Index
393
Gene regulatory network, 160, 162, 166, 168,
354–355
Gene repertoire, 146, 163, 315, 354–355
Genetic cline, 92
Genetic diversity, 6, 21, 23, 78–79, 224, 251,
255–256, 300
Genetic hitch-hiking, 86
Genetic lineages, 2
Genetic maps, 4, 87, 219, 243
Genetic marker, 80, 84
Genetic transformation, 197, 201–202
Genomes, 55, 83, 93, 99–100, 127–128,
155–156, 166, 183–186, 190, 196–198,
220, 292, 316–321, 337–339, 349–350,
354–355
annotation, 55, 147, 315, 337–342,
345, 349
annotation systems, 55, 338–339, 345
scan, 85–86, 88–93, 257–258, 261
sequence analysis, 61, 315
Genomics, 1–25, 35, 37, 55–57, 78, 83–90,
96–97, 100, 179–204, 213–264,
288–291, 296, 301, 303–305, 326, 331,
342, 345, 355
Genomic Standards Consortium (GSC), 61
Geochemical cycles, 34, 180, 197, 293
Germ layer, 122–123, 137, 151, 152, 154,
158, 160
Gilthead seabream, 214, 218, 240, 242
Glaucophyte, 180, 182, 197
Glimmer, 54, 56, 332–336
Global Ocean Sampling (GOS), 36, 57–58,
293, 296, 352
Glycymeris sp, 20
Gordon and Betty Moore Foundation, 55
G-protein coupled receptors (GPCR), 166
Graphical user interface (GUI), 57, 366–367
Green algae, 183, 187, 303–305
Grooved carpet shell, 246
Growth, 7, 17, 23, 87–89, 94–96, 165, 168,
190, 194–195, 201, 222–232, 234,
241–243, 256, 261–262, 303, 316,
318, 322
Guillardia theta, 186, 192, 198
H
Haematococcus pluvialis, 305–306
Haemophilus influenzae, 316
Haliotis discus hannai, 121, 225
Haliotis kamtschatkana, 20
Halogen metabolism, 200
Haploid-diploid life cycle, 201
Haptophytes, 182, 191, 198
Hardy-Weinberg, 80
Hedgehog, 147–149
Helicolenus dactylopterus, 20
Helix-loop-helix, 149
Hemichordates, 122, 133, 160
Heterocapsa triquetra, 191, 199
Heterokonts, 182, 188, 191–192, 198, 306
Heterosis, 94–95, 222, 225
Heterotroph, 12, 181–182, 188, 190
Hidden Markov Models (HMMs), 331–332,
335–336, 340–341
High throughput DNA sequencing, 6, 11,
15, 36, 166, 169, 179, 188–191, 215,
290, 356
High-scoring segment pair (HSP), 74, 98,
326–327, 329
Homeobox, 149–150, 153–154
Homeodomain proteins, 151
Homeodomain, 126, 151
Homologue, 155, 218
Homoplasy, 80, 129–130
Horizontal (or lateral) gene transfer, 183
Horizontal gene transfer, 183, 194, 332,
344–345
Host-pathogen interaction, 240–249
Hox cluster, 144, 156–157, 167
Hox genes, 119, 123, 126, 144, 154, 156–157
Hybrid vigour, 81, 93–95
Hybrid, 81, 92–95, 216, 218–219, 222, 322
Hybridisation, 13, 19, 38, 49, 92, 188, 202,
250, 258
Hydra, 7, 130, 154–155
Hydra vulgaris, 155
Hydractinia echinata, 155
Hydrothermal, 2, 20–21, 73, 100–102, 105,
288–289
Hydrothermal vent mussel, 18, 76, 102
Hydrozoan, 155, 159–160
Hyperthermus butylicus DSM 5456, 294
Hyporhamphus melanochir, 18
Hyporhamphus regularis, 18
I
Ictalurus punctatus, 240
Immediate upright (imm), 201
Inbreeding, 77, 79, 84, 94, 224
Innate immunity, 166, 242, 261
Insert-end sequencing, 36–37, 49, 52
In situ hybridization, 13, 20, 40, 44
The Integrated Microbial Genomes system
(IMG), 55
Internal transcribed space, length heterogeneity
PCR (ITS-LH-PCR), 11
