Phylogenetic relationships within the hyper-diverse genus Eugenia (Myrtaceae: Myrteae) based on target enrichment sequencing
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ABSTRACT:
PROVIDER: PRJEB49071 | ENA |
REPOSITORIES: ENA
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Project description:Phylogenomics of Eugenia
| PRJEB49982 | ENA
Project description:Eugenia is one of the most taxonomically challenging lineages of flowering plants, in which morphological delimitation has changed over the last few years resulting from recent phylogenetic study based on molecular data. Efforts, until now, have been limited to Sanger sequencing of mostly plastid markers. These phylogenetic studies indicate 11 clades formalized as infrageneric groups. However, relationships among these clades are poorly supported at key nodes and inconsistent between studies, particularly along the backbone and within Eugenia sect. Umbellatae encompasses ca. 700 species. To resolve and better understand systematic discordance, 54 Eugenia taxa were subjected to phylogenomic Hyb-Seq using 353 low-copy nuclear genes. Twenty species trees based on coding and non-coding loci of nuclear and plastid datasets were recovered using coalescent and concatenated approaches. Concordant and conflicting topologies were assessed by comparing tree landscapes, topology tests, and gene and site concordance factors. The topologies are similar except between nuclear and plastid datasets. The coalescent trees better accommodate disparity in the intron dataset, which contains more parsimony informative sites, while concatenated trees recover more conservative topologies, as they have narrower distribution in the tree landscape. This suggests that highly supported phylogenetic relationships determined in previous studies do not necessarily indicate overwhelming concordant signal. Congruence must be interpreted carefully especially in concatenated datasets. Despite this, the congruence between the multi-species coalescent (MSC) approach and concatenated tree topologies found here is notable. Our analysis does not support Eugenia subg. Pseudeugenia or sect. Pilothecium, as currently circumscribed, suggesting necessary taxonomic reassessment. Five clades are further discussed within Eugenia sect. Umbellatae progress toward its division into workable clades. While targeted sequencing provides a massive quantity of data that improves phylogenetic resolution in Eugenia, uncertainty still remains in Eugenia sect. Umbellatae. The general pattern of higher site coefficient factor (CF) than gene CF in the backbone of Eugenia suggests stochastic error from limited signal. Tree landscapes in combination with concordance factor scores, as implemented here, provide a comprehensive approach that incorporates several phylogenetic hypotheses. We believe the protocols employed here will be of use for future investigations on the evolutionary history of Myrtaceae.
| S-EPMC8855041 | biostudies-literature
Project description:miRNAs are small non-coding regulatory RNAs that play important functions in the regulation of gene expression at the post-transcriptional level by targeting mRNAs for degradation or by inhibiting protein translation. Eugenia uniflora is a plant native to tropical America with pharmacological and ecological importance without previous studies about its gene expression and regulation. To date, there is not miRNAs reported in species of Myrtaceae. A small RNA library was constructed to identify miRNAs in Eugenia uniflora. Solexa technology was used to perform high throughput sequencing of the library and the data obtained was analysed using bioinformatics tools. From 14,489,131 clean reads, we obtained 1,852,722 small RNAs representing 45 known miRNA families that have been identified in other plant species. Further analysis using contigs assembled from Illumina mRNA sequencing of leaves from the same individual allowed the prediction of secondary structures of 25 known and 17 novel miRNAs. Potential targets were predicted for the most abundant mature miRNAs in the identified pre-miRNAs based on sequence homology. This study provide the first large scale identification of miRNAs and their potential targets of a species from Myrtaceae without previous genomic sequence resources. Our study provides more information about the evolutionary conservation of the regulatory network of miRNAs in plants and highlights the miRNAs species-specific. mRNA profiles in 1 leaf library of Eugenia uniflora by deep sequencing (Illumina HiSeq2000)
2013-01-07 | E-GEOD-38210 | biostudies-arrayexpress
Project description:miRNAs are small non-coding regulatory RNAs that play important functions in the regulation of gene expression at the post-transcriptional level by targeting mRNAs for degradation or by inhibiting protein translation. Eugenia uniflora is a plant native to tropical America with pharmacological and ecological importance without previous studies about its gene expression and regulation. To date, there is not miRNAs reported in species of Myrtaceae. A small RNA library was constructed to identify miRNAs in Eugenia uniflora. Solexa technology was used to perform high throughput sequencing of the library and the data obtained was analysed using bioinformatics tools. From 14,489,131 clean reads, we obtained 1,852,722 small RNAs representing 45 known miRNA families that have been identified in other plant species. Further analysis using contigs assembled from Illumina mRNA sequencing of leaves from the same individual allowed the prediction of secondary structures of 25 known and 17 novel miRNAs. Potential targets were predicted for the most abundant mature miRNAs in the identified pre-miRNAs based on sequence homology. This study provide the first large scale identification of miRNAs and their potential targets of a species from Myrtaceae without previous genomic sequence resources. Our study provides more information about the evolutionary conservation of the regulatory network of miRNAs in plants and highlights the miRNAs species-specific. microRNA profiles in 1 leaf library of Eugenia uniflora by deep sequencing (Illumina HiSeq2000)
