The Chlamydomonas reinhardtii Plastid Chromosome: Islands of Genes in a Sea of Repeats
The Chlamydomonas reinhardtii Plastid Chromosome: Islands of Genes in a Sea of Repeats
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发表时间：
2002
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通讯作者：
J. Maul;J. W. Lilly;Liying Cui;C. dePamphilis;W. Miller;E. H. Harris;D. Stern
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作者：
J. Maul;J. W. Lilly;Liying Cui;C. dePamphilis;W. Miller;E. H. Harris;D. Stern
莱茵衣藻是一种单细胞真核植物，具有单一的叶绿体，被广泛用作光合作用过程研究的模型系统。本报告分析了完全测序的203，395 bp质体染色体的惊人结构和进化特征。基因组由21.2 kb反向重复序列分为两个80 kb的单拷贝区域，仅包含99个基因，包括完整的tRNA和编码RNA聚合酶的非典型基因。一个显着的特征是，20%的基因组是重复DNA：大多数基因间区域由许多类型的短分散重复序列（SDR）组成，这可能具有结构或进化意义。在其他已测序的绿藻质体基因组中，只有绿色小球藻的质体基因组似乎具有这一特征。用MultiPipMaker程序比较了衣原体与其他叶绿体基因组的基因互补序列，并扫描了基因组的序列相似性和重复DNA。在这些结果中，有证据表明SDR不是来自现存的编码序列，尽管一些SDR可能来自其他基因组片段。质体基因组含量的变化的系统发育重建显示，加速的基因丢失率也具有衣原体/小球藻谱系的特征，这种现象可能是独立的SDR的增殖。总之，我们的研究结果揭示了一个动态的和不寻常的质体基因组，其存在于模式生物中将允许其功能进行测试。
Chlamydomonas reinhardtii is a unicellular eukaryotic alga possessing a single chloroplast that is widely used as a model system for the study of photosynthetic processes. This report analyzes the surprising structural and evolutionary features of the completely sequenced 203,395-bp plastid chromosome. The genome is divided by 21.2-kb inverted repeats into two single-copy regions of (cid:2) 80 kb and contains only 99 genes, including a full complement of tRNAs and atypical genes encoding the RNA polymerase. A remarkable feature is that (cid:2) 20% of the genome is repetitive DNA: the majority of intergenic regions consist of numerous classes of short dispersed repeats (SDRs), which may have structural or evolutionary significance. Among other sequenced chlorophyte plastid genomes, only that of the green alga Chlorella vulgaris appears to share this feature. The program MultiPipMaker was used to compare the genic complement of Chlamydomonas with those of other chloroplast genomes and to scan the genomes for sequence similarities and repetitive DNAs. Among the results was evidence that the SDRs were not derived from extant coding sequences, although some SDRs may have arisen from other genomic fragments. Phylogenetic reconstruction of changes in plastid genome content revealed that an accelerated rate of gene loss also characterized the Chlamydomonas/Chlorella lineage, a phenomenon that might be independent of the proliferation of SDRs. Together, our results reveal a dynamic and unusual plastid genome whose existence in a model organism will allow its features to be tested functionally.