHAL A. & VALENTIN K. 2000. The structure and gene repertoire of an ancient red algal plastid genome. Journal of Molecular Evolution 51: 382-390.
21. GRAY M.W. 1999. Evolution of organellar genomes. Current Opinion in Genetics and Development 9: 678-687.
22. GUIRY M.D. & GUIRY G.M. 2013. AlgaeBase. World-wide electronic publication, National University of Ireland, Galway. http://www.algaebase.org; searched on 16 April 2013.
23. GURGEL C.F.D., FREDERICQ S. & NORRIS J.N. 2004a. Gracilaria flabelliformis (Gracilariaceae, Rhodophyta): restoring old names for common tropical western Atlantic species, including the recognition of three new subspecies, and a replacement name for ''G. lacinulata''. Cryptogamie, Algologie 25: 367-396.
24. GURGEL C.F.D., FREDERICQ S. & NORRIS J.N. 2004b. Molecular systematics and taxonomy of flattened species of Gracilaria Greville (Gracilariaceae, Gracilariales, Rhodophyta) from the Western Atlantic. In: Taxonomy of economic seaweeds with reference to the Pacific and other locations, vol. IX (Ed. by I.A. Abbott & K.J. McDermid), pp. 159-200. Hawaii Sea Grant College Program, Honolulu.
25. GURGEL C.F.D., FREDERICQ S., NORRIS J.N. & YONESHIGUEVALENTIN Y. 2008. Two new flat species of Gracilaria (Gracilariales, Rhodophyta) from Brazil: G. abyssalis sp nov and G. brasiliensis sp nov Phycologia 47: 249-264.
26. HAGOPIAN J.C., REIS M., KITAJIMA J.P., BHATTACHARYA D. & DE OLIVEIRA M.C. 2004. Comparative analysis of the complete plastid genome sequence of the red alga Gracilaria tenuistipitata var. liui provides insights into the evolution of rhodoplasts and their relationship to other plastids. Journal of Molecular Evolution 59: 464-477.
27. HANCOCK L., GOFF L. & LANE C. 2010. Red algae lose key mitochondrial genes in response to becoming parasitic. Genome Biology and Evolution 2: 897-910.
28. HAYASHI-ISHIMARU Y., EHARA M., INAGAKI Y. & OHAMA T. 1997. A deviant mitochondrial genetic code in prymnesiophytes (yellowalgae): UGA codon for tryptophan. Current Genetics 32: 296-299.
29. IYER R., TRONCHIN E.M., BOLTON J.J. & COYNE V.E. 2005. Molecular systematics of the Gracilariaceae (Gracilariales, Rhodophyta) with emphasis on Southern Africa. Journal of Phycology 41: 672-684.
30. JANOÜSKOVEC J., LIU S.L., MARTONE P.T., CARŔe W., LEBLANC C., COLĹ EN 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.
31. KAZlOWSKI B., CHIU Y.-H., KAZlOWSKI K., PAN C.-L. & WU C.-J. 2012. Prevention of Japanese encephalitis virus infections by lowdegree- polymerisation sulfated saccharides from Gracilaria sp. and Monostroma nitidum. Food Chemistry 133: 866-874.
32. KIM M.-S, YANG E.C. & BOO S.M. 2006. Taxonomy and phylogeny of flattened species of Gracilariaceae (Gracilariceae, Rhodophyta) from Korea based on morphology and protein-coding plastid rbcL and psbA sequences. Phycologia 45: 520-528.
33. LIN S.-M. & DE CLERCK O. 2006. A new flattened species of Gracilaria (Gracilariales, Rhodophyta) from Taiwan. Cryptogamie, Algologie 27: 233-244.
34. MCCUTCHEON J.P. & MORAN N.A. 2012. Extreme genome reduction in symbiotic bacteria. Nature Reviews Microbiology 10: 13-26.
