130
normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief
Bioinform 14:671–683
Exadactylos A (2015) Molecular approach of seagrasses response related to tolerance acquisition
to abiotic stress. In: Çalişkan M, Oz GC, Kavakli IH, Ozcan B (eds) Molecular approaches to
genetic diversity. InTech-Open Access, Rijeka, pp 75–91
Fourqurean JW, Duarte CM, Kennedy H, Marba N, Holmer M, Mateo MA, Apostolaki ET,
Kendrick GA, Krause-Jensen D, Mcglathery KJ, Serrano O (2012) Seagrass ecosystems as a
globally significant carbon stock. Nat Geosci 5:505–509
Franssen SU, Gu J, Bergmann N, Winters G, Klostermeier UC, Rosenstiel P, Bornberg-Bauer
E, Reusch TBH (2011) Transcriptomic resilience to global warming in the seagrass Zostera
marina, a marine foundation species. Proc Natl Acad Sci U S A 108:19276–19281
Franklin L, Osmond CB, Larkum AD (2003) Photoinhibition, UV-B and algal photosynthesis. In:
Larkum AD, Douglas S, Raven J (eds) Photosynthesis in algae, vol 14. Springer, Dordrecht,
pp 351–384
Garrard SL, Gambi MC, Scipione MB, Patti FP, Lorenti M, Zupo V, Paterson DM, Buia MC
(2014) Indirect effects may buffer negative responses of seagrass invertebrate communities to
ocean acidification. J Exp Mar Biol Ecol 461:31–38
Golicz AA, Schliep M, Lee HT, Larkum AW, Dolferus R, Batley J, Chan CK, Sablok G, Ralph PJ,
Edwards D (2015) Genome-wide survey of the seagrass Zostera muelleri suggests modification
of the ethylene signalling network. J Exp Bot 66:1489–1498
Greco M, Chiappetta A, Bruno L, Bitonti MB (2013) Effects of light deficiency on genome methylation in Posidonia oceanica. Mar Ecol Prog Ser 473:103–114
Green S (2017) Philosophy of systems biology. Perspectives from scientists and philosophers.
Springer, Cham. doi:10.1007/978-3-319-47000-9
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D,
Li B, Lieber M, Macmanes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R,
William T, Dewey CN, Henschel R, Leduc RD, Friedman N, Regev A (2013) De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512
Hasler-Sheetal H, Fragner L, Holmer M, Weckwerth W (2015) Diurnal effects of anoxia on the
metabolome of the seagrass Zostera marina. Metabolomics 11:1208–1218
Hemminga MA, Duarte CM (2000) Ecology. Cambridge University Press, Cambridge
Hiroaki K (2002) Computational systems biology. Nature 450:206–210
Hunt L, Gray JE (2009) The signaling peptide EPF2 controls asymmetric cell divisions during
stomatal development. Curr Biol 19:864–869
Hsu P, Lander E, Zhang F (2014) Development and applications of CRISPR-Cas9 for genome
engineering. Cell 157:1262–1278
Iyapparaj P, Revathi P, Ramasubburayan R, Prakash S, Palavesam A, Immanuel G, Anantharaman
P, Sautreau A, Hellio C (2014) Antifouling and toxic properties of the bioactive metabolites
from the seagrasses Syringodium isoetifolium and Cymodocea serrulata. Ecotoxicol Environ
Saf 103:54–60
Jain M (2015) Function genomics of abiotic stress tolerance in plants: a CRISPR approach. Front
Plant Sci 6:375
Jiang ZJ, Huang XP, Zhang JP (2010) Effects of CO 2 enrichment on photosynthesis, growth,
and biochemical composition of seagrass Thalassia hemprichii (Ehrenb.) Aschers. PubMed
10:904–913
Khalafallah AA, Geneid YA, Shaetaey SA, Shaaban B (2013) Responses of the seagrass Halodule
uninervis (Forssk.) Aschers. to hypersaline conditions. Egypt J Aquat Res 39:167–176
Koce JD, Vilhar B, Bohanec B, Dermastia M (2003) Genome size of Adriatic seagrasses. Aquat
Bot 77:17–25
Koch MS, Schopmeyer SA, Kyhn-Hansen C, Madden CJ, Peters JS (2007) Tropical seagrass species tolerance to hypersalinity stress. Aquat Bot 86:14–24
Kong FN, Li H, Sun PP, Zhou Y, Mao YX (2014) De novo assembly and characterization of the
transcriptome of seagrass Zostera marina using Illumina paired-end sequencing. PLoS One
9:e112245
E.E. Malandrakis et al.
normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief
Bioinform 14:671–683
Exadactylos A (2015) Molecular approach of seagrasses response related to tolerance acquisition
to abiotic stress. In: Çalişkan M, Oz GC, Kavakli IH, Ozcan B (eds) Molecular approaches to
genetic diversity. InTech-Open Access, Rijeka, pp 75–91
Fourqurean JW, Duarte CM, Kennedy H, Marba N, Holmer M, Mateo MA, Apostolaki ET,
Kendrick GA, Krause-Jensen D, Mcglathery KJ, Serrano O (2012) Seagrass ecosystems as a
globally significant carbon stock. Nat Geosci 5:505–509
Franssen SU, Gu J, Bergmann N, Winters G, Klostermeier UC, Rosenstiel P, Bornberg-Bauer
E, Reusch TBH (2011) Transcriptomic resilience to global warming in the seagrass Zostera
marina, a marine foundation species. Proc Natl Acad Sci U S A 108:19276–19281
Franklin L, Osmond CB, Larkum AD (2003) Photoinhibition, UV-B and algal photosynthesis. In:
Larkum AD, Douglas S, Raven J (eds) Photosynthesis in algae, vol 14. Springer, Dordrecht,
pp 351–384
Garrard SL, Gambi MC, Scipione MB, Patti FP, Lorenti M, Zupo V, Paterson DM, Buia MC
(2014) Indirect effects may buffer negative responses of seagrass invertebrate communities to
ocean acidification. J Exp Mar Biol Ecol 461:31–38
Golicz AA, Schliep M, Lee HT, Larkum AW, Dolferus R, Batley J, Chan CK, Sablok G, Ralph PJ,
Edwards D (2015) Genome-wide survey of the seagrass Zostera muelleri suggests modification
of the ethylene signalling network. J Exp Bot 66:1489–1498
Greco M, Chiappetta A, Bruno L, Bitonti MB (2013) Effects of light deficiency on genome methylation in Posidonia oceanica. Mar Ecol Prog Ser 473:103–114
Green S (2017) Philosophy of systems biology. Perspectives from scientists and philosophers.
Springer, Cham. doi:10.1007/978-3-319-47000-9
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D,
Li B, Lieber M, Macmanes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R,
William T, Dewey CN, Henschel R, Leduc RD, Friedman N, Regev A (2013) De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512
Hasler-Sheetal H, Fragner L, Holmer M, Weckwerth W (2015) Diurnal effects of anoxia on the
metabolome of the seagrass Zostera marina. Metabolomics 11:1208–1218
Hemminga MA, Duarte CM (2000) Ecology. Cambridge University Press, Cambridge
Hiroaki K (2002) Computational systems biology. Nature 450:206–210
Hunt L, Gray JE (2009) The signaling peptide EPF2 controls asymmetric cell divisions during
stomatal development. Curr Biol 19:864–869
Hsu P, Lander E, Zhang F (2014) Development and applications of CRISPR-Cas9 for genome
engineering. Cell 157:1262–1278
Iyapparaj P, Revathi P, Ramasubburayan R, Prakash S, Palavesam A, Immanuel G, Anantharaman
P, Sautreau A, Hellio C (2014) Antifouling and toxic properties of the bioactive metabolites
from the seagrasses Syringodium isoetifolium and Cymodocea serrulata. Ecotoxicol Environ
Saf 103:54–60
Jain M (2015) Function genomics of abiotic stress tolerance in plants: a CRISPR approach. Front
Plant Sci 6:375
Jiang ZJ, Huang XP, Zhang JP (2010) Effects of CO 2 enrichment on photosynthesis, growth,
and biochemical composition of seagrass Thalassia hemprichii (Ehrenb.) Aschers. PubMed
10:904–913
Khalafallah AA, Geneid YA, Shaetaey SA, Shaaban B (2013) Responses of the seagrass Halodule
uninervis (Forssk.) Aschers. to hypersaline conditions. Egypt J Aquat Res 39:167–176
Koce JD, Vilhar B, Bohanec B, Dermastia M (2003) Genome size of Adriatic seagrasses. Aquat
Bot 77:17–25
Koch MS, Schopmeyer SA, Kyhn-Hansen C, Madden CJ, Peters JS (2007) Tropical seagrass species tolerance to hypersalinity stress. Aquat Bot 86:14–24
Kong FN, Li H, Sun PP, Zhou Y, Mao YX (2014) De novo assembly and characterization of the
transcriptome of seagrass Zostera marina using Illumina paired-end sequencing. PLoS One
9:e112245
E.E. Malandrakis et al.