Index
397
Prymnesium parvum, 191, 197
Pseudogene, 335
Pseudomonas bromoutilis, 288
Pseudo-nitzschia, 186, 191–192, 195
Pulsed field gel electrophoresis, 47
PUMA, 2, 55
p-value, 364
Pyrobaculum aerophilum, 294
Pyrococcus abyssi GE5, 294
Pyrococcus furiosus JCM 8422, 294
Pyrococcus horikoshii OT3, 294
Pyrodictium abyssi DSM 6198, 294
Pyrolobus fumarii, 294
Pyrosequencing, 11, 36–39, 50–51, 58, 61,
80–81, 249, 316, 318–321
Q
Q-PCR, qPCR or qRT-PCR, 81–84, 91,
242–243, 357, 369
Quantitative or Real Time PCR (Q-PCR), 5,
11, 74, 81–83, 91–92, 227, 258
Quantitative trait locus/loci (QTL), 4, 21,
74, 81, 87–90, 217, 223–225, 232,
242–243, 261, 263
R
Rainbow trout, 78, 99, 223, 227–231, 235,
242, 260
Random Amplification of Polymorphic DNA
(RAPD), 215, 233
Rapid Annotation using Subsystem Technology
(RAST), 55, 166, 333
Rare genomic changes, 121, 128–131
Reactive Oxygen species (ROS), 248
Recombination, 84, 86, 95, 153, 217, 219, 306
Red algae, 187, 198, 201–203
Red tides, 190–191
Reganor, 56, 333–334
Regulatory Networks, 146, 149, 160, 162, 166,
168–170, 315, 354, 356
Replicate, 362
Reporter/Probe, 12–13, 40, 45, 197, 359–360
Reproduction, 23, 153, 160, 222–225, 255–256
Restriction length polymorphism (RFLP), 10,
14, 18–19, 49, 243
Reverse taxonomy, 15, 18
Rhizaria, 181–182
Rhodopirellula baltica, 301
2R hypothesis, 144, 167
Ribosomal Database Project II, 58
Ribosomal probes, 12–13
Rice cluster I, 36, 40
Riftia pachyptila, 20, 79
RNA interference (RNAi), 201
18s rRNA, 10, 12–13, 15
Rolling circle amplification, 42
Ruditapes decussates, 246
Ruditapes philippinarum, 19
S
Saccaromyces cerevisiae, 7
Saccharina (Laminaria) japonica, 306
Saccharomyces cerevisae, 322
Salmo salar, 77–79, 84, 214, 217, 223, 225,
229, 233, 240, 242, 254, 257, 259–260
Salmonella typhimurium, 344
Salmo trutta, 233, 258
Sargasso Sea, 8, 50, 189, 290, 293, 297, 300
Scaffolds, 51–52, 54, 57, 220
Scatter-plot, 362
Scomber scombrus, 20
Scophthalmus maximus, 222, 260
Scophthalmus rhombus, 20
Screening, 4–5, 38–39, 45–46, 49, 52, 78,
82–84, 88, 99, 201, 237–239, 291,
296–298
Scyphozoan, 160
SDS-PAGE, 239
Sea anemone, 154–155
Seagrasses, 174
Sea hare, 163
Sea-ice, 190
Sea urchin, 7, 160, 166, 169
Seaweed, 199, 201
Secondary endosymbiosis, 175–177, 198
Selective sweep, 4–5, 86, 92, 96
Selenoenzymes, 196
Self Organizing Maps (SOM), 53, 334
Senegalese sole, 222
Sequence databases, 58, 324, 347, 348–353
Sequence trace file, 317, 327
Sequence-tagged markers, 4
Sequencing, 10–11, 15, 19, 35–39, 44–45,
49–52, 73, 80–81, 125–126, 151, 162,
166, 179, 186, 190, 204, 220, 248,
290–293, 315–323, 355
Sequencing (454), 80, 105, 257, 320
Serial Analysis of Gene Expression (SAGE),
220–221, 225, 249, 356–358, 369
Seriola quinquerdiata, 242
Serpulidae, 19
Serranus cabrilla, 20
Settlement, 91, 128, 149–150
Sex, 105, 153
Short Read Archive (SRA), 57–58
Signalling, 91, 147, 149–151, 155–157, 166,
204, 242, 245, 247, 356
