Hirao Tomonori, Watanabe Atsushi, Kurita Manabu, Kondo Teiji, Takata Katsuhiko
Institute of Wood Technology, Akita Prefectural University, 11-1 Kaieisaka, Noshiro, Akita 016-0876, Japan.
BMC Plant Biol. 2008 Jun 23;8:70. doi: 10.1186/1471-2229-8-70.
The recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species, Cycas taitungensis, Pinus thunbergii, and Pinus koraiensis have been established. The lack of information regarding the gene content and genomic structure of gymnosperm cp genomes may severely hamper further progress of plant and cp genome evolutionary studies. To address this need, we report here the complete nucleotide sequence of the cp genome of Cryptomeria japonica, the first in the Cupressaceae sensu lato of gymnosperms, and provide a comparative analysis of their gene content and genomic structure that illustrates the unique genomic features of gymnosperms.
The C. japonica cp genome is 131,810 bp in length, with 112 single copy genes and two duplicated (trnI-CAU, trnQ-UUG) genes that give a total of 116 genes. Compared to other land plant cp genomes, the C. japonica cp has lost one of the relevant large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperms, such as Cycas and Gingko, and additionally has completely lost its trnR-CCG, partially lost its trnT-GGU, and shows diversification of accD. The genomic structure of the C. japonica cp genome also differs significantly from those of other plant species. For example, we estimate that a minimum of 15 inversions would be required to transform the gene organization of the Pinus thunbergii cp genome into that of C. japonica. In the C. japonica cp genome, direct repeat and inverted repeat sequences are observed at the inversion and translocation endpoints, and these sequences may be associated with the genomic rearrangements.
The observed differences in genomic structure between C. japonica and other land plants, including pines, strongly support the theory that the large IRs stabilize the cp genome. Furthermore, the deleted large IR and the numerous genomic rearrangements that have occurred in the C. japonica cp genome provide new insights into both the evolutionary lineage of coniferous species in gymnosperm and the evolution of the cp genome.
近期多种植物物种完整叶绿体（cp）基因组序列的测定，使得大量的比较分析以及植物和基因组进化研究取得了进展。在被子植物中，约70个物种的完整cp基因组序列已被测定，而裸子植物中仅有三种物种，即台东苏铁、黑松和红松的完整cp基因组序列已被确定。裸子植物cp基因组的基因内容和基因组结构信息的缺乏，可能会严重阻碍植物和cp基因组进化研究的进一步发展。为满足这一需求，我们在此报告日本柳杉cp基因组的完整核苷酸序列，这是裸子植物广义柏科中的首个序列，并对其基因内容和基因组结构进行了比较分析，以阐明裸子植物独特的基因组特征。
日本柳杉cp基因组长度为131,810 bp，有112个单拷贝基因和两个重复基因（trnI-CAU、trnQ-UUG），共计116个基因。与其他陆地植物cp基因组相比，日本柳杉cp基因组缺失了在被子植物（如苏铁和银杏）、蕨类植物、苔类植物和裸子植物中发现的一个相关的大反向重复序列（IR），此外还完全缺失了trnR-CCG，部分缺失了trnT-GGU，并显示出accD的多样化。日本柳杉cp基因组的基因组结构也与其他植物物种有显著差异。例如，我们估计至少需要15次倒位才能将黑松cp基因组的基因组织转变为日本柳杉的基因组织。在日本柳杉cp基因组中，在倒位和易位端点观察到直接重复和反向重复序列，这些序列可能与基因组重排有关。
观察到的日本柳杉与包括松树在内的其他陆地植物在基因组结构上的差异，有力地支持了大IR稳定cp基因组的理论。此外，日本柳杉cp基因组中缺失的大IR和发生的众多基因组重排，为裸子植物中针叶树种的进化谱系以及cp基因组的进化提供了新的见解。
