@article{SchwarteWegnerHavensteinetal.2015,
  author    = {Schwarte, Sandra and Wegner, Fanny and Havenstein, Katja and Groth, Detlef and Steup, Martin and Tiedemann, Ralph},
  title     = {Sequence variation, differential expression, and divergent evolution in starch-related genes among accessions of Arabidopsis thaliana},
  series = {Plant molecular biology : an international journal of fundamental research and genetic engineering},
  volume    = {87},
  journal   = {Plant molecular biology : an international journal of fundamental research and genetic engineering},
  number    = {4-5},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {0167-4412},
  doi       = {10.1007/s11103-015-0293-2},
  pages     = {489 -- 519},
  year      = {2015},
  abstract  = {Transitory starch metabolism is a nonlinear and highly regulated process. It originated very early in the evolution of chloroplast-containing cells and is largely based on a mosaic of genes derived from either the eukaryotic host cell or the prokaryotic endosymbiont. Initially located in the cytoplasm, starch metabolism was rewired into plastids in Chloroplastida. Relocation was accompanied by gene duplications that occurred in most starch-related gene families and resulted in subfunctionalization of the respective gene products. Starch-related isozymes were then evolutionary conserved by constraints such as internal starch structure, posttranslational protein import into plastids and interactions with other starch-related proteins. 25 starch-related genes in 26 accessions of Arabidopsis thaliana were sequenced to assess intraspecific diversity, phylogenetic relationships, and modes of selection. Furthermore, sequences derived from additional 80 accessions that are publicly available were analyzed. Diversity varies significantly among the starch-related genes. Starch synthases and phosphorylases exhibit highest nucleotide diversities, while pyrophosphatases and debranching enzymes are most conserved. The gene trees are most compatible with a scenario of extensive recombination, perhaps in a Pleistocene refugium. Most genes are under purifying selection, but disruptive selection was inferred for a few genes/substitutiones. To study transcript levels, leaves were harvested throughout the light period. By quantifying the transcript levels and by analyzing the sequence of the respective accessions, we were able to estimate whether transcript levels are mainly determined by genetic (i.e., accession dependent) or physiological (i.e., time dependent) parameters. We also identified polymorphic sites that putatively affect pattern or the level of transcripts.},
  language  = {en}
}
@article{SchwarteBrustSteupetal.2013,
  author    = {Schwarte, Sandra and Brust, Henrike and Steup, Martin and Tiedemann, Ralph},
  title     = {Intraspecific sequence variation and differential expression in starch synthase genes of Arabidopsis thaliana},
  doi       = {10.1186/1756-0500-6-84},
  year      = {2013},
  language  = {en}
}
@article{SchwarteTiedemann2011,
  author    = {Schwarte, Sandra and Tiedemann, Ralph},
  title     = {A Gene Duplication/Loss Event in the Ribulose-1,5-Bisphosphate-Carboxylase/Oxygenase (Rubisco) Small Subunit Gene Family among Accessions of Arabidopsis thaliana},
  series = {Molecular biology and evolution},
  volume    = {28},
  journal   = {Molecular biology and evolution},
  number    = {6},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0737-4038},
  doi       = {10.1093/molbev/msr008},
  pages     = {1861 -- 1876},
  year      = {2011},
  abstract  = {Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39), the most abundant protein in nature, catalyzes the assimilation of CO(2) (worldwide about 10(11) t each year) by carboxylation of ribulose-1,5-bisphosphate. It is a hexadecamer consisting of eight large and eight small subunits. Although the Rubisco large subunit (rbcL) is encoded by a single gene on the multicopy chloroplast genome, the Rubisco small subunits (rbcS) are encoded by a family of nuclear genes. In Arabidopsis thaliana, the rbcS gene family comprises four members, that is, rbcS-1a, rbcS-1b, rbcS-2b, and rbcS-3b. We sequenced all Rubisco genes in 26 worldwide distributed A. thaliana accessions. In three of these accessions, we detected a gene duplication/loss event, where rbcS-1b was lost and substituted by a duplicate of rbcS-2b (called rbcS-2b*). By screening 74 additional accessions using a specific polymerase chain reaction assay, we detected five additional accessions with this duplication/loss event. In summary, we found the gene duplication/loss in 8 of 100 A. thaliana accessions, namely, Bch, Bu, Bur, Cvi, Fei, Lm, Sha, and Sorbo. We sequenced an about 1-kb promoter region for all Rubisco genes as well. This analysis revealed that the gene duplication/loss event was associated with promoter alterations (two insertions of 450 and 850 bp, one deletion of 730 bp) in rbcS-2b and a promoter deletion (2.3 kb) in rbcS-2b* in all eight affected accessions. The substitution of rbcS-1b by a duplicate of rbcS-2b (i.e., rbcS-2b*) might be caused by gene conversion. All four Rubisco genes evolve under purifying selection, as expected for central genes of the highly conserved photosystem of green plants. We inferred a single positive selected site, a tyrosine to aspartic acid substitution at position 72 in rbcS-1b. Exactly the same substitution compromises carboxylase activity in the cyanobacterium Anacystis nidulans. In A. thaliana, this substitution is associated with an inferred recombination. Functional implications of the substitution remain to be evaluated.},
  language  = {en}
}
@phdthesis{Schwarte2010,
  author    = {Schwarte, Sandra},
  title     = {Genetic variation of photosynthesis and starch metabolism genes in Arabidopsis thaliana},
  address   = {Potsdam},
  year      = {2010},
  language  = {en}
}