Index

A Amborella, 26, 31 Abiotic stress Anacardium occidentale, 33 genetic control, angiosperm tolerance Anagyris foetida, 29 antioxidant defense machinery, 290 Annotated reference genomes, of angiosperm damage control and repair, 292 and gymnosperm , 122, detoxification, 292 123 gene expression, 286–289 Annual rings, wood development, 206 photosynthesis and growth control, Antioxidant defense machinery, abiotic stress, 290–291 290 quantitative trait loci, drought stress Apical control, 185–187 response, 285–286 Apical dominance, 185–187 reactive oxygen species, 290 Aquaporins signaling, 289–290 drought tolerance, 291 stress sensing, 289–290 water transport, 291 transcription control, 289–290 “Aquatic palaeoherb” hypothesis, 7 transporter activity and osmotic Arabidopsis sp., 4 adjustments, 291–292 A. thaliana geographic and environmental distribution, evolutionary loss in, 336 276 genome-wide scan, 171 morphological and anatomical changes Qua-Qine Starch, 128 roots, 277–280 wood production in, 22–23 shoots and , 282–284 Arabinogalactan protein epitopes, 220 stem, 280–282 ARBORKNOX1 (ARK1) and ARK2, 210 Populus euphratica, 276 Archaefructus, 6 Abscisic acid (ABA), 251 Archaeopteris, 5 Acer pseudoplatanus, 36, 37 Architecture, hierarchical scales, 180 Activation tagging, 72–73 Asimina triloba, 28 Activator-inhibitor dynamics, 193 Autoallopolyploids, 167 Adansonia digitata, 41 Autopolyploidy, 104, 167 Adenia pechuelii, 41 Axial parenchyma, 38–39 ADHoRe, 113 Aeonium urbicum, 23 All-against-all BLASTP (protein BLAST) B search, 112 Bateson-Dobzhansky-Muller incompatibilities Allopatric speciation, 160 (BDMI), 165 Allopolyploidy, 104, 167 Begonia fruticosa, 43

© Springer International Publishing AG 2017 357 A.T. Groover and Q.C.B. Cronk (eds.), Comparative and Evolutionary Genomics of Angiosperm Trees, Genetics and Genomics: Crops and Models, DOI 10.1007/978-3-319-49329-9 358 Index

Benchmarking Universal Single-Copy Cornus sericea, 246 Orthologs (BUSCO), 62 C-repeat binding factors (CBFs), 251 Betula sp. Cryphonectria parasitica, 340 B. nana (see Dwarf birch) C-value paradox, 109 B. pendula, 90 Cyathea, 4–5 B. platyphylla, 90 Cyclostemon sp., 36, 37 β-glucosidases, 340 Cyphostemma juttae, 41 Biological pattern formation, 180 Cyto-nuclear interactions, 164 Botryosphaeria dothidea, 341 Branching angle, 187–188 Brighamia insignis, 41 D DAM6, 252 Damage control and repair, abiotic stress, 292 C “Dark and disturbed” hypothesis, 7 Callixylon wood, 5 The Dendrome portal, 90 Cambium, 19–22, 24–25, 34, 38, 39, 41, 42, Dendrosicyos socotrana, 41 44–46 Detoxification, abiotic stress, 292 Canarium mehenbethene, 36, 37 Dicksonia, 4–5 Candidate gene, local adaptation, 307–311 Diffuse porous woods, 27, 29 Carica papaya, 154 Dioecious trees evolutionary stratum, age of, 149 sex determination, 147–148 homologous sex-linked loci, 153 tropical, 140 non-recombining SDR, sequencing of, Diploidization, 106 149 Diploidy, restoration of, 106 Carlquistia muirii, 23 Dormancy Carya ovata var. australis, 33 and growth resumption, 252–253 Castanea sp. induction, 247 C. dentata, 28 Dorstenia gigas, 41 C. mollissima (see Chinese chestnut) Drought tolerance Castanopsis fordii, 28 aquaporins, 291 Causuarina glauca, 342 genome×environment interactions, 285 Celtis ehrenbergiana, 33 Populus euphratica, 276, 283 Centurion, 1–2 Dubautia laxa, 23 Chestnut blight, 340 Durio oxleyanas, 36, 37 Chinese chestnut, 86–87 Dutch elm disease, 341 Chitinases, 340 Dwarf birch, 88–89 Chondodendron platyphylla, 43 Chromosomal speciation, 165–166 Circadian clock, 247 E Cissus sulcicaulis, 43 Echinopsis mamillosa, 41 Clades, angiosperms, 9 Echium sp. Cladoxylales, 5 E. creticum, 23 Clonal propagation, of Populus genotypes, E. simplex, 23 68 Embolism, 29–31, 38 Comparative genome (CoGe) resource, 113 Endohydric mosses, 3 Compatible interactions, 337 Endophytes ComPlEx tool, 114 Colletotrichum tropicale, 345 Conserved non-coding DNA sequences mutualistic relationship, 344 (CNS), 101 nitrogen metabolism, 345 Conserved non-coding elements (CNE), 101, physical defence pathways, 345 102 and Theobroma cacao, 345 Conspecific pollen precedence (CPP), Endoreduplication, 105 163–164 Endospermum peltatum, 36, 37 Index 359

Ensembl project, 113 whole genome duplication events, Epigenetics role, local adaptation, 320 124–126 Eucalyptus sp. gains and losses E. globulus, 229 all-vs-all BLASTp search, 129 E. grandis, singleton genes, 128 evolution of vascular , 130 E. regnans, 1–2, 36, 37 full-length protein sequence collection, genomes of, 70 129 , clades of, 8, 10 InterProScan, 129 Eukaryotic genomes Leucine rich repeat domains, 130, 131 feature of, 109 molecular function and biological repeats in, 110 process terms, 129, 131 European ash, 87–88 MutS-related domain, 130 Expressed sequence tags (ESTs), 70 Pentatricopeptide repeat, 130 protein tyrosine kinase domain, 130 Toll/interleukin-1 receptor domains, F 131, 132 Fabids, 10 Z-score, 129 Fagus sylvatica, 338 Genetic control, abiotic stress Ferns, 3–6 antioxidant defense machinery, 290 Fiber, 32–33 damage control and repair, 292 Fiber-tracheids, 31, 32 detoxification, 292 Ficus sp. gene expression, 286–289 F. benghalensis, 2 photosynthesis and growth control, F. maxima, 33 290–291 Flowering time gene homologs, 239 quantitative trait loci, drought stress Fragments Per Kilobase of transcript per response, 285–286 Million mapped reads (FPKM), reactive oxygen species, 290 72 signaling, 289–290 Fraxinus sp. stress sensing, 289–290 F. americana, 34–35 transcription control, 289–290 F. excelsior (see European ash) transporter activity and osmotic FT gene, 255 adjustments, 291–292 Genetic theory sex chromosomes, evolution of, 148 G Genic speciation, 166 Gelatinous fiber, 32 Genome sequencing projects, 85 Gene breeding programmes, 85, 86 duplication Chinese chestnut, 86–87 fate of, 106–108 dwarf birch, 88–89 segmental duplication, 108–109 European ash, 87–88 expression, abiotic stress, 286–289 fruit and nut trees, 89–90 flow and population structure, future research, 91–93 305–307 pedunculate oak, 87 phenology and maturation in woody plants, purple willow, 88 235–238 selection of, 93–95 Gene-environment associations (GEA), 309 willow, 88 Gene families Genome structure, repeat content and, 109–112 evolutionary mechanisms Genome-wide association studies (GWAS), horizontal gene transfer, 127–128 local adaptation “orphan” genes, 128 adaptive genomic evolution, 314 protein domains, 126–127 P. trichocarpa, 312 segmental and single-gene duplications, RNASeq study, 313 126 SNP arrays, 311 360 Index

