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首页> 外文学位 >Using comparative plastomics to identify potentially informative non-coding regions for basal angiosperms, with a focus on Illicium (Schisandraceae).
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Using comparative plastomics to identify potentially informative non-coding regions for basal angiosperms, with a focus on Illicium (Schisandraceae).

机译：使用比较质体组学来识别基础被子植物的潜在信息丰富的非编码区，重点是八角茴香（Schisandraceae）。

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Chapter 2.;• Premise of study: Comparative plastomics provides a method for choosing the most informative tools for a given study group, often a difficult process due to limited available data for targeted taxa. Many of the most commonly used chloroplast DNA regions for phylogenetic analyses are not the regions predicted to be most variable by pairwise taxonomic comparisons across varying study groups, and therefore may not be the most useful regions available, demonstrating the need for testing the top potential informative regions. This research seeks to add to the groundwork of basal angiosperm phylogenetics by providing an understanding of the tools available in this important group of flowering plants.;• Methods: A comparative analysis was completed using the whole plastomes of five members of Illicium: I. oligandrum, I. henryi, I. cubense, I. floridanum, and I. ekmanii. An additional analysis was completed using representatives of the broader basal angiosperms: Amborella trichopoda, Nymphaea alba, Nymphaea mexicana, Nuphar advena, and Trithuria inconspicua . Perl scripts were written to expedite the comparative screening analysis. In each case, the objective was to identify the most potentially variable non-coding chloroplast DNA regions for phylogeny reconstruction and phylogeographic analyses.;• Key results: The most variable regions identified for Illicium were petN-psbM, rpl32-trnL, cemA-petA, petB intron, and psaC-ndhE. The most variable regions across the basal angiosperms were psbE-petL , rpoB-trnC, matK, trnE-trnT , and psbM-trnD. Four regions, ndhF-rpl32 , ndhC-trnV, rps16-trnQ, and trnT-psbD, were listed as top performers in a previous study, but were unable to be sequenced in Illicium and were excluded.;• Conclusions: The most variable regions differed between different taxonomic levels in the Illicium and basal angiosperm comparative analyses. The Illicium regions that did not amplify and were therefore excluded may be the most variable regions in Illicium, and warrant further testing. While a few regions stand out as variable in all analyses at lower taxonomic levels, there are clear differences in which regions will likely be phylogenetically informative at different taxonomic scales. Therefore, researchers who choose not to use next-generation sequencing methods should employ a screening process in the group of interest before beginning a phylogenetic analysis.;Chapter 3.;• Premise of study: As next-generation sequencing becomes more accessible to researchers, it becomes more important that researchers have the appropriate tools for a given study. Comparative plastomics have become a common tool for screening plastomes for potentially informative regions.;• Methods and results: The PIC Counter scripts were developed using Perl and are executable on the command line. The PIC Counter scripts count number of SNPs in a pairwise or multiple alignment, length of the alignment, and position and base pairs of SNPs. The script for the pairwise alignment also counts indels.;• Conclusions: The PIC Counter scripts make the plastome screening process easier and faster, and decrease the likelihood of human error in counts. The scripts are not interactive, require no additional downloaded software, minimal computational knowledge, and little computer RAM.
机译：第2章；研究前提：比较质体组学提供了一种方法，可以为给定的研究组选择最有用的工具，由于目标分类单元的可用数据有限，通常这是一个困难的过程。系统发育分析中，许多最常用的叶绿体DNA区域并不是通过成对分类学比较在不同研究组中预测的变化最大的区域，因此可能不是可用的最有用的区域，这表明需要测试潜在的最高信息量地区。这项研究旨在通过了解这一重要的开花植物中可用的工具，为基础被子植物的系统发育研究打下基础。;•方法：使用八角茴香的五种成员的完整质体进行了比较分析： ，I。henryi，I。cubense，I。floridanum和I. ekmanii。使用更广泛的基础被子植物的代表完成了另外的分析：伞形毛虫（Amborella trichopoda），白睡莲（Nymphaea alba），墨西哥睡莲（Nymphaea mexicana），Nuphar advena和Trithuria inconspicua。编写Perl脚本可以加快比较筛选分析的速度。在每种情况下，目的都是为了确定系统发育重建和系统地理分析中最具潜在可变性的非编码叶绿体DNA区域。•主要结果：Illicium鉴定出的最具可变性的区域是petN-psbM，rpl32-trnL，cemA-petA ，petB内含子和psaC-ndhE。整个被子植物中变化最大的区域是psbE-petL，rpoB-trnC，matK，trnE-trnT和psbM-trnD。在以前的研究中，ndhF-rpl32，ndhC-trnV，rps16-trnQ和trnT-psbD这四个区域被列为表现最佳的区域，但无法在Illicium中进行测序，因此被排除在外。；•结论：变化最大的区域在八角茴香和基础被子植物的比较分析中，不同的生物分类水平之间存在差异。未扩增并因此被排除的Illicium区域可能是Illicium中变化最大的区域，需要进一步测试。尽管在较低的生物分类学水平上，一些区域在所有分析中均表现出可变性，但在不同的生物分类学尺度上，哪些区域可能在系统发育信息上存在明显差异。因此，选择不使用下一代测序方法的研究人员应在开始系统发育分析之前在目标人群中采用筛选过程。;第3章；•研究前提：随着研究人员更容易使用下一代测序，研究人员为特定研究提供适当的工具变得越来越重要。比较质体组学已经成为筛查潜在信息区域的质体组的常用工具。；•方法和结果：PIC Counter脚本是使用Perl开发的，可以在命令行上执行。 PIC计数器脚本以成对或多重比对对SNP的数量，比对的长度以及SNP的位置和碱基对进行计数。成对比对的脚本也计入插入缺失。•结论：PIC Counter脚本使质子组筛选过程更加轻松，快捷，并减少了人为错误计数的可能性。脚本不是交互式的，不需要额外的下载软件，最少的计算知识和很少的计算机RAM。

著录项

  • 作者

    Leonard, Opal Rayne.;

  • 作者单位

    Middle Tennessee State University.;

  • 授予单位 Middle Tennessee State University.;
  • 学科 Biology.;Genetics.;Plant sciences.
  • 学位 M.S.
  • 年度 2015
  • 页码 81 p.
  • 总页数 81
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

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