The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms.
The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms.
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DOI：
10.1186/1471-2229-6-21
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发表时间：
2006-09-30
影响因子：
5.3
通讯作者：
Daniell H
中科院分区：
文献类型：
--
作者：
Bausher MG;Singh ND;Lee SB;Jansen RK;Daniell H
柑橘是世界上最大的水果作物，其生产受到柑橘溃疡病的威胁。通过植物育种和核转基因方法来防治这种疾病没有取得重大进展。与核转化相比，叶绿体基因工程具有许多优势;它不仅增加转基因表达，而且促进转基因遏制，这是转基因树木发展的主要障碍之一。我们已经测序了柑橘叶绿体基因组，以促进这种作物的遗传改良，并评估被子植物主要谱系之间的系统发育关系。柑橘叶绿体基因组全长160，129 bp，包含133个基因（89个蛋白质编码基因，4个rRNA和30个tRNA）。基因组结构与推测的祖先被子植物叶绿体基因组非常相似。然而，在柑橘中，infA基因是不存在的。反向重复区已扩展为重复rps 19和rpl 22的前84个氨基酸。在IRb区域中的rpl 22基因具有导致9个终止密码子的无义突变。这通过使用IR/LSC边界侧翼的引物进行PCR扩增和测序来证实。重复序列分析鉴定出29个30 bp或更长的正向和反向重复序列，序列同一性≥ 90%。蛋白质编码序列与表达序列标签的比较揭示了6个推定的RNA编辑，其中5个导致petL、psbH、ycf 2和ndhA中的非同义修饰。利用最大简约法（MP）和最大似然法（ML）对30个类群的61个蛋白质编码基因进行系统发育分析，为单子叶植物、真双子叶植物、蔷薇科植物和被子植物等几个主要类群的单系性提供了有力的支持。MP树和ML树在三个方面不一致：Amborella和Nymphaeales的位置，木兰科Calycanthus属的关系，Eurosid I分支的单系性。MP和ML树的单系性的eurosids II和放置柑橘（无患子目）姐妹的一个分支，包括锦葵目/apricales提供了强有力的支持。这是第一个完整的叶绿体基因组序列的成员芸香科和无患子目。反向重复区的扩展，包括rps 19和rpl 22的一部分，并存在两个截断拷贝的rpl 22是不寻常的测序叶绿体基因组。柑橘叶绿体基因组全序列的获得为叶绿体基因工程提供了基因间区和内源调控序列的信息。系统发育分析解决了几个主要的被子植物分支之间的关系，并提供了强有力的支持eurosid II分支的单系性和Sapindales姐妹的apericales/Malvales的位置。
The production of Citrus, the largest fruit crop of international economic value, has recently been imperiled due to the introduction of the bacterial disease Citrus canker. No significant improvements have been made to combat this disease by plant breeding and nuclear transgenic approaches. Chloroplast genetic engineering has a number of advantages over nuclear transformation; it not only increases transgene expression but also facilitates transgene containment, which is one of the major impediments for development of transgenic trees. We have sequenced the Citrus chloroplast genome to facilitate genetic improvement of this crop and to assess phylogenetic relationships among major lineages of angiosperms. The complete chloroplast genome sequence of Citrus sinensis is 160,129 bp in length, and contains 133 genes (89 protein-coding, 4 rRNAs and 30 distinct tRNAs). Genome organization is very similar to the inferred ancestral angiosperm chloroplast genome. However, in Citrus the infA gene is absent. The inverted repeat region has expanded to duplicate rps19 and the first 84 amino acids of rpl22. The rpl22 gene in the IRb region has a nonsense mutation resulting in 9 stop codons. This was confirmed by PCR amplification and sequencing using primers that flank the IR/LSC boundaries. Repeat analysis identified 29 direct and inverted repeats 30 bp or longer with a sequence identity ≥ 90%. Comparison of protein-coding sequences with expressed sequence tags revealed six putative RNA edits, five of which resulted in non-synonymous modifications in petL, psbH, ycf2 and ndhA. Phylogenetic analyses using maximum parsimony (MP) and maximum likelihood (ML) methods of a dataset composed of 61 protein-coding genes for 30 taxa provide strong support for the monophyly of several major clades of angiosperms, including monocots, eudicots, rosids and asterids. The MP and ML trees are incongruent in three areas: the position of Amborella and Nymphaeales, relationship of the magnoliid genus Calycanthus, and the monophyly of the eurosid I clade. Both MP and ML trees provide strong support for the monophyly of eurosids II and for the placement of Citrus (Sapindales) sister to a clade including the Malvales/Brassicales. This is the first complete chloroplast genome sequence for a member of the Rutaceae and Sapindales. Expansion of the inverted repeat region to include rps19 and part of rpl22 and presence of two truncated copies of rpl22 is unusual among sequenced chloroplast genomes. Availability of a complete Citrus chloroplast genome sequence provides valuable information on intergenic spacer regions and endogenous regulatory sequences for chloroplast genetic engineering. Phylogenetic analyses resolve relationships among several major clades of angiosperms and provide strong support for the monophyly of the eurosid II clade and the position of the Sapindales sister to the Brassicales/Malvales.
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影响因子：
5.6
作者：
Daniell, H;Lee, SB;Panchal, T;Wiebe, PO
通讯作者：
Wiebe, PO
影响因子：
3
作者：
Graham, SW;Olmstead, RG
通讯作者：
Olmstead, RG
影响因子：
10.7
作者：
Goremykin, VV;Holland, B;Hellwig, FH
通讯作者：
Hellwig, FH
影响因子：
5.1
作者：
Dufourmantel, N;Pelissier, B;Tissot, G
通讯作者：
Tissot, G
影响因子：
46.9
作者：
De Cosa, B;Moar, W;Daniell, H
通讯作者：
Daniell, H