Genomics Hill-Robertson effect, 150, 151 adaptive introgression prevalence, 321–322 Hopea nutans, 36, 37 candidate gene studies, local adaptation, Hydraulic conductance, 277, 279, 280 307–311 Hydrome, 3 challenges and solutions collinear environmental, 314–315 genotypic axes, 314–315 I investment in phenotyping, Ilex sp. 316–318 I. cassine, 29 phenotypic, 314–315 I. decidua, 29 validating adaptive associations, natural Illegitimate recombination (IR), populations, 315–316 110–112 epigenetics role, 320 Illumina-based short RNAseq reads, 71 gene flow and population structure, Incompatible interactions, 337 305–307 Indian banyan tree, 2 genome-wide studies, local adaptation, Insular woodiness, 22 311–314 Internode elongation, 183–185 genomic predictions, climate change and Ipomoea arborescens var. pachylutea, 41 local adaptation, 320–321 Isoetes, 4 growing genomic resources outside of Populus, 318–319 incorporating gene expression studies, K 319–320 Karyotype changes, 104 populations for, 308 KNOX proteins, 3 predictions, climate change and local Koeberlinia spinosa, 28 adaptation, 320–321 scale and scope, revisiting, 323 seeking out understudied systems and L questions, 322 Land plants wood formation early, 2–3 comparative and evolutionary genomic evolution, timeline of, 2 studies, 215–219 Landscape genetics evolutionary origins and variation, adaptive introgression prevalence, 205–207 321–322 post-transcriptional regulation, candidate gene studies, local adaptation, 212–215 307–311 regulatory mechanisms regulating, challenges and solutions 207–208 collinear environmental, transcriptional regulation, 314–315 208–211 genotypic axes, 314–315 Genotype to phenotype mapping, 209 investment in phenotyping, Giant herbs, 4, 5 316–318 Gibberellic acid (GA), 211 phenotypic, 314–315 Ginkgo, 6 validating adaptive associations, Glomus intraradices, 342 natural populations, 315–316 Gnetales, 6 epigenetics role, 320 Growth control, abiotic stress, 290–291 gene flow and population structure, Guilfoylia monostylis, 36, 37 305–307 genome-wide studies, local adaptation, 311–314 H genomic predictions, climate change and Habitat isolation, 161–162 local adaptation, 320–321 Hartig net, 342 growing genomic resources outside of Heartwood formation, 39–40 Populus, 318–319 Index 361

incorporating gene expression studies, high-affinity ammonium importer family 319–320 (AMT1), 344 populations for, 308 oxidative stress tolerance, 343 scale and scope, revisiting, 323 pathogenesis-related (PR) proteins, 343 seeking out understudied systems and questions, 322 N abiotic stress, 282–284 NAC transcription factors, 3 mutualistic interactions, endophytes, NBS-LRR resistance proteins, 340 344–346 Nelumbo, 22 pathogens 24 nt siRNAs, biogenesis of, 111 Melampsora, 340 Nymphaeales, 22 Phytophthora, 340 Sphaerulina, 340 Leptome, 3 O Liana, 40–44 Optical mapping, 91 Lignin pathway, 3 orthoMCL tool, 112 Liquidambar styraciflua, 29 Oxford Nanopore sequencing, 91 Long interspersed (retro) elements (LINEs), 109 Long-terminal repeat TEs (LTR-TEs), 109, P 111–112 lealii, 41 Lycophytes, 3–6 Palaquium galatoxylum, 36, 37 Palm wood, 7–8 Panax elegans, 36, 37 M Pando (tree), 2 Macrospatial isolation, 161–162 Parapatric speciation, 160–161 Madhuca utilis, 36, 37 Parenchyma, 20, 27, 33 Malvids, 10 axial parenchyma, 38–39 Manoxylic wood, 6 expansion in woody succulents and lianas, Meiotic non-reduction, 167 40–42 Meiotic non-reduction mechanisms, longevity and heartwood formation, 104–105 39–40 Melampsora, 340 rays and rayless woods, 34–38 Meristem function Pathogenesis-related (PR) proteins, 337 rib, 184 Pathogenic invasion root apical, 194 tree defences against, 336–337 shoot apical, 181, 183 Paullinia pinnata, 43 subapical rib, 183 Pedunculate oak, 87 Microarrays, 70, 71 Pelargonium carnosum, 41 Microbes at home, plant tissues, 339 Phase change/maturation Microspatial isolation, 161–162 description, 227 Miniature inverted-repeat TEs (MITEs), juvenile and adult vegetative phases, 109 228–230 miRNA regulation, 212–213 reproductive Mixed-mating model, 142–143 environmental and hormonal Moringa ovalifolia, 41 regulation, 233–234 Mueller’s ratchet, 150 population, functional and comparative Mutualistic interactions genomics, 234, 239 in leaf, endophytes, 344–346 vegetative, 230–231 in root, mycorrhizal fungi, 341–344 environmental and hormonal Mycorrhizal fungi regulation, 231 arbuscular, 341–342 population, functional and comparative ectomycorrhizal, 341–342 genomics, 231–233 362 Index

