Complete chloroplast genome of Macadamia integrifolia confirms the position of the Gondwanan early-diverging eudicot family Proteaceae.
Complete chloroplast genome of Macadamia integrifolia confirms the position of the Gondwanan early-diverging eudicot family Proteaceae.
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DOI：
10.1186/1471-2164-15-s9-s13
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发表时间：
2014
期刊：
影响因子：
4.4
通讯作者：
King GJ
中科院分区：
文献类型：
--
作者：
Nock CJ;Baten A;King GJ
叶绿体基因组的序列数据在阐明开花植物被子植物的进化史中发挥了核心作用。在过去的十年中，完整叶绿体基因组的数量迅速增加，导致被子植物系统发育得到很好的支持。然而，一些关系，特别是早期分化谱系之间的关系，仍然没有解决。多样的南半球植物变形科在被子植物历史的早期出现在古超大陆冈瓦纳，是适应气候条件变化的适应辐射的模式群。该家族的基因组资源有限，到目前为止，它是为数不多的早期分化的“基础edidiot”谱系之一，没有在叶绿体系统基因组学分析中表现出来。利用Illumina配对末端序列重新组装了澳大利亚坚果作物澳洲坚果（Macadamia integrifolia）叶绿体基因组。三个contigs，对应于一个塌陷的倒置重复序列，一个大的和一个小的单拷贝区域，并用于基因组重建。全基因组长度为159,714bp，在深度覆盖下组装（329万reads； ~2000 x）。基于83个基因和反向重复区域比对的系统发育分析，为包括基础eudicot家族Proteaceae的最大序列丰富的数据集提供了强有力的支持，包括Macadamia， Platanus和Nelumbo的Proteales分支。基因组结构和内容遵循祖先被子植物的模式，在Proteales中高度保守，而大小差异在很大程度上是由单拷贝区域的相对收缩和反向重复序列的扩张来解释的。澳洲坚果叶绿体基因组是Proteaceae中的第一个基因组，并证实了该科与Plantanaceae（梧桐树科）和Nelumbonaceae（神莲科）在形态上存在差异的基础上的位置。它为未来的进化研究提供了一个高质量的参考基因组，并将有利于类群丰富的系统基因组分析，旨在解决早期分化被子植物之间的关系，以及更广泛地跨越植物生命树。
Sequence data from the chloroplast genome have played a central role in elucidating the evolutionary history of flowering plants, Angiospermae. In the past decade, the number of complete chloroplast genomes has burgeoned, leading to well-supported angiosperm phylogenies. However, some relationships, particulary among early-diverging lineages, remain unresolved. The diverse Southern Hemisphere plant family Proteaceae arose on the ancient supercontinent Gondwana early in angiosperm history and is a model group for adaptive radiation in response to changing climatic conditions. Genomic resources for the family are limited, and until now it is one of the few early-diverging 'basal eudicot' lineages not represented in chloroplast phylogenomic analyses. The chloroplast genome of the Australian nut crop tree Macadamia integrifolia was assembled de novo from Illumina paired-end sequence reads. Three contigs, corresponding to a collapsed inverted repeat, a large and a small single copy region were identified, and used for genome reconstruction. The complete genome is 159,714bp in length and was assembled at deep coverage (3.29 million reads; ~2000 x). Phylogenetic analyses based on 83-gene and inverted repeat region alignments, the largest sequence-rich datasets to include the basal eudicot family Proteaceae, provide strong support for a Proteales clade that includes Macadamia, Platanus and Nelumbo. Genome structure and content followed the ancestral angiosperm pattern and were highly conserved in the Proteales, whilst size differences were largely explained by the relative contraction of the single copy regions and expansion of the inverted repeats in Macadamia. The Macadamia chloroplast genome presented here is the first in the Proteaceae, and confirms the placement of this family with the morphologically divergent Plantanaceae (plane tree family) and Nelumbonaceae (sacred lotus family) in the basal eudicot order Proteales. It provides a high-quality reference genome for future evolutionary studies and will be of benefit for taxon-rich phylogenomic analyses aimed at resolving relationships among early-diverging angiosperms, and more broadly across the plant tree of life.