The Complete Chloroplast Genome of Tree Fern Cyathea delgadii and Its Comparison to Other Cyatheales.

IF 1.6 4区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochemical Genetics Pub Date : 2025-09-11 DOI:10.1007/s10528-025-11248-3

Geferson Fernando Metz, Tiego De la Vega Ferreira, Rafael De la Vega Ferreira, Cristiane Barbosa D'Oliveira Matielo, Rafael Plá Matielo Lemos, Filipe de Carvalho Victoria

{"title":"The Complete Chloroplast Genome of Tree Fern Cyathea delgadii and Its Comparison to Other Cyatheales.","authors":"Geferson Fernando Metz, Tiego De la Vega Ferreira, Rafael De la Vega Ferreira, Cristiane Barbosa D'Oliveira Matielo, Rafael Plá Matielo Lemos, Filipe de Carvalho Victoria","doi":"10.1007/s10528-025-11248-3","DOIUrl":null,"url":null,"abstract":"<p><p>The chloroplast (cp) genome of the tree fern Cyathea delgadii Pohl ex Sternb. was assembled and annotated to investigate its structure and evolution within the Cyatheales order. The genome, sequenced using Oxford Nanopore Technologies, has a total size of 165,248 bp, comprising a large single-copy (LSC) region of 94,738 bp, a small single-copy (SSC) region of 22,012 bp, and two inverted repeat (IR) regions of 24,251 bp each. It contains 89 protein-coding genes, eight rRNAs, and 33 tRNAs. Comparative phylogenomic analyses involving 19 species of Cyatheales have revealed that the cp genome of C. delgadii shares similarities in gene content with other ferns of the Cyatheaceae family; however, it demonstrates variations in both genome size and GC content. Variations in cp genome size were observed across the Cyatheales species, ranging from 154,046 bp in Gymnosphaera denticulata (Baker) Copel to 168,244 bp in Dicksonia squarrosa (G.Forst) SW. Gene content analysis showed that most species have a conserved number of protein-coding genes, rRNAs, and tRNAs, suggesting structural stability. However, Cibotium spp. has a reduced number of protein-coding genes (87), possibly due to gene loss or transfer to the nuclear genome. Phylogenetic analyses using both whole genome and SNP data showed comparable clustering among Alsophila and Gymnosphaera species, while C. delgadii occupied a basal to intermediate position. The overall guanine-cytosine (GC) content of C. delgadii was calculated to be 40.95%, with a significantly higher content of 44.03% observed in the intragenic regions. An analysis of codon usage bias indicated a preference for codons ending with adenine or thymine, which aligns with the genome's adenine-thymine (AT) richness. This study provides valuable genomic resources and insights into the evolution of Cyatheales cp genomes, emphasizing both conserved features and specific adaptations within this group of ferns.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":1.6000,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Biochemical Genetics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s10528-025-11248-3","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

The chloroplast (cp) genome of the tree fern Cyathea delgadii Pohl ex Sternb. was assembled and annotated to investigate its structure and evolution within the Cyatheales order. The genome, sequenced using Oxford Nanopore Technologies, has a total size of 165,248 bp, comprising a large single-copy (LSC) region of 94,738 bp, a small single-copy (SSC) region of 22,012 bp, and two inverted repeat (IR) regions of 24,251 bp each. It contains 89 protein-coding genes, eight rRNAs, and 33 tRNAs. Comparative phylogenomic analyses involving 19 species of Cyatheales have revealed that the cp genome of C. delgadii shares similarities in gene content with other ferns of the Cyatheaceae family; however, it demonstrates variations in both genome size and GC content. Variations in cp genome size were observed across the Cyatheales species, ranging from 154,046 bp in Gymnosphaera denticulata (Baker) Copel to 168,244 bp in Dicksonia squarrosa (G.Forst) SW. Gene content analysis showed that most species have a conserved number of protein-coding genes, rRNAs, and tRNAs, suggesting structural stability. However, Cibotium spp. has a reduced number of protein-coding genes (87), possibly due to gene loss or transfer to the nuclear genome. Phylogenetic analyses using both whole genome and SNP data showed comparable clustering among Alsophila and Gymnosphaera species, while C. delgadii occupied a basal to intermediate position. The overall guanine-cytosine (GC) content of C. delgadii was calculated to be 40.95%, with a significantly higher content of 44.03% observed in the intragenic regions. An analysis of codon usage bias indicated a preference for codons ending with adenine or thymine, which aligns with the genome's adenine-thymine (AT) richness. This study provides valuable genomic resources and insights into the evolution of Cyatheales cp genomes, emphasizing both conserved features and specific adaptations within this group of ferns.

