Unraveling the nuclear and chloroplast genomes of an agar producing red macroalga, Gracilaria changii (Rhodophyta, Gracilariales)

Smith, 1944

Renn, 1984, Agar and agarose: indispensable partners in biotechnology, Ind. Eng. Chem. Prod. Res. Dev., 23, 17, 10.1021/i300013a004

Cock, 2010, The Ectocarpus genome and the independent evolution of multicellularity in brown algae, Nature, 465, 617, 10.1038/nature09016

Collén, 2013, Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida, Proc. Natl. Acad. Sci. U. S. A., 110, 5247, 10.1073/pnas.1221259110

Matsuzaki, 2004, Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D, Nature, 428, 653, 10.1038/nature02398

Schönknecht, 2013, Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote, Science, 339, 1207, 10.1126/science.1231707

Bhattacharya, 2013, Genome of the red alga Porphyridium purpureum, Nat. Commun., 4, 1941, 10.1038/ncomms2931

Nakamura, 2013, The first symbiont-free genome sequence of marine red alga, susabi-nori (Pyropia yezoensis), PLoS One, 8

Porse, 2017, The seaweed hydrocolloid industry: 2016 updates, requirements, and outlook, J. Appl. Phycol., 10.1007/s10811-017-1144-0

Teo, 2007, Analyses of expressed sequence tags (ESTs) from an agarophyte, Gracilaria changii (Gracilariales, Rhodophyta), Eur. J. Phycol., 42, 41, 10.1080/09670260601012461

Teo, 2009, Transcriptomic analysis of Gracilaria changii (Rhodophyta) in response to hyper- and hypo-osmotic stresses, J. Phycol., 45, 1093, 10.1111/j.1529-8817.2009.00724.x

Ho, 2009, Profiling the transcriptome of Gracilaria changii (Rhodophyta) in response to light deprivation, Mar. Biotechnol., 11, 1436, 10.1007/s10126-008-9166-x

Lim, 2016, Global transcriptome analysis of Gracilaria changii (Rhodophyta) in response to agarolytic enzyme and bacterium, Mar. Biotechnol., 18, 189, 10.1007/s10126-015-9680-6

Lee, 2017, Transcriptome profiling of sulfate deprivation responses in two agarophytes Gracilaria changii and Gracilaria salicornia (Rhodophyta), Sci Rep, 7, 46563, 10.1038/srep46563

Campbell, 2014, Highly conserved organellar genomes in the Gracilariales as inferred using new data from the Hawaiian invasive red alga Gracilaria salicornia (Rhodophyta), Phycologia, 53, 109, 10.2216/13-222.1

Hagopian, 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, J. Mol. Evol., 59, 464, 10.1007/s00239-004-2638-3

Chung, 2007, Sequencing cucumber (Cucumis sativus L.) chloroplast genomes identifies differences between chilling-tolerant and -susceptible cucumber lines, Genome, 50, 215, 10.1139/G07-003

Gordon, 2011, Comparative analysis of chilling response in cucumber through plastidic and nuclear genetic effects component analysis, J. Am. Soc. Hortic. Sci., 136, 256, 10.21273/JASHS.136.4.256

Goecke, 2010, Chemical interactions between marine macroalgae and bacteria, Mar. Ecol. Prog. Ser., 409, 267, 10.3354/meps08607

Miranda, 2013, Diversity and abundance of the bacterial community of the red macroalga Porphyra umbilicalis: did bacterial farmers produce macroalgae?, PLoS One, 8, 10.1371/journal.pone.0058269

Stanke, 2006, Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources, BMC Bioinf., 7, 62, 10.1186/1471-2105-7-62

Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2

Simao, 2015, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, 31, 3210, 10.1093/bioinformatics/btv351

Falda, 2000, Argot2: a large scale function prediction tool relying on semantic similarity of weighted gene ontology terms, BMC Bioinf., 13, 2012

Chenna, 2003, Multiple sequence alignment with the Clustal series of programs, Nucleic Acids Res., 31, 3497, 10.1093/nar/gkg500