Phenology Plant form alleles selection, 240 comparative genomics role, 194–196 description, 227 study of, 179, 180 reproductive, 228 themes, 193–194 anther dehiscence, 254 PlantGenIE, 114 anthesis, 254 Plant Genome Duplication Database (PGDD), bud flush time, 254 113 environmental and hormonal factors, Plant Genome Integrative Explorer Resource 254–255 (PlantGenIE), 73 flowering process, 254 Plant genomes molecular regulation, seasonal all-against-all BLASTP search, 112 flowering, 255–257 analysis, challenges and methods, 112–113 short-day (SD)-induced growth cessation Comparative Genome resource, 113 and dormancy induction, 240 ComPlEx tool, 114 vegetative, 228 Ensembl project, 113 annual growth patterns, 242 feature of, 102 annual shoot, 241 future research, 114 apical bud and cambial growth Phytozome, 113 cessation, 241 PlaNet resource, 114 depth of dormancy, 241 PlantGenIE, 114 dormancy induction, 245 Plant Genome Duplication Database, 113 environmental regulation, 243–247 PLAZA, 113, 114 environmental signals, 244 quality of genome assemblies, 113 freezing tolerance, 246 Plant mating systems insolation maxima, 247 definition, 140, 142 molecular regulation, 247–253 distribution of, 143–145 photoperiod, 247 estimating/inferring, 142–143 photoperiod and temperature, 246 evolutionary transitions, 141 photoperiodic responsive species, 245 genetic diversity, levels and distribution of, storage proteins, 243 145, 146 temperate and boreal trees, 243 mixed-mating model, 142–143 Phosphatidylethanolamine-binding protein outcrossing (PEBP) family, 251 advantages, 145 Photosynthesis, abiotic stress, 290–291 estimates, 142–145 PHYB2, 308–309 self-fertilization, 141 Phylostratigraphy, 128 selfing rates, 141–142 Physcomitrella patens, 2, 129, 130, 132 Plasmodesmata (PD) apertures, 253 Phytohormone based defences, 337 PLAZA, 113, 114 Phytophthora sp. Plectranthus ernstii, 41 endophyte, 345 Polar auxin transport (PAT), 4 P. citricola, 338 Pollinator preference, 163–164 root infection, 337–338 Polyploidy, 102 Phytozome, 113 definition, 166–167 PlaNet resource, 114 importance, 103 Plant breeding systems role in speciation, 167–168 definition, 140 types, 104–105 dioecy, 140–141, 147, 149 Polyspermy, 167 monoecy, 140–141 Poplar Genome Integrative Explorer Plant defences (PopGenIE), 73 categories, 337 Poplar tree, 63 general stress/pathogen responses, 337 Agrobacterium tumefaciens-mediated phytohormone based responses, 337 transformation, 69 Index 363