35. OHTA N., MATSUZAKI M., MISUMI O., MIYAGISHIMA S., NOZAKI H., TANAKA K., SHIN-I T., KOHARA Y. & KUROIWA T. 2003. Complete sequence and analysis of the plastid genome of the unicellular red alga Cyanidioschyzon merolae. DNA Research 10: 67-77.
36. PAGANI I., LIOLIOS K., JANSSON J., CHEN I.A., SMIRNOVA T., NOSRAT B., MARKOWITZ V.M. & KYRPIDES N.C. 2012. The genomes online database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Research 40: D571-D579.
37. PAREEK M., MISHRA A. & JHA B. 2010. Molecular phylogeny of Gracilaria species inferred from molecular markers belonging to three different genomes. Journal of Phycology 46: 1322-1328.
38. REITH M. & MUNHOLLAND J. 1995. Complete nucleotide sequences of the Porphyra purpurea chloroplast genome. Plant Molecular Biology Reporter 13: 333-335.
39. SABATER-MUNOZ B., VAN HAM R.C.H.J., MOYA A., SILVA F.J. & LATORRE A. 2004. Evolution of the Leucine gene cluster in Buchnera aphidicola: insights from chromosomal versions of the cluster. Journal of Bacteriology 186: 2646-2654.
40. SANTELICES B. & DOTY M.S. 1989. A review of Gracilaria farming. Aquaculture 78: 95-133.
41. SCHATTNER P., BROOKS A.N. & LOWE T.M. 2005. The tRNAscan- SE, snoscan and snoGPS servers for the detection of tRNAs and snoRNAs. Nucleic Acids Research 33: W686-689.
42. SHERWOOD A.R., & PRESTING G.G. 2013. HADB: The Hawaiian Algal Database. World-wide electronic publication, University of Hawaii, Honolulu. http://algae.manoa.hawaii.edu/hadb; searched on 23 December 2013.
43. SMITH J.E., HUNTER C.L. & SMITH C.M. 2002. Distribution and reproductive characteristics of nonindigenous and invasive marine algae in the Hawaiian Islands. Pacific Science 56: 299-315.
44. SLOT J.C. & ROKAS A. 2010. Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi. Proceedings of the National Academy of Sciences of the United States of America 107: 10136-10141.
45. TAMAKOSHI M., YAMAGISHI A. & OSHIMA T. 1998. The organization of the leuC, leuD and leuB genes of the extreme thermophile Thermus thermophilus. Gene 222: 125-132.
46. TSENG C. K. & XIA B.-M. 1999. On the Gracilaria in the Western Pacific and the Southeastern Asia region. Botanica Marina 42: 209-217.
47. TURMEL M., OTIS C. & LEMIEUX C. 2005. The complete chloroplast DNA sequences of the charophycean green algae Staurastrum and Zygnema reveal that the chloroplast genome underwent extensive changes during the evolution of the Zygnematales. BMC Biology 3: 22.
48. VAN LEUVEN J.T. & MCCUTCHEON J.P. 2011. An AT mutational bias in the tiny GC-rich endosymbiont genome of Hodgkinia. Genome Biology and Evolution 4: 24-27.
49. VOGEL K.J. & MORAN N.A. 2013. Functional and evolutionary analysis of the genome of an obligate fungal symbiont. Genome Biology and Evolution. 5: 891-904.
50. WANG L., MAO Y., KONG F., LI G., MA F., ZHANG B., SUN P., BI G., ZHANG F., XUE H. & CAO M. 2013. Complete sequence and analysis of plastid genomes of two economically important red algae: Pyropia haitanensis and Pyropia yezoensis. PLoS One. 8: e65902.
51. ZEMKE-WHITE W. L. & OHNO M. 1999. World seaweed utilisation: an end-of-century summary. Journal of Applied Phycology 11: 369-376.
52. ZHANG L., WANG X., QIAN H., CHI S., LIU C. & LIU T. 2012. Complete sequences of the mitochondrial DNA of the wild Gracilariopsis lemanaeformis and two mutagenic cultivated breeds (Gracilariaceae, Rhodophyta). PLoS One 7: e40241.