Yang, Xiaohan; Hu, Rongbin; Yin, Hengfu; Jenkins, Jerry; Shu, Shengqiang; Tang, Haibao; Liu, Degao; Weighill, Deborah A.; Cheol Yim, Won; Ha, Jungmin; Heyduk, Karolina; Goodstein, David M.; Guo, Hao-Bo; Moseley, Robert C.; Fitzek, Elisabeth; Jawdy, Sara; Zhang, Zhihao; Xie, Meng; Hartwell, James; Grimwood, Jane; Abraham, Paul E.; Mewalal, Ritesh; Beltrán, Juan D.; Boxall, Susanna F.; Dever, Louisa V.; Palla, Kaitlin J.; Albion, Rebecca; Garcia, Travis; Mayer, Jesse A.; Don Lim, Sung; Man Wai, Ching; Peluso, Paul; Van Buren, Robert; De Paoli, Henrique Cestari; Borland, Anne M.; Guo, Hong; Chen, Jin-Gui; Muchero, Wellington; Yin, Yanbin; Jacobson, Daniel A.; Tschaplinski, Timothy J.; Hettich, Robert L.; Ming, Ray; Winter, Klaus; Leebens-Mack, James H.; Smith, J. Andrew C.; Cushman, John C.; Schmutz, Jeremy; Tuskan, Gerald A.: The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism. In: Nature Communications. Jg.8 H. 1. 2017
Inhalt
- Results
- Kalanchoë genome assembly and annotation
- The phylogenetic placement of Kalanchoë
- Kalanchoë genome duplication
- Gene co-expression modules and clusters in Kalanchoë
- Overview of genes that have undergone convergent evolution
- Convergent evolution of genes involved in CO2 fixation
- Convergent evolution of genes involved in stomatal movement
- Convergent evolution of genes involved in heat tolerance
- Convergent evolution of genes in the circadian clock
- Convergent evolution of genes in carbohydrate metabolism
- Discussion
- Methods
- Plant material
- Estimation of DNA content
- Chromosome counting
- Illumina sequencing of genome
- Transcriptome sequencing
- Genome assembly and improvement
- Protein-coding gene annotation
- Construction of orthologous groups
- Construction of species phylogeny
- Construction of protein tribes and phylogenetic analysis
- Analysis of convergence in protein sequences in CAM species
- Gene Ontology analysis and pathway annotation
- Analysis of carbohydrate active enzymes
- Estimation of transcript abundance in Kalanchoë
- Co-expression network analysis in Kalanchoë
- Cluster analysis of gene expression in Kalanchoë
- Comparative analysis of gene expression
- Genome synteny analysis
- Protein 3D structural simulation
- Gas chromatography-mass spectrometry metabolite profiling
- In vitro protein expression and analysis of enzyme activity
- Data availability
- References
- Acknowledgements
- Author contributions
- ACKNOWLEDGEMENTS
- ACKNOWLEDGEMENTS
- Competing interests