查看原文本刊更多论文

桫椤（Cyathea delgadii）叶绿体全基因组及其与其他桫椤属植物的比较。

树蕨Cyathea delgadii Pohl ex Sternb的叶绿体（cp）基因组。对其进行了组装和注释，以研究其在Cyatheales目中的结构和演变。使用牛津纳米孔技术测序的基因组总大小为165,248 bp，包括94,738 bp的大单拷贝（LSC）区域，22,012 bp的小单拷贝（SSC）区域和两个24,251 bp的反向重复（IR）区域。它包含89个蛋白质编码基因，8个rrna和33个trna。对19种Cyatheaceae蕨类植物的系统基因组分析表明，C. delgadii的cp基因组在基因含量上与其他Cyatheaceae蕨类植物具有相似性；然而，它显示了基因组大小和GC含量的变化。不同Cyatheales物种的cp基因组大小存在差异，从Gymnosphaera denticulata (Baker) Copel的154,046 bp到Dicksonia squarrosa (g.f ost) SW的168,244 bp不等。基因含量分析表明，大多数物种具有保守数量的蛋白质编码基因、rrna和trna，表明结构稳定。然而，Cibotium spp.的蛋白质编码基因数量减少（87），可能是由于基因丢失或转移到核基因组。利用全基因组和SNP数据进行的系统发育分析表明，Alsophila和Gymnosphaera物种之间的聚类具有可比性，而C. delgadii处于基础到中间位置。结果表明，该菌的总鸟嘌呤-胞嘧啶（GC）含量为40.95%，其中种内区GC含量最高，达44.03%。对密码子使用偏好的分析表明，密码子倾向于以腺嘌呤或胸腺嘧啶结尾，这与基因组的腺嘌呤胸腺嘧啶（AT）丰富度一致。这项研究为Cyatheales cp基因组的进化提供了宝贵的基因组资源和见解，强调了这类蕨类植物的保守特征和特定适应性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Biochemical Genetics 生物-生化与分子生物学

CiteScore

3.90

自引率

0.00%

发文量

133

审稿时长

4.8 months

期刊介绍： Biochemical Genetics welcomes original manuscripts that address and test clear scientific hypotheses, are directed to a broad scientific audience, and clearly contribute to the advancement of the field through the use of sound sampling or experimental design, reliable analytical methodologies and robust statistical analyses. Although studies focusing on particular regions and target organisms are welcome, it is not the journal’s goal to publish essentially descriptive studies that provide results with narrow applicability, or are based on very small samples or pseudoreplication. Rather, Biochemical Genetics welcomes review articles that go beyond summarizing previous publications and create added value through the systematic analysis and critique of the current state of knowledge or by conducting meta-analyses. Methodological articles are also within the scope of Biological Genetics, particularly when new laboratory techniques or computational approaches are fully described and thoroughly compared with the existing benchmark methods. Biochemical Genetics welcomes articles on the following topics: Genomics; Proteomics; Population genetics; Phylogenetics; Metagenomics; Microbial genetics; Genetics and evolution of wild and cultivated plants; Animal genetics and evolution; Human genetics and evolution; Genetic disorders; Genetic markers of diseases; Gene technology and therapy; Experimental and analytical methods; Statistical and computational methods.