Bayesian network learning procedure, gene duplication, 106, 107 75 genome, 336 biological character, 65, 67–69 habitats of, 64 biology, 64–65 Illumina Infinium SNP genotyping cultivation, 65 arrays, 72 distributions, 64 range-wide collection, 76, 77 feed-forward transcriptional regulatory salicoid duplication, 168 network, 74 sex determining locus on chromosome flowering strategies, 75–76 19, 67 genomics singleton genes, 128 activation tagging, 72–73 transcriptional regulation, wood formation expressed sequence tags, 70 genomics, 208–211 genome assembly and annotation, 71 Post-transcriptional regulation, wood genome-wide single nucleotide formation polymorphism, 72 miRNA regulation, 212–213 microarrays, 70, 71 protein abundance regulation, 213–215 random gene dosage variants, Post-zygotic barriers, to gene flow generation of, 73 Bateson-Dobzhansky-Muller resources, 70 incompatibilities, 165 RNA sequencing, 71–72 chromosomal speciation, 165–166 habitats, 64 ecological and sexual selection, hybridization, 64 164–165 local environments, adaptation to, 76–78 extrinsic/ecological barriers, 164 maturation and seasonality, 75–76 genic speciation, 166 networks in wood formation, 74–75 hybrid incompatibility, 164 phenotypic variation, genetic basis of, intrinsic/genetic barriers, 164 76–78 Pre-zygotic barriers, to gene flow plantations, 65 conspecific pollen precedence, 163–164 rationale and history, 69–70 habitat preference/eco-geographic single nucleotide polymorphisms, 68 isolation, 161–162 species and hybrids, selection of, 65, 66 immigrant inviability, 162–163 systems biology approach, 74 pollinator preference, 163–164 systems genetics approach, 74, 75 reproductive isolation, 161–163 Population genetics, 112 temporal isolation, 162 Populus sp., 305, 340. See also Poplar tree Primary Xylem, 19–20 growing genomic resources outside of, Procambium, 20 318–319 Profile-based protein databases, 122 P. alba, 168 Progymnosperms, 5–6 P. angustifolia, 307 Protein-coding angiosperm gene families. See P. balsamifera, 67, 68, 76, 77, 307 Gene families sex determination genes, 148 Proteomics P. deltoides, 29, 68, 73 culture-based systems, tracheary element P. euphratica, 64 differentiation, 215 P. nigra, 78, 306 integration, 215 Illumina Infinium SNP genotyping lignification, 213 arrays for, 72 phenylpropanoid pathway, 213 vegetative propagation, 68 reaction wood formation, 214 protein abundance regulation, 213–215 wood formation, 213 P. tremula, 67, 68, 168 Pseudoautosomal regions (PAR), 148 P. tremuloides, 2, 67, 306 Pseudotsuga menziesii, 311 P. trichocarpa, 67, 73, 307 Purple willow, 88 clonal propagation, 68 Pycnoxylic wood, 6 364 Index

Q Semi-ring/semi-diffuse porous woods, 27–29 Quantitative trait loci (QTL) Senescence and self-pruning, 189–190 drought stress response, abiotic stress, Sequenced angiosperm tree genomes, 102, 103 285–286 Serjania ichthyoctona, 43 Dw1 and Dw2, 234 Sex determination genes, 147, 148, 153 Qua-Qine Starch (QQS), 128 Sex determination region (SDR) Quercus sp., 305 C. papaya Y, 149 Q. alba, 319 in cucurbits, 148 Q. lobata, 319 dioecious tree species, 148 Q. robur, 318 (see also Pedunculate oak) Hill-Robertson effect, 150, 151 locations and ages, 149, 150 in Populus and Salix, 148, 149 R Salicaceae, 149 Random gene dosage variants, generation of, sexually antagonistic fitness effects, 73 148–149 Rays and rayless woods, 34–38 Sexual polyploidisation, 105 Reactive oxygen species (ROS), abiotic stress, Shoot apex, patterning, 181–183 290 Shoot apical meristem (SAM), 181 Reproductive maturation, 228 Shoot development, lateral, 185–187 Reproductive phenology, 228 Shoots, abiotic stress, 282–284 anther dehiscence, 254 Short-day (SD)-induced growth cessation and anthesis, 254 dormancy induction, 240 bud flush time, 254 Short interspersed (retro)elements (SINEs), environmental and hormonal factors, 109 254–255 Shrub willow, 88 flowering process, 254 Signaling, abiotic stress, 289–290 molecular regulation, seasonal flowering, SMRT sequencing, 91 255–257 Soft sweep phenomenon, 171 REVOLUTA, 211 Somatic doubling, 167 Rhamnus chugokuensis, 29 Somatic genome duplication, 104 Ring porous woods, 27–28 Sophora affinis, 28 RNA sequencing (RNAseq), 71–72 Speciation Root allopatric, 160 abiotic stress, 277–280 gene flow mutualistic interactions, mycorrhizal fungi, post-zygotic barriers, 164–166 341–344 pre-zygotic barriers, 161–164 pathogens, Phytophthora, 337–338 genomic islands of divergence, 169–170 Rosid clades, evolution of, 10 genomics of, 169–171 Rust pathogens, 340 hybridization, 167–168 local adaptation, 160 modes of, 159–161 S non-allopatric divergence, 160 Salicaceae, 63 parapatric, 160–161 Salix sp. polyploidy, 166–168 S. caerulea, 36, 37 Sphaerulina sp., 340 S. purpurea (see Purple willow) Stem S. suchowensis (see Shrub willow) abiotic stress, 280–282 Sapindus mukorossi, 33 canker, 341 Sapwood, 28, 39, 40 pathogens, 338–341 Sarcandra, 26, 27 Stizophyllum riparium, 44 Secondary woodiness, 22–25 Stress sensing, 276 Secondary xylem, 19–21 genetic control, abiotic stress, 289–290 Seed dispersal, in wind-pollinated trees, 160 Stylites, 4 Segmental gene duplication, 108–109 Successive cambia, 45 Selaginella moellendorffii, 132 Succulents, 40–42 Index 365

