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九种毛茛科Ranunculeae 物种的完整质体基因组及其系统发育推断。

Complete Plastid Genomes of Nine Species of Ranunculeae (Ranunculaceae) and Their Phylogenetic Inferences.

机构信息

State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China.

College of Agriculture and Forestry, Longdong University, Qingyang 745000, China.

出版信息

Genes (Basel). 2023 Nov 27;14(12):2140. doi: 10.3390/genes14122140.

Abstract

The tribe Ranunculeae, Ranunculaceae, comprising 19 genera widely distributed all over the world. Although a large number of Sanger sequencing-based molecular phylogenetic studies have been published, very few studies have been performed on using genomic data to infer phylogenetic relationships within Ranunculeae. In this study, the complete plastid genomes of nine species (eleven samples) from , , and were de novo assembled using a next-generation sequencing method. Previously published plastomes of and other related genera of the family were downloaded from GenBank for comparative analysis. The complete plastome of each Ranunculeae species has 112 genes in total, including 78 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The plastome structure of Ranunculeae samples is conserved in gene order and arrangement. There are no inverted repeat (IR) region expansions and only one IR contraction was found in the tested samples. This study also compared plastome sequences across all the samples in gene collinearity, codon usage, RNA editing sites, nucleotide variability, simple sequence repeats, and positive selection sites. Phylogeny of the available Ranunculeae species was inferred by the plastome data using maximum-likelihood and Bayesian inference methods, and data partitioning strategies were tested. The phylogenetic relationships were better resolved compared to previous studies based on Sanger sequencing methods, showing the potential value of the plastome data in inferring the phylogeny of the tribe.

摘要

毛茛科 Ranunculeae 族,包含广泛分布于世界各地的 19 属。尽管已经发表了大量基于桑格测序的分子系统发育研究,但利用基因组数据推断 Ranunculeae 内系统发育关系的研究却很少。本研究采用新一代测序方法,从头组装了 、 、 等 9 个种(11 个样本)的完整质体基因组。从 GenBank 下载了 和其他相关科的已发表的质体基因组进行比较分析。每个 Ranunculeae 种的完整质体基因组共有 112 个基因,包括 78 个蛋白质编码基因、30 个转移 RNA 基因和 4 个核糖体 RNA 基因。 Ranunculeae 样本的质体基因组结构在基因顺序和排列上是保守的。在测试样本中没有发现反向重复(IR)区域的扩张,只有一个 IR 收缩。本研究还比较了所有样本的质体序列在基因共线性、密码子使用、RNA 编辑位点、核苷酸变异性、简单重复序列和正选择位点上的差异。利用最大似然法和贝叶斯推断法,根据质体数据推断了现有 Ranunculeae 种的系统发育,并测试了数据分区策略。与基于桑格测序方法的先前研究相比,系统发育关系得到了更好的解决,表明质体数据在推断该族的系统发育方面具有潜在价值。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f206/10742492/57379f22085d/genes-14-02140-g001.jpg

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