Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species.
Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species.
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DOI：
10.1186/1471-2229-8-70
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发表时间：
2008-06-23
影响因子：
5.3
通讯作者：
Takata K
中科院分区：
文献类型：
--
作者：
Hirao T;Watanabe A;Kurita M;Kondo T;Takata K
最近确定的完整叶绿体（cp）基因组序列的各种植物物种，使许多比较分析以及植物和基因组进化研究的进展。在被子植物中，大约70个物种的完整cp基因组序列已经确定，而只有三个裸子植物物种，苏铁台东，黑松，红松已经建立。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严重阻碍植物和cp基因组进化研究的进一步进展。为了解决这一问题，我们在这里报告的完整核苷酸序列的CP基因组的柳杉，第一个在柏科广义裸子植物，并提供了一个比较分析的基因内容和基因组结构，说明了独特的基因组特征的裸子植物。梭粳稻cp基因组全长131，810 bp，包含112个单拷贝基因和2个双拷贝基因（trnI-CAU，trnQ-UUG），共116个基因。与其它陆生植物cp基因组相比，C. japonica cp已经丢失了在被子植物、蕨类植物、苔类植物和裸子植物如苏铁和银杏中发现的一个相关的大反向重复序列（IR），另外已经完全丢失了其trnR-CCG，部分丢失了其trnT-GGU，并显示出accD的多样化。对C.粳稻cp基因组也与其它植物物种的cp基因组显著不同。例如，我们估计至少需要15个倒位才能将黑松基因组的基因结构转化为C。日本。在C.在粳稻cp基因组中，在倒位和易位末端观察到了正向重复和反向重复序列，这些序列可能与基因组重排有关。C.日本和其他陆地植物，包括松树，强烈支持大IR稳定cp基因组的理论。此外，C. japonica cp基因组的研究为裸子植物中针叶植物的进化谱系和cp基因组的进化提供了新的视角。
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.
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DOI：
10.1007/bf02464880
发表时间：
1989-06-01
期刊：
MOLECULAR AND GENERAL GENETICS
影响因子：
--
作者：
HIRATSUKA, J;SHIMADA, H;SUGIURA, M
通讯作者：
SUGIURA, M
影响因子：
3.4
作者：
Cai Z;Penaflor C;Kuehl JV;Leebens-Mack J;Carlson JE;dePamphilis CW;Boore JL;Jansen RK
通讯作者：
Jansen RK
影响因子：
5.3
作者：
Bausher MG;Singh ND;Lee SB;Jansen RK;Daniell H
通讯作者：
Daniell H
影响因子：
10.7
作者：
Chaw, SM;Zharkikh, A;Li, WH
通讯作者：
Li, WH
影响因子：
5.1
作者：
CLARKE, AK;GUSTAFSSON, P;LIDHOLM, JA
通讯作者：
LIDHOLM, JA