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A bioinformatic study on the evolution of bamboos and other graminoid poales.

机译:关于竹子和其他类粉虱的进化的生物信息学研究。

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摘要

For the past decade, next-generation sequencing (NGS) has been used to undertake genomics-scale projects in molecular biology. This method of sequencing involves randomly fragmenting a sample of nucleic acid and randomly generating millions of short reads. The large number of reads moves the assembly and other analyses to be performed by computer algorithms. As well as sequencing full chromosomes, full RNA extracts can be sequenced to determine levels of gene expression and exon boundaries.;In this study, NGS is used to examine the evolution of bamboos (Bambusoideae), which are a subfamily of grasses (Poaceae). Bamboos are divided into two main phenotypes: woody and herbaceous. Woody bamboos are characterized by lignified culms, bisexual florets and undergo gregarious monocarpy, while herbaceous bamboos have less lignified shoots, unisexual florets and flower annually.;The evolution of this subfamily was examined in a phylogenomic framework using full chloroplast genome (plastome) sequences. First, a set of methods for plastome assembly was developed using automatable scripts and accuracy-testing steps. These methods were then used to generate full plastomes from bamboos. Full plastomes were then analyzed phylogenomically under a maximum-likelihood and Bayesian framework. This analysis revealed paraphyly between the temperate woody and tropical woody clades. Previously established tribal and subtribal relationships were also confirmed.;Nuclear transcripts were assembled from four bamboo species by sequencing RNA from floral tissue using NGS. Two assembly methods were performed: a de novo assembly used only overlapping reads to produce transcripts and a reference-based assembly used a previously sequenced nuclear genome from a bamboo to place reads and assemble them into transcripts. After quality assessment, the reference-based produced about double the number of transcripts than then de novo assembly, but may be biased toward the number of nuclear genes found in the reference genome. Floral development transcripts were examined as gene trees. Several preliminary correlations to phenotype were determined using putative gene function. The nuclear transcripts were then used to perform a phylogenetic analysis. After 3,878 transcripts were determined to be single-copy, they were concatenated and analyzed under a maximum-likelihood framework. Each of the 3,878 transcripts were also analyzed individually. This analysis strongly supported a monophyletic relationship between the woody bamboos, which contrasted with the plastome analysis.;Finally, a plastome was generated for a near-grass Joinvillea ascendens (Joinvilleaceae). The plastome was generated using completely de novo methods and was found to have undergone two large-scale inversions. These inversions occurred after two other large-scale inversions in the Poaceae-Joinvilleaceae lineage, which had been previously documented using PCR amplification. The two previously documented inversions were verified by comparing grasses to a plastome with an ancestral gene arrangement. Several gene and intron losses were also verified in grasses.
机译:在过去的十年中,下一代测序(NGS)已用于开展分子生物学的基因组规模的项目。这种测序方法涉及随机裂解核酸样品并随机产生数百万个短读。大量的读取移动了装配和其他要由计算机算法执行的分析。除了对完整染色体进行测序外,还可以对完整RNA提取物进行测序,以确定基因表达水平和外显子边界。在本研究中,NGS用于检查竹子(禾本科)的进化(竹子)。 。竹子分为两种主要表型:木质和草本。木本竹的特征是木质化茎秆,双性恋小花和经历合掌的单掌状,而草本竹子的木质化芽少,单性小花和一年生花。首先,使用自动化脚本和准确性测试步骤开发了一套质体组装方法。然后将这些方法用于从竹子中产生完整的质体。然后在最大似然和贝叶斯框架下对完整的质体进行系统发育分析。该分析揭示了温带木质和热带木质进化枝之间的副生。还证实了以前建立的部落和部落之间的关系。使用NGS对来自花木组织的RNA进行测序,从四个竹种中组装了核转录本。进行了两种组装方法:从头组装仅使用重叠的读段来产生转录本,而基于参考的组装则使用先前从竹子中测序的核基因组来放置读段并将其组装成转录本。经过质量评估后,基于参考的基因产生的转录物数量约为从头组装的两倍,但可能会偏向于参考基因组中发现的核基因数量。将花发育记录作为基因树进行检查。使用推定的基因功能确定了一些与表型的初步相关性。然后将核转录本用于进行系统发育分析。在确定3,878个转录本为单拷贝后,将它们连接起来并在最大似然框架下进行分析。还分别分析了3,878个转录本中的每一个。该分析有力地支持了木质竹子之间的单亲关系,这与塑性组分析形成了鲜明的对比。使用完全从头方法生成质体组,发现它经历了两次大规模的反转。这些倒转发生在禾本科-Joinvilleaceae谱系中的另外两次大规模倒转之后,先前已使用PCR扩增对其进行了记录。通过将草与具有祖先基因排列的质体组进行比较,验证了两个先前记录的倒置。在草中也证实了几种基因和内含子的损失。

著录项

  • 作者

    Wysocki, William P.;

  • 作者单位

    Northern Illinois University.;

  • 授予单位 Northern Illinois University.;
  • 学科 Bioinformatics.;Evolution development.;Botany.
  • 学位 Ph.D.
  • 年度 2016
  • 页码 178 p.
  • 总页数 178
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

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