Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes

Gonçalves, Deise Josely Pereira; Simpson, Beryl B.; Shimizu, Gustavo Hiroaki; Jansen, Robert K.

doi:10.1016/j.ympev.2019.05.022

Cited by 145 publications

(143 citation statements)

References 90 publications

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“…A possible explanation for the incongruence observed in dataset1 could be that Ruhfel et al [3] used only protein coding data of 78 genes from 360 taxa to build their phylogenetic tree. Gene conflicts in plastome-based phylogenies have recently been highlighted as a major cause of incongruence among studies [31,32], and differences in methodology between our study and the study by Ruhfel et al [3] could explain the observed incongruence. The analyses performed here were based on complete plastome data and include non-coding, fast evolving regions.…”

Section: Discussioncontrasting

confidence: 54%

Peer Review #3 of "ECuADOR—Easy Curation of Angiosperm Duplicated Organellar Regions, a tool for cleaning and curating plastomes assembled from next generation sequencing pipelines (v0.1)"

2020

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Background:With the rapid increase in availability of genomic resources offered by Next-Generation Sequencing (NGS) and the availability of free online genomic databases, efficient and standardised metadata curation approaches have become increasingly critical for the post-processing stages of biological data. Especially in organelle-based studies using circular chloroplast genome datasets, the assembly of the main structural regions in random order and orientation represents a major limitation in our ability to easily generate "ready-to-align" datasets for phylogenetic reconstruction, at both small and large taxonomic scales. In addition, current practices discard the most variable regions of the genomes to facilitate the alignment of the remaining coding regions. Nevertheless, no software is currently available to perform curation to such a degree, through simple detection, organization and positioning of the main plastome regions, making it a time-consuming and error-prone process. Here we introduce a fast and user friendly software ECuADOR, a Perl script specifically designed to automate the detection and reorganization of newly assembled plastomes obtained from any source available (NGS, sanger sequencing or assembler output). Methods:ECuADOR uses a sliding-window approach to detect long repeated sequences in draft sequences, which then identifies the inverted repeat regions (IRs), even in case of artifactual breaks or sequencing errors, and automates the rearrangement of the sequence to the widely used LSC-Irb-SSC-IRa order. This facilitates rapid post-editing steps such as creation of genome alignments, detection of variable regions, SNP detection and phylogenomic analyses. Results:ECuADOR was successfully tested on plant families throughout the angiosperm phylogeny by curating 161 chloroplast datasets. ECuADOR first identified and reordered the central regions (LSC-Irb-SSC-IRa) for each dataset and then produced a new annotation for the chloroplast sequences. The process took less than 20 minutes with a maximum memory requirement of 150 MB, and an accuracy of over 99 %. Abstract Background:With the rapid increase in availability of genomic resources offered by Next-Generation Sequencing (NGS) and the availability of free online genomic databases, efficient and standardised metadata curation approaches have become increasingly critical for the postprocessing stages of biological data. Especially in organelle-based studies using circular 49 50 51 52 53 54 55 56 57 PeerJ reviewing PