Plastid Genome Evolution, Volume 85

398 Pages·2018·12.571 MB·English

by  Shu-Miaw Chaw, Robert K. Jansen

VOLUMEEIGHTYFIVE
A
DVANCES IN
BOTANICAL RESEARCH
Plastid Genome Evolution
ADVANCES IN BOTANICAL RESEARCH
Series Editors
Jean-PierreJacquot
Professor, Membre deL’InstitutUniversitaire deFrance, Unite´ Mixte deRecherche
INRA,UHP1136 “InteractionArbresMicroorganismes”, Universit(cid:1)edeLorraine,
Facult(cid:1)edesSciences, Vandoeuvre, France
PierreGadal
Honorary Professor, Universit(cid:1)eParis-Sud XI, InstitutBiologiedes Plantes, Orsay, France
VOLUMEEIGHTYFIVE
A
DVANCES IN
BOTANICAL RESEARCH
Plastid Genome Evolution
Volume Editors
SHU-MIAW CHAW
Biodiversity Research Center, Academia Sinica;
Biodiversity Program, Taiwan International
Graduate Program, Academia Sinica and National Taiwan
Normal University, Taipei, Taiwan
ROBERT K. JANSEN
Department of Integrative Biology,
University of Texas at Austin, Austin, TX, United States;
Genomics and Biotechnology Research Group,
Faculty of Science, King Abdulaziz University,
Jeddah, Saudi Arabia
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CONTENTS
Contributors ix
Preface xiii
1.Plastid Autonomy vs Nuclear Control Over Plastid Function 1
Jande Vries and JohnM. Archibald
1. Introduction:EndosymbiosisandtheGenomicRemnantsofCyanobacteriain
Archaeplastida 2
2. CyanobacterialGenesinTwoGeneticCompartments 6
3. PlastidGenomes:CodingCapacityandFunctionalDiversity 7
4. RoleofGeneticAutonomyinEndosymbiosis 11
5. KleptoplastyandGeneticSemiautonomyof(Stolen)Plastids 13
6. PlastidAutonomyandtheEvolutionofLandPlants 16
7. Outlook 19
Acknowledgements 20
References 20
2.Lost in the Light: Plastid Genome Evolution in
Nonphotosynthetic Algae 29
DavidR.Smith
1. Introduction 30
2. AndThenThereWasLight 33
3. BurningOut:TheEvolutionaryLossofPhotosynthesis 36
4. GeneticBallandChain:PlastomesinColourlessAlgae 39
5. AdiósptDNA:TheOutrightLossofaPlastome 43
6. NonphotosyntheticptDNA:NotsoSmallAfterAll 46
7. ConcludingThoughts 48
Acknowledgements 49
References 49
FurtherReading 53
3.Plastid Genomes in the Myzozoa 55
SergioA. Muñoz-Gómezand Claudio H.Slamovits
1. Introduction 56
2. TheMyzozoa 56
3. TheOriginofMyzozoanPlastids 60
v
vi Contents
4. DiversityofPlastidsintheMyzozoa 61
5. ThePlastomesofMyzozoans 68
6. GeneTransferinMyzozoans 81
7. ConclusionsandFutureDirections 86
Acknowledgements 87
References 87
4.Comparative Plastid Genomics of Glaucophytes 95
AdrianReyes-Prieto, SarahRussell,Francisco Figueroa-Martinez,
andChristopher Jackson
1. Introduction 96
2. TheGlaucophytaPlastids,OrganellesWithAncestralMorphologicalTraits 98
3. TheGeneticRepertoireoftheBlue-GreenPlastids 103
4. InterspecificComparativeGenomics 110
5. Phylogenomics,theOriginofthePrimaryPlastidsandtheArchaeplastida
Hypothesis 115
6. TheKnownGlaucophyteGroupsRepresentLineagesofPutativeAncient
Divergence 117
7. Conclusions 119
References 121
5.Evolution of the Plastid Genomes in Diatoms 129
MengjieYu, MattP.Ashworth, Nahid H.Hajrah, MohammadA. Khiyami,
MumdoohJ. Sabir,AlawiahM. Alhebshi,Abdulrahman L.Al-Malki,
Jamal S.M.Sabir, EdwardC.Theriot, and RobertK. Jansen
1. Introduction 130
2. MaterialsandMethods 133
3. Results 137
4. Discussion 146
Acknowledgements 151
AuthorContributions 152
References 152
6.Evolution of the Plastid Genome in Green Algae 157
MoniqueTurmel and Claude Lemieux
1. Introduction 158
2. ClassificationandPhylogenyofGreenAlgae 159
3. PlastomeArchitectureoftheCommonAncestorofAllGreenAlgae 164
Contents vii
4. PlastomeEvolutionintheChlorophyta 165
5. PlastomeEvolutioninStreptophyteAlgae 182
6. FutureDirections 186
References 188
7.Evolution of Gymnosperm Plastid Genomes 195
Shu-MiawChaw, Chung-Shien Wu, andEdi Sudianto
1. Introduction 196
2. SequencingthePlastomesofGymnosperms 198
3. PlastomeCharacteristicsinGymnosperms 201
4. PlastomeRearrangements 206
5. EvolutionofNucleotideSubstitutionRates 209
6. PlastidPhylogenomicsofGymnosperms 212
7. ConclusionsandFutureDirections 216
Acknowledgments 216
References 216
8.Aberration or Analogy? The Atypical Plastomes of Geraniaceae 223
Tracey A.Ruhlman and RobertK. Jansen
1. Introduction 224
2. TheGreatandtheSmall 225
3. ChangeorStaytheSame 231
4. KeepingUpWiththeRateRace:AccelerationandCoevolution 242
5. StayinginSync:HybridHarmonyorDissonance 251
6. AberrationorAnalogy? 254
Acknowledgements 255
References 255
9.Structural Diversity Among Plastid Genomes of Land Plants 263
Jeffrey P.Mowerand Trisha L.Vickrey
1. Introduction 264
2. TypicalStructureofaLandPlantPlastome 264
3. ConservedPlastomesandInferenceofAncestralStructures 266
4. StructuralDiversityofthePlastomeAmongPlants 270
5. FunctionalEffectofStructuralChange 277
6. WhatIsLeftinPlastomeStructuralResearch? 281
Acknowledgements 283
References 283
viii Contents
10.Plastome Phylogenetics: 30 Years of Inferences Into Plant
Evolution 293
MatthewA.Gitzendanner, PamelaS. Soltis, Ting-Shuang Yi,De-ZhuLi,
andDouglas E. Soltis
1. Introduction 294
2. ThePlastidGenomeandPlantSystematics 294
3. PlastomePhylogeny:StateoftheTree 300
4. PlastomePhylogenetics:OngoingChallenges 306
5. Conclusions 307
References 308
11.Molecular Evolution of Plastid Genomes in Parasitic Flowering
Plants 315
SusannWicke and JuliaNaumann
1. Introduction 316
2. PlastomeSizeDiversityinHeterotrophicLandPlants 317
3. ReconstructingandAnnotatingDivergentPlastomesofHeterotrophs 321
4. AreWeAlwaysDealingWith(Pseudo)genes? 324
5. EvolutionofPlastomeStructureUnderRelaxedSelectiveConstraints 326
6. FunctionalReductionAlongtheTransitiontoaNonphotosyntheticLifestyle 329
7. EvolutionofSubstitutionRates 332
8. ModelsofPlastomeDegradation 335
9. ConclusionsandFutureDirections 339
Acknowledgements 340
Glossary 341
References 341
SubjectIndex 349
AuthorIndex 357
CONTRIBUTORS
AbdulrahmanL.Al-Malki
DepartmentofBiochemistry,FacultyofScience,KingAbdulazizUniversity,Jeddah,21589,
SaudiArabia
AlawiahM.Alhebshi
GenomicsandBiotechnologyResearchGroup,FacultyofScience,KingAbdulaziz
University,Jeddah,21589,SaudiArabia
JohnM.Archibald
DalhousieUniversity,Halifax,NS;PrograminIntegratedMicrobialBiodiversity,Canadian
InstituteforAdvancedResearch,Toronto,ON,Canada
MattP.Ashworth
DepartmentofIntegrativeBiology,UniversityofTexasatAustin,Austin,TX,UnitedStates
Shu-MiawChaw
BiodiversityResearchCenter,AcademiaSinica;BiodiversityProgram,TaiwanInternational
GraduateProgram,AcademiaSinicaandNationalTaiwanNormalUniversity,Taipei,
Taiwan
JandeVries
DalhousieUniversity,Halifax,NS,Canada
FranciscoFigueroa-Martinez
CONACyT-UniversidadAuto´nomaMetropolitana,M(cid:1)exicoCity,M(cid:1)exico
MatthewA.Gitzendanner
DepartmentofBiology,UniversityofFlorida,Gainesville,FL,UnitedStates
NahidH.Hajrah
GenomicsandBiotechnologyResearchGroup,FacultyofScience,KingAbdulaziz
University,Jeddah,21589,SaudiArabia
ChristopherJackson
SchoolofBiosciences,UniversityofMelbourne,Melbourne,VIC,Australia
RobertK.Jansen
DepartmentofIntegrativeBiology,UniversityofTexasatAustin,Austin,TX,UnitedStates;
GenomicsandBiotechnologyResearchGroup,FacultyofScience,KingAbdulaziz
University,Jeddah,SaudiArabia
MohammadA.Khiyami
KingAbdulazizCityforScienceandTechnology,Riyadh,11442,SaudiArabia
ClaudeLemieux
Universit(cid:1)eLaval,Qu(cid:1)ebec,QC,Canada
De-ZhuLi
GermplasmBankofWildSpecies,KunmingInstituteofBotany,ChineseAcademyof
Sciences,Kunming,PRChina
ix