Tamura, 2007, MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0, Mol. Biol. Evol., 24, 1596, 10.1093/molbev/msm092

Saitou, 1987, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol., 4, 406

van Dongen, 2000

Besemer, 2001, GeneMarkS: a self-training method for prediction of gene starts in microbial genomes implications for finding sequence motifs in regulatory regions, Nucleic Acids Res., 29, 2607, 10.1093/nar/29.12.2607

Wyman, 2004, Automatic annotation of organellar genomes with DOGMA, Bioinformatics, 20, 3252, 10.1093/bioinformatics/bth352

Schattner, 2005, The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs, Nucleic Acids Res., 33, W686, 10.1093/nar/gki366

Lohse, 2007, OrganellarGenomeDRAW (OGDRAW) - a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes, Curr. Genet., 52, 267, 10.1007/s00294-007-0161-y

Wang, 2007, Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl. Environ. Microbiol., 73, 5261, 10.1128/AEM.00062-07

Cole, 2009, The ribosomal database project: improved alignments and new tools for rRNA analysis, Nucleic Acids Res., 37, D141, 10.1093/nar/gkn879

de Oliveira, 2012, Transcriptomic analysis of the red seaweed Laurencia dendroidea (Florideophyceae, Rhodophyta) and its microbiome, BMC Genomics, 13, 487, 10.1186/1471-2164-13-487

Yoon, 2004, A molecular timeline for the origin of photosynthetic eukaryotes, Mol. Biol. Evol., 21, 809, 10.1093/molbev/msh075

Meeuse, 1960, Floridean starch, J. Exp. Bot., 11, 129, 10.1093/jxb/11.2.129

McCracken, 1981, Amylose in floridean starch, New Phytol., 88, 67, 10.1111/j.1469-8137.1981.tb04568.x

Ekman, 1991, Effects of altered salinity, darkness and algal nutrient status on floridoside and starch content, a-galactosidase activity and agar yield of cultivated Gracilaria sordida, Br. Phycol. J., 126, 123, 10.1080/00071619100650091

Lobban, 1985

Rincones, 1993, Effect of dark treatment on the starch degradation and the agar quality of cultivated Gracilariopsis lemaneiformis (Rhodophyta, Gracilariales) from Venezuela, Hydrobiologia, 260, 633, 10.1007/BF00049082

Nyvall, 1999, Purification and characterisation of a novel starch synthase selective for uridine 5′-diphosphate glucose from the red alga Gracilaria tenuistipitata, Planta, 209, 143, 10.1007/s004250050616

Sesma, 1998, Synthesis of floridean starch in the red alga Gracilaria gracilis occurs via ADP-glucose, vol. V, 3537

Yu, 1993, α-1,4-Glucan lyase, a new class of starch/glycogen degrading enzyme I: efficient purification and characterization from red seaweeds, Biochim. Biophys. Acta, 1156, 313, 10.1016/0304-4165(93)90049-E

Pade, 2014, Floridoside and isofloridoside are synthesized by trehalose 6-phosphate synthase-like enzymes in the red alga Galdieria sulphuraria, New Phytol., 205, 1227, 10.1111/nph.13108

Kirst, 1990, Salinity tolerance of eukaryotic marine algae, Annu. Rev. Plant Physiol. Plant Mol. Biol., 41, 21, 10.1146/annurev.pp.41.060190.000321

Yu, 1990, The effect of salinity changes on the activity of α-galactosidase of the red algae Gracilaria sordida and G tenuistipitata, Bot. Mar., 33, 385, 10.1515/botm.1990.33.5.385

Yu, 1990, The α-galactosidase of Gracilaria tenuistipitata and G sordida (Gracilariales, Rhodophyta), Phycologia, 29, 454, 10.2216/i0031-8884-29-4-454.1

Craigie, 1990, Cell walls, 221

Lahaye, 1991, Chemical structure and physico-chemical properties of agar, Hydrobiology, 221, 137, 10.1007/BF00028370