T insolation maxima, 247 TDIF RECEPTOR/PHLOEM molecular regulation, 247–253 INTERCALATED WITH XYLEM abscisic acid (ABA), 251 (TDR/PXY), 210 circadian clock, 247 Tension wood, 32 cold acclimation, 247 Tetracentron sinense, 27 C-repeat binding factors (CBFs), Timber 251 families, 10–12 DAM6, 252 phylogenetic distribution, 10, 13 dormancy and growth resumption, Tracheids 252–253 and co-occurrence of vessels, 30–31 dormancy induction, 247 fiber-tracheids, 31, 32 environmental and endogenous Transcriptomic analysis signaling pathways, 250 compatible vs. incompatible plant, 341 evg peach genotype, 252 genetic control, abiotic stress, 289–290 FT genes expression, 249 mycorrhizal symbiosis, 342 FT-like (FTL) genes, 251 with Phytophthora concentrate, 338 growth cessation, 247 wood formation genomics, 208–211 phosphatidylethanolamine-binding Transporter activity and osmotic adjustments, protein (PEBP) family, 251 291–292 plasmodesmata (PD) apertures, 253 Transposable elements (TEs), 109–111 SD response, transcriptomic time Tree defences, pathogenic invasion, 336–337 series, 250 Tree height, 192–193 photoperiod, 247 Tree responses responsive species, 245 to common pathogens, 337 and temperature, 246 mirrored, 347 storage proteins, 243 Triploid block, 105 temperate and boreal trees, 243 Trochodendraceae, 26, 27 Vesselless woods, 26–27 Tylecodon paniculatus, 41 Vessels, angiosperm distribution patterns and hydraulic consequences, 27–30 U patterning, 25–26 Ulmus americana, 28 tracheids and co-occurrence of, 30–31 Unequal intra-strand homologous vesselless woods, 26–27 recombination (UR), 110–112 Viburnum stellatotomentosum, 33

V W Vascular cambium (VC), 190, 206 Waterlilies, 7 vascular tissue production, 121 Water use efficiency (WUE), 283 Vascularization, 3–4 in Quercus robur, 286 VASCULAR-RELATED NAC-DOMAIN6 Whole genome duplication (WGD), 105–106 (VND6), 210 importance, 102 Vascular system and plant girth regulation, Wood 190–191 definition, 19 Vegetative phenology, 228 evolution of annual growth patterns, 242 Amborella, 7, 8 annual shoot, 241 Austrobaileyales, 7 apical bud and cambial growth cessation, molecular dating studies, 6 241 monocot clade, 7 depth of dormancy, 241 Nymphaeales, 7 dormancy induction, 245 pollen grains, 6 environmental regulation, 243–247 formation genomics environmental signals, 244 comparative and evolutionary genomic freezing tolerance, 246 studies, 215–219 366 Index

Wood (cont.) trunks, evolution of, 5–6 evolutionary origins and variation, Woody-herbaceous continuum, 205–207 21–25 post-transcriptional regulation, Woody herbs, 21 212–215 Woody plant, 19 regulatory mechanisms regulating, Woody succulents, 40–42 207–208 WRKY transcription factors, 340 transcriptional regulation, 208–211 stem biology, angiosperm trees, 19–21 structure in X primary xylem, 19–20 Xylem procambium, 20 vs. phloem cylinder production, 42–45 secondary xylem, 19–20 primary, 19–20 woodiness, variation in, 21–25 secondary, 19–21 woody-herbaceous continuum, 21–25 water transport, 25–31 woody stem biology, 19–21 Xylogenesis, 3, 7, 8