397
Prymnesium parvum, 191, 197
Pseudogene, 335
Pseudomonas bromoutilis, 288
Pseudo-nitzschia, 186, 191–192, 195
Pulsed field gel electrophoresis, 47
PUMA, 2, 55
p-value, 364
Pyrobaculum aerophilum, 294
Pyrococcus abyssi GE5, 294
Pyrococcus furiosus JCM 8422, 294
Pyrococcus horikoshii OT3, 294
Pyrodictium abyssi DSM 6198, 294
Pyrolobus fumarii, 294
Pyrosequencing, 11, 36–39, 50–51, 58, 61,
80–81, 249, 316, 318–321
Q
Q-PCR, qPCR or qRT-PCR, 81–84, 91,
242–243, 357, 369
Quantitative or Real Time PCR (Q-PCR), 5,
11, 74, 81–83, 91–92, 227, 258
Quantitative trait locus/loci (QTL), 4, 21,
74, 81, 87–90, 217, 223–225, 232,
242–243, 261, 263
R
Rainbow trout, 78, 99, 223, 227–231, 235,
242, 260
Random Amplification of Polymorphic DNA
(RAPD), 215, 233
Rapid Annotation using Subsystem Technology
(RAST), 55, 166, 333
Rare genomic changes, 121, 128–131
Reactive Oxygen species (ROS), 248
Recombination, 84, 86, 95, 153, 217, 219, 306
Red algae, 187, 198, 201–203
Red tides, 190–191
Reganor, 56, 333–334
Regulatory Networks, 146, 149, 160, 162, 166,
168–170, 315, 354, 356
Replicate, 362
Reporter/Probe, 12–13, 40, 45, 197, 359–360
Reproduction, 23, 153, 160, 222–225, 255–256
Restriction length polymorphism (RFLP), 10,
14, 18–19, 49, 243
Reverse taxonomy, 15, 18
Rhizaria, 181–182
Rhodopirellula baltica, 301
2R hypothesis, 144, 167
Ribosomal Database Project II, 58
Ribosomal probes, 12–13
Rice cluster I, 36, 40
Riftia pachyptila, 20, 79
RNA interference (RNAi), 201
18s rRNA, 10, 12–13, 15
Rolling circle amplification, 42
Ruditapes decussates, 246
Ruditapes philippinarum, 19
S
Saccaromyces cerevisiae, 7
Saccharina (Laminaria) japonica, 306
Saccharomyces cerevisae, 322
Salmo salar, 77–79, 84, 214, 217, 223, 225,
229, 233, 240, 242, 254, 257, 259–260
Salmonella typhimurium, 344
Salmo trutta, 233, 258
Sargasso Sea, 8, 50, 189, 290, 293, 297, 300
Scaffolds, 51–52, 54, 57, 220
Scatter-plot, 362
Scomber scombrus, 20
Scophthalmus maximus, 222, 260
Scophthalmus rhombus, 20
Screening, 4–5, 38–39, 45–46, 49, 52, 78,
82–84, 88, 99, 201, 237–239, 291,
296–298
Scyphozoan, 160
SDS-PAGE, 239
Sea anemone, 154–155
Seagrasses, 174
Sea hare, 163
Sea-ice, 190
Sea urchin, 7, 160, 166, 169
Seaweed, 199, 201
Secondary endosymbiosis, 175–177, 198
Selective sweep, 4–5, 86, 92, 96
Selenoenzymes, 196
Self Organizing Maps (SOM), 53, 334
Senegalese sole, 222
Sequence databases, 58, 324, 347, 348–353
Sequence trace file, 317, 327
Sequence-tagged markers, 4
Sequencing, 10–11, 15, 19, 35–39, 44–45,
49–52, 73, 80–81, 125–126, 151, 162,
166, 179, 186, 190, 204, 220, 248,
290–293, 315–323, 355
Sequencing (454), 80, 105, 257, 320
Serial Analysis of Gene Expression (SAGE),
220–221, 225, 249, 356–358, 369
Seriola quinquerdiata, 242
Serpulidae, 19
Serranus cabrilla, 20
Settlement, 91, 128, 149–150
Sex, 105, 153
Short Read Archive (SRA), 57–58
Signalling, 91, 147, 149–151, 155–157, 166,
204, 242, 245, 247, 356