Haberle Rosemarie C, Fourcade H Matthew, Boore Jeffrey L, Jansen Robert K
Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA.
J Mol Evol. 2008 Apr;66(4):350-61. doi: 10.1007/s00239-008-9086-4. Epub 2008 Mar 11.
Chloroplast genome organization, gene order, and content are highly conserved among land plants. We sequenced the chloroplast genome of Trachelium caeruleum L. (Campanulaceae), a member of an angiosperm family known for highly rearranged genomes. The total genome size is 162,321 bp, with an inverted repeat (IR) of 27,273 bp, large single-copy (LSC) region of 100,114 bp, and small single-copy (SSC) region of 7,661 bp. The genome encodes 112 different genes, with 17 duplicated in the IR, a tRNA gene (trnI-cau) duplicated once in the LSC region, and a protein-coding gene (psbJ) with two duplicate copies, for a total of 132 putatively intact genes. ndhK may be a pseudogene with internal stop codons, and clpP, ycf1, and ycf2 are so highly diverged that they also may be pseudogenes. ycf15, rpl23, infA, and accD are truncated and likely nonfunctional. The most conspicuous feature of the Trachelium genome is the presence of 18 internally unrearranged blocks of genes inverted or relocated within the genome relative to the ancestral gene order of angiosperm chloroplast genomes. Recombination between repeats or tRNA genes has been suggested as a mechanism of chloroplast genome rearrangements. The Trachelium chloroplast genome shares with Pelargonium and Jasminum both a higher number of repeats and larger repeated sequences in comparison to eight other angiosperm chloroplast genomes, and these are concentrated near rearrangement endpoints. Genes for tRNAs occur at many but not all inversion endpoints, so some combination of repeats and tRNA genes may have mediated these rearrangements.
叶绿体基因组的组织、基因顺序和内容在陆地植物中高度保守。我们对天蓝刺头（桔梗科）的叶绿体基因组进行了测序，桔梗科是一个被子植物科，以基因组高度重排而闻名。其基因组总大小为162,321 bp，其中反向重复序列（IR）为27,273 bp，大单拷贝（LSC）区域为100,114 bp，小单拷贝（SSC）区域为7,661 bp。该基因组编码112种不同的基因，其中17种在IR中重复，一个tRNA基因（trnI-cau）在LSC区域重复一次，一个蛋白质编码基因（psbJ）有两个重复拷贝，总共132个可能完整的基因。ndhK可能是一个带有内部终止密码子的假基因，而clpP、ycf1和ycf2高度分化，它们也可能是假基因。ycf15、rpl23、infA和accD被截断，可能无功能。天蓝刺头基因组最显著的特征是存在18个内部未重排的基因块，相对于被子植物叶绿体基因组的祖先基因顺序，这些基因块在基因组内发生了倒置或重新定位。重复序列或tRNA基因之间的重组被认为是叶绿体基因组重排的一种机制。与其他八个被子植物叶绿体基因组相比，天蓝刺头叶绿体基因组与天竺葵和茉莉属植物都具有更多的重复序列和更大的重复序列，并且这些序列集中在重排端点附近。tRNA基因出现在许多但不是所有的倒置端点处，因此重复序列和tRNA基因的某种组合可能介导了这些重排。
