The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae)
The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae)
复制标题
DOI：
10.1016/j.gene.2005.01.018
复制
发表时间：
2005-05-09
期刊：
影响因子：
3.5
通讯作者：
Boore, JL
中科院分区：
文献类型：
--
作者：
Wolf, PG;Karol, KG;Boore, JL
我们使用了一种独特的技术组合来测序石松，石杉的第一个完整的叶绿体基因组。本植物属于一个重要的分支，假设代表姐妹组的所有其他维管植物。我们使用荧光激活细胞分选（FACS）分离细胞器，使用滚环扩增（RCA）扩增基因组，并使用鸟枪测序至8x深度覆盖以获得完整的叶绿体基因组序列。基因组全长154，373 bp，包含15，314 bp的反向重复序列，104，088 bp的大单拷贝区和19，657 bp的小单拷贝区。与其他维管植物的基因顺序相比，苔藓、地钱和金鱼藻的基因顺序更相似。例如，石杉属叶绿体基因组具有先前表征的30 kb倒位的bratite基因顺序，从而支持石松植物与所有其他现存维管植物是姐妹的假设。石松植物叶绿体基因组数据也使基维管植物基因组的更好的重建，这是有用的推断brandites谱系之间的关系。在石杉属中观察到几个独特的特征，例如ndhF基因从小的单拷贝区域移动到反向重复区域。我们提出了几个陆地植物之间的进化关系的分析，通过使用核苷酸数据，推断的氨基酸序列，并通过比较叶绿体基因组的基因排列。这些结果，虽然仍然是暂时的，等待大量的叶绿体基因组从其他关键的谱系，很快被测序，是耐人寻味的本身，并有助于不断增长的比较数据库的基因组和形态数据的绿色植物。(c)2005 Elsevier B.V.保留所有权利。
We used a unique combination of techniques to sequence the first complete chloroplast genome of a lycophyte, Huperzia lucidula. This plant belongs to a significant clade hypothesized to represent the sister group to all other vascular plants. We used fluorescence-activated cell sorting (FACS) to isolate the organelles, rolling circle amplification (RCA) to amplify the genome, and shotgun sequencing to 8x depth coverage to obtain the complete chloroplast genome sequence. The genome is 154,373 bp, containing inverted repeats of 15,314 bp each, a large single-copy region of 104,088 bp, and a small single-copy region of 19,657 bp. Gene order is more similar to those of mosses, liverworts, and hornworts than to gene order for other vascular plants. For example, the Huperzia chloroplast genome possesses the bryophyte gene order for a previously characterized 30 kb inversion, thus supporting the hypothesis that lycophytes are sister to all other extant vascular plants. The lycophyte chloroplast genome data also enable a better reconstruction of the basal tracheophyte genome, which is useful for inferring relationships among bryophyte lineages. Several unique characters are observed in Huperzia, such as movement of the gene ndhF from the small single copy region into the inverted repeat. We present several analyses of evolutionary relationships among land plants by using nucleotide data, inferred amino acid sequences, and by comparing gene arrangements from chloroplast genomes. The results, while still tentative pending the large number of chloroplast genomes from other key lineages that are soon to be sequenced, are intriguing in themselves, and contribute to a growing comparative database of genomic and morphological data across the green plants. (c) 2005 Elsevier B.V. All rights reserved.