Kitagawa, 2001, Molecular cloning and expression of a human chondroitin synthase, J. Biol. Chem., 276, 38721, 10.1074/jbc.M106871200

Fukuta, 1995, Molecular cloning and expression of chick chondrocyte chondroitin 6-sulfotransferase, J. Biol. Chem., 270, 18575, 10.1074/jbc.270.31.18575

Fukuta, 1997, Molecular cloning and characterization of human keratan sulfate Gal-6-sulfotransferase, J. Biol. Chem., 272, 32321, 10.1074/jbc.272.51.32321

Mazany, 1998, Human chondroitin 6-sulfotransferase: cloning, gene structure, and chromosomal localization, Biochim. Biophys. Acta, 1407, 92, 10.1016/S0925-4439(98)00028-3

Chi, 2012, Agar degradation by microorganisms and agar-degrading enzymes, Appl. Microbiol. Biotechnol., 94, 917, 10.1007/s00253-012-4023-2

Préchoux, 2013, Controlling carrageenan structure using a novel formylglycine-dependent sulfatase, an endo-4S-iota-carrageenan sulfatase, Mar. Biotechnol., 15, 265, 10.1007/s10126-012-9483-y

Janouškovec, 2013, Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers, PLoS One, 8, 10.1371/journal.pone.0059001

Manhart, 1990, The gain of two chloroplast tRNA introns marks the green algal ancestors of land plants, Nature, 345, 268, 10.1038/345268a0

Turmel, 2006, The chloroplast genome sequence of Chara vulgaris sheds new light into the closest green algal relatives of land plants, Mol. Biol. Evol., 23, 1324, 10.1093/molbev/msk018

Binder, 2007, Branched-chain amino acid metabolism in higher plants, Physiol. Plant., 129, 68, 10.1111/j.1399-3054.2006.00800.x

Hughey, 2001, Solving taxonomic and nomenclatural problems in Pacific Gigartinaceae (Rhodophyta) using DNA from type material, J. Phycol., 1109, 1091, 10.1046/j.1529-8817.2001.01048.x

Song, 2017, Complete mitochondrial genome of Gracilaria changii (Rhodophyta, Gracilariaceae), J. Appl. Phycol., 10.1007/s10811-017-1100-z

Vairappan, 2010, Role of secondary metabolites as defense chemicals against ice-ice disease bacteria in biofouler at carrageenophyte farms, J. Appl. Phycol., 22, 305, 10.1007/s10811-009-9460-7

Nasrolahi, 2012, A protective coat of microorganisms of macroalgae: inhibitory effects of bacterial microfilms and epibiotic microbial assemblages on barnacle attachment, FEMS Microbiol. Ecol., 81, 583, 10.1111/j.1574-6941.2012.01384.x

Longford, 2007, Comparisons of diversity of bacterial communities associated with three sessile marine eukaryotes, Aquat. Microb. Ecol., 48, 217, 10.3354/ame048217

Tujula, 2010, Variability and abundance of the epiphytic bacterial community associated with a green marine Ulvacean alga, ISME J., 4, 301, 10.1038/ismej.2009.107

Burke, 2011, Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis, ISME J., 5, 590, 10.1038/ismej.2010.164

Lachnit, 2011, Epibacterial community patterns on marine macroalgae are host-specific but temporally variable, Environ. Microbiol., 13, 655, 10.1111/j.1462-2920.2010.02371.x

Staufenberger, 2008, Phylogenetic analysis of bacteria associated with Laminaria saccharina, FEMS Microbiol. Ecol., 64, 65, 10.1111/j.1574-6941.2008.00445.x

Gl, 2011, Structural analysis of the degradation products of porphyran digested by Zobellia galactanivorans β-porphyranase A, Carbohydr. Polym., 83, 277, 10.1016/j.carbpol.2010.07.060

Aravindraja, 2013, Ultradeep 16S rRNA sequencing A analysis of geographically similar but diverse unexplored marine samples reveal varied bacterial community composition, PLoS One, 8, 10.1371/journal.pone.0076724