393
Gene regulatory network, 160, 162, 166, 168,
354–355
Gene repertoire, 146, 163, 315, 354–355
Genetic cline, 92
Genetic diversity, 6, 21, 23, 78–79, 224, 251,
255–256, 300
Genetic hitch-hiking, 86
Genetic lineages, 2
Genetic maps, 4, 87, 219, 243
Genetic marker, 80, 84
Genetic transformation, 197, 201–202
Genomes, 55, 83, 93, 99–100, 127–128,
155–156, 166, 183–186, 190, 196–198,
220, 292, 316–321, 337–339, 349–350,
354–355
annotation, 55, 147, 315, 337–342,
345, 349
annotation systems, 55, 338–339, 345
scan, 85–86, 88–93, 257–258, 261
sequence analysis, 61, 315
Genomics, 1–25, 35, 37, 55–57, 78, 83–90,
96–97, 100, 179–204, 213–264,
288–291, 296, 301, 303–305, 326, 331,
342, 345, 355
Genomic Standards Consortium (GSC), 61
Geochemical cycles, 34, 180, 197, 293
Germ layer, 122–123, 137, 151, 152, 154,
158, 160
Gilthead seabream, 214, 218, 240, 242
Glaucophyte, 180, 182, 197
Glimmer, 54, 56, 332–336
Global Ocean Sampling (GOS), 36, 57–58,
293, 296, 352
Glycymeris sp, 20
Gordon and Betty Moore Foundation, 55
G-protein coupled receptors (GPCR), 166
Graphical user interface (GUI), 57, 366–367
Green algae, 183, 187, 303–305
Grooved carpet shell, 246
Growth, 7, 17, 23, 87–89, 94–96, 165, 168,
190, 194–195, 201, 222–232, 234,
241–243, 256, 261–262, 303, 316,
318, 322
Guillardia theta, 186, 192, 198
H
Haematococcus pluvialis, 305–306
Haemophilus influenzae, 316
Haliotis discus hannai, 121, 225
Haliotis kamtschatkana, 20
Halogen metabolism, 200
Haploid-diploid life cycle, 201
Haptophytes, 182, 191, 198
Hardy-Weinberg, 80
Hedgehog, 147–149
Helicolenus dactylopterus, 20
Helix-loop-helix, 149
Hemichordates, 122, 133, 160
Heterocapsa triquetra, 191, 199
Heterokonts, 182, 188, 191–192, 198, 306
Heterosis, 94–95, 222, 225
Heterotroph, 12, 181–182, 188, 190
Hidden Markov Models (HMMs), 331–332,
335–336, 340–341
High throughput DNA sequencing, 6, 11,
15, 36, 166, 169, 179, 188–191, 215,
290, 356
High-scoring segment pair (HSP), 74, 98,
326–327, 329
Homeobox, 149–150, 153–154
Homeodomain proteins, 151
Homeodomain, 126, 151
Homologue, 155, 218
Homoplasy, 80, 129–130
Horizontal (or lateral) gene transfer, 183
Horizontal gene transfer, 183, 194, 332,
344–345
Host-pathogen interaction, 240–249
Hox cluster, 144, 156–157, 167
Hox genes, 119, 123, 126, 144, 154, 156–157
Hybrid vigour, 81, 93–95
Hybrid, 81, 92–95, 216, 218–219, 222, 322
Hybridisation, 13, 19, 38, 49, 92, 188, 202,
250, 258
Hydra, 7, 130, 154–155
Hydra vulgaris, 155
Hydractinia echinata, 155
Hydrothermal, 2, 20–21, 73, 100–102, 105,
288–289
Hydrothermal vent mussel, 18, 76, 102
Hydrozoan, 155, 159–160
Hyperthermus butylicus DSM 5456, 294
Hyporhamphus melanochir, 18
Hyporhamphus regularis, 18
I
Ictalurus punctatus, 240
Immediate upright (imm), 201
Inbreeding, 77, 79, 84, 94, 224
Innate immunity, 166, 242, 261
Insert-end sequencing, 36–37, 49, 52
In situ hybridization, 13, 20, 40, 44
The Integrated Microbial Genomes system
(IMG), 55
Internal transcribed space, length heterogeneity
PCR (ITS-LH-PCR), 11