Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids.
Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids.
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DOI：
10.1186/1471-2148-6-77
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发表时间：
2006-10-04
影响因子：
3.4
通讯作者：
Jansen RK
中科院分区：
文献类型：
--
作者：
Cai Z;Penaflor C;Kuehl JV;Leebens-Mack J;Carlson JE;dePamphilis CW;Boore JL;Jansen RK
木兰科植物有4目19科8,500种，是早期分叉被子植物中最大的分支之一。尽管最近的一些被子植物系统发育分析支持木兰科的单系性，并提出了各目之间的关系，但所研究的基因数量有限，导致仅有微弱的支持，这些问题仍然存在争议。此外，相当大的不一致导致了系统发育重建，支持木兰科和两个大的被子植物支系--单子叶植物和优生植物之间的三组不同的关系。我们测定了三个木兰科植物Drimys(Canellales)、鹅掌菇(Magnoliales)和胡椒属(Piper)的叶绿体基因组序列，并结合其他32个被子植物的叶绿体基因组分析了木兰科植物之间的系统发育关系和GC含量的变化规律。Drimys、Liriodendron和Piper叶绿体基因组的大小非常相似，分别为160、604、159、886bp和160,624bp。基因内容和序列与许多其他未经重排的被子植物叶绿体基因组几乎相同，包括另一个已发表的木兰状基因组--蜡梅。总体而言，GC含量在34-39%之间，编码区的GC含量显著高于非编码区。在蛋白质编码基因中，GC含量因密码子位置不同而不同，第1密码子>；第2密码子>；第3密码子；不同功能基团的GC含量也不同，其中光合作用基因所占比例最高，NADH基因所占比例最低。利用简约和似然方法进行的系统发育分析和61个蛋白质编码基因的序列为木兰科的单系性提供了强有力的支持，并确定了两个支持较强的类群，即Canellales/Piperales和Laurales/Magnoliales。据报道，单子叶植物和优子叶植物得到了强有力的支持，因为在单子叶植物和优子叶植物分裂之前，它们的姐妹支系中有木兰体的分叉。这些树木还为Amborella作为包括所有其他被子植物在内的一个支系的姐妹的地位提供了中等或强烈的支持。三个新的木兰体基因组序列的进化比较，结合其他已发表的被子植物基因组，证实了GC含量在基因组中的位置、密码子位置和功能群分布不均匀。此外，系统发育分析提供了迄今为止最有力的支持假设，即木兰科植物是包括单子叶植物和真双子叶植物的大型分支的姊妹植物。
The magnoliids with four orders, 19 families, and 8,500 species represent one of the largest clades of early diverging angiosperms. Although several recent angiosperm phylogenetic analyses supported the monophyly of magnoliids and suggested relationships among the orders, the limited number of genes examined resulted in only weak support, and these issues remain controversial. Furthermore, considerable incongruence resulted in phylogenetic reconstructions supporting three different sets of relationships among magnoliids and the two large angiosperm clades, monocots and eudicots. We sequenced the plastid genomes of three magnoliids, Drimys (Canellales), Liriodendron (Magnoliales), and Piper (Piperales), and used these data in combination with 32 other angiosperm plastid genomes to assess phylogenetic relationships among magnoliids and to examine patterns of variation of GC content. The Drimys, Liriodendron, and Piper plastid genomes are very similar in size at 160,604, 159,886 bp, and 160,624 bp, respectively. Gene content and order are nearly identical to many other unrearranged angiosperm plastid genomes, including Calycanthus, the other published magnoliid genome. Overall GC content ranges from 34–39%, and coding regions have a substantially higher GC content than non-coding regions. Among protein-coding genes, GC content varies by codon position with 1st codon > 2nd codon > 3rd codon, and it varies by functional group with photosynthetic genes having the highest percentage and NADH genes the lowest. Phylogenetic analyses using parsimony and likelihood methods and sequences of 61 protein-coding genes provided strong support for the monophyly of magnoliids and two strongly supported groups were identified, the Canellales/Piperales and the Laurales/Magnoliales. Strong support is reported for monocots and eudicots as sister clades with magnoliids diverging before the monocot-eudicot split. The trees also provided moderate or strong support for the position of Amborella as sister to a clade including all other angiosperms. Evolutionary comparisons of three new magnoliid plastid genome sequences, combined with other published angiosperm genomes, confirm that GC content is unevenly distributed across the genome by location, codon position, and functional group. Furthermore, phylogenetic analyses provide the strongest support so far for the hypothesis that the magnoliids are sister to a large clade that includes both monocots and eudicots.
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影响因子：
1.9
作者：
Goremykin, V;Hirsch-Ernst, KI;Hellwig, FH
通讯作者：
Hellwig, FH
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3
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通讯作者：
Hellwig, FH
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作者：
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Ito, M