Wolf Paul G, Karol Kenneth G, Mandoli Dina F, Kuehl Jennifer, Arumuganathan K, Ellis Mark W, Mishler Brent D, Kelch Dean G, Olmstead Richard G, Boore Jeffrey L
Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322-5305, USA.
Gene. 2005 May 9;350(2):117-28. doi: 10.1016/j.gene.2005.01.018. Epub 2005 Mar 19.
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.
我们运用了一系列独特的技术，对石松科植物亮叶石杉的首个完整叶绿体基因组进行了测序。该植物属于一个重要的进化枝，据推测它是所有其他维管植物的姐妹群。我们采用荧光激活细胞分选技术（FACS）分离细胞器，通过滚环扩增技术（RCA）扩增基因组，并进行鸟枪法测序以达到8倍深度覆盖，从而获得完整的叶绿体基因组序列。该基因组大小为154,373碱基对，包含两个长度均为15,314碱基对的反向重复序列、一个大小为104,088碱基对的大单拷贝区域以及一个大小为19,657碱基对的小单拷贝区域。其基因排列顺序与苔藓植物、地钱和角苔的更为相似，而与其他维管植物的不同。例如，亮叶石杉叶绿体基因组具有苔藓植物特有的、先前已被鉴定的30千碱基对倒位的基因排列顺序，这支持了石松类植物是所有其他现存维管植物姐妹群的假说。石松类植物的叶绿体基因组数据也有助于更好地重建基部维管植物基因组，这对于推断苔藓植物谱系之间的关系很有用。在亮叶石杉中观察到了几个独特的特征，比如基因ndhF从小单拷贝区域转移到了反向重复序列中。我们通过使用核苷酸数据、推断的氨基酸序列以及比较叶绿体基因组的基因排列，对陆地植物之间的进化关系进行了多项分析。尽管由于即将测序的其他关键谱系的大量叶绿体基因组，这些结果目前仍具有不确定性，但它们本身很有趣，并且为绿色植物中不断增长的基因组和形态数据比较数据库做出了贡献。