2013-01-07 | E-GEOD-38211 | biostudies-arrayexpress
Project description:miRNAs are small non-coding regulatory RNAs that play important functions in the regulation of gene expression at the post-transcriptional level by targeting mRNAs for degradation or by inhibiting protein translation. Eugenia uniflora is a plant native to tropical America with pharmacological and ecological importance without previous studies about its gene expression and regulation. To date, there is not miRNAs reported in species of Myrtaceae. A small RNA library was constructed to identify miRNAs in Eugenia uniflora. Solexa technology was used to perform high throughput sequencing of the library and the data obtained was analysed using bioinformatics tools. From 14,489,131 clean reads, we obtained 1,852,722 small RNAs representing 45 known miRNA families that have been identified in other plant species. Further analysis using contigs assembled from Illumina mRNA sequencing of leaves from the same individual allowed the prediction of secondary structures of 25 known and 17 novel miRNAs. Potential targets were predicted for the most abundant mature miRNAs in the identified pre-miRNAs based on sequence homology. This study provide the first large scale identification of miRNAs and their potential targets of a species from Myrtaceae without previous genomic sequence resources. Our study provides more information about the evolutionary conservation of the regulatory network of miRNAs in plants and highlights the miRNAs species-specific.
2013-01-07 | GSE38210 | GEO
Project description:miRNAs are small non-coding regulatory RNAs that play important functions in the regulation of gene expression at the post-transcriptional level by targeting mRNAs for degradation or by inhibiting protein translation. Eugenia uniflora is a plant native to tropical America with pharmacological and ecological importance without previous studies about its gene expression and regulation. To date, there is not miRNAs reported in species of Myrtaceae. A small RNA library was constructed to identify miRNAs in Eugenia uniflora. Solexa technology was used to perform high throughput sequencing of the library and the data obtained was analysed using bioinformatics tools. From 14,489,131 clean reads, we obtained 1,852,722 small RNAs representing 45 known miRNA families that have been identified in other plant species. Further analysis using contigs assembled from Illumina mRNA sequencing of leaves from the same individual allowed the prediction of secondary structures of 25 known and 17 novel miRNAs. Potential targets were predicted for the most abundant mature miRNAs in the identified pre-miRNAs based on sequence homology. This study provide the first large scale identification of miRNAs and their potential targets of a species from Myrtaceae without previous genomic sequence resources. Our study provides more information about the evolutionary conservation of the regulatory network of miRNAs in plants and highlights the miRNAs species-specific.
2013-01-07 | GSE38211 | GEO
Project description:Background and Aims:Comparative floral ontogeny represents a valuable tool to understand angiosperm evolution. Such an approach may elucidate subtle changes in development that discretely modify floral architecture and underlie reproductive lability in groups with superficial homogeneous morphology. This study presents a comparative survey of floral development in Eugenia (Myrtaceae), one of the largest genera of angiosperms, and shows how previously undocumented ontogenetic trends help to explain the evolution of its megadiversity in contrast to its apparent flower uniformity. Methods:Using scanning electron microscopy, selected steps of the floral ontogeny of a model species (Eugenia punicifolia) are described and compared with 20 further species representing all ten major clades in the Eugenia phylogenetic tree. Additional floral trait data are contrasted for correlation analysis and character reconstructions performed against the Myrtaceae phylogenetic tree. Key results:Eugenia flowers show similar organ arrangement patterns: radially symmetrical, (most commonly) tetramerous flowers with variable numbers of stamens and ovules. Despite a similar general organization, heterochrony is evident from size differences between tissues and structures at similar developmental stages. These differences underlie variable levels of investment in protection, subtle modifications to symmetry, herkogamic effects and independent androecium and gynoecium variation, producing a wide spectrum of floral display and contributing to fluctuations in fitness. During Eugenia's bud development, the hypanthium (as defined here) is completely covered by stamen primordia, unusual in other Myrtaceae. This is the likely plesiomorphic state for Myrteae and may have represented a key evolutionary novelty in the tribe. Conclusions:Floral evolution in Eugenia depends on heterochronic patterns rather than changes in complexity to promote flexibility in floral strategies. The successful early establishment of Myrteae, previously mainly linked to the key innovation of fleshy fruit, may also have benefitted from changes in flower structure.
| S-EPMC5786242 | biostudies-literature