Cahoon A Bruce, Sharpe Richard M, Mysayphonh Chansamone, Thompson Elizabeth J, Ward Andrea D, Lin Anhua
Department of Biology, Middle Tennessee State University, Box 60, Murfreesboro, Tennessee 37132 USA.
Am J Bot. 2010 Jan;97(1):49-58. doi: 10.3732/ajb.0900008. Epub 2009 Dec 18.
In this paper, we describe the complete chloroplast genome of Lolium arundinaceum. This sequence is the culmination of a long-term project completed by >400 undergraduates who took general genetics at Middle Tennessee State University from 2004-2007. It was undertaken in an attempt to introduce these students to an open-ended experiential/exploratory lesson to produce and analyze novel data. The data they produced should provide the necessary information for both phylogenetic comparisons and plastome engineering of tall fescue. The fescue plastome (GenBank FJ466687) is 136048 bp with a typical quadripartite structure and a gene order similar to other grasses; 56% of the plastome is coding region comprised of 75 protein-coding genes, 29 tRNAs, four rRNAs, and one hypothetical coding region (ycf). Comparisons of Poaceae plastomes reveal size differences between the PACC (subfamilies Panicoideae, Arundinoideae, Centothecoideae, and Chloridoideae) and BOP (subfamilies Bambusoideae, Oryzoideae, and Pooideae) clades. Alignment analysis suggests that several potentially conserved large deletions in previously identified intergenic length polymorphic regions are responsible for the majority of the size discrepancy. Phylogenetic analysis using whole plastome data suggests that fescue closely aligns with Lolium perenne. Some unique features as well as phylogenetic branch length calculations, however, suggest that a number of changes have occurred since these species diverged.
在本文中，我们描述了黑麦草的完整叶绿体基因组。该序列是一个长期项目的成果，该项目由400多名于2004年至2007年在中田纳西州立大学修读普通遗传学的本科生完成。开展这个项目旨在让这些学生参与一门开放式的实践/探索性课程，以生成和分析新数据。他们生成的数据应为高羊茅的系统发育比较和质体基因组工程提供必要信息。高羊茅质体基因组（GenBank登录号FJ466687）为136048 bp，具有典型的四分体结构，基因顺序与其他禾本科植物相似；质体基因组的56%为编码区，由75个蛋白质编码基因、29个tRNA、4个rRNA和1个假定编码区（ycf）组成。禾本科质体基因组的比较揭示了黍亚科（Panicoideae）、芦竹亚科（Arundinoideae）、百簕草亚科（Centothecoideae）和虎尾草亚科（Chloridoideae）组成的PACC分支与竹亚科（Bambusoideae）、稻亚科（Oryzoideae）和早熟禾亚科（Pooideae）组成的BOP分支之间的大小差异。比对分析表明，先前确定的基因间长度多态性区域中几个潜在保守的大缺失是造成大部分大小差异的原因。使用全质体基因组数据进行的系统发育分析表明，高羊茅与多年生黑麦草密切相关。然而，一些独特特征以及系统发育分支长度计算表明，自这些物种分化以来已经发生了许多变化。
