A reappraisal of chloroplast genetic SNPs in phylogeny and barcoding of Pteris species (genus Pteris L.): Multispecies coalescence analysis, ancient hybridization, and deep coalescence

IF 1 Q4 GENETICS & HEREDITY

Gene Reports Pub Date : 2025-04-16 DOI:10.1016/j.genrep.2025.102224

Maedeh Alaeifar, Masoud Sheidai, Fahimeh Koohdar

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引用次数: 0

Abstract

The genus Pteris L. (Pteridaceae) is one of the largest fern genera, comprising about 200 to 250 species distributed globally. There is ongoing debate regarding species classification and phylogeny within Pteris, as phylogenetic studies have revealed incongruences between trees constructed from various genetic regions. To address this, we conducted a multispecies coalescence analysis of matK and rbcL sequences using publicly available data, aiming to identify genetic regions suitable for phylogenetic analysis and molecular barcoding of Pteris. We employed methods such as STAR-BEAST and contained gene coalescence analyses for phylogenetic reconstruction, as well as redundancy analysis (RDA) and latent factor mixed model analysis to pinpoint biologically significant SNPs.

Our study highlights phylogenetic relationships among Pteris species based on chloroplast DNA sequences, revealing discordance between matK and rbcL. Findings indicated deep coalescence and incomplete lineage sorting (ILS) within the genus. Both D-statistics and admixture analyses showed evidence of genetic admixture and introgression. Notably, matK sequences demonstrated higher success in species delineation than rbcL, with combined data enhancing taxonomic resolution and indicating the role of SNPs in adaptations to local environments. Additionally, species delineation analyses using the GMYC and ASAP methods revealed congruent results, with most species clustering closely, although a few exceptions were observed. The use of concatenated DNA sequences successfully delineated sections within Pteris, highlighting the taxonomic utility of these markers. Divergence time estimation from the concatenated sequences indicated a deep evolutionary history for P. tremula, with the majority of species diverging more recently within the past 1 to 15 million years, further supporting rapid speciation within the genus.

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重新评估叶绿体基因 SNPs 在紫檀属物种系统发育和条形码中的作用：多物种聚合分析、远古杂交和深度聚合

翼蕨属（Pteris L.）是世界上最大的蕨类植物属之一，约有200 ~ 250种，分布在世界各地。关于翼属植物的物种分类和系统发育存在持续的争论，因为系统发育研究揭示了不同遗传区域构建的树之间的不一致性。为了解决这个问题，我们利用公开的数据对Pteris的matK和rbcL序列进行了多物种聚结分析，旨在确定适合系统发育分析和分子条形码的遗传区域。我们采用STAR-BEAST和内含基因聚结分析等方法进行系统发育重建，以及冗余分析（RDA）和潜在因素混合模型分析来确定具有生物学意义的snp。我们的研究基于叶绿体DNA序列强调了翼类物种之间的系统发育关系，揭示了matK和rbcL之间的不一致。结果表明，属内存在深度聚并和不完全谱系分类（ILS）。d统计和外源分析均显示了遗传外源和遗传渐渗的证据。值得注意的是，与rbcL相比，matK序列在物种描述方面表现出更高的成功率，结合数据提高了分类分辨率，并表明snp在适应当地环境中的作用。此外，采用GMYC和ASAP方法进行的物种圈定分析结果一致，大多数物种聚类紧密，但也有少数例外。使用连接的DNA序列成功地描绘了翼龙内的部分，突出了这些标记的分类效用。从串联序列中估计的分化时间表明，震耳蕨具有较深的进化史，大多数物种在过去的100万至1500万年间分化较晚，进一步支持了该属内快速的物种形成。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Gene Reports Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

3.30

自引率

7.70%

发文量

246

审稿时长

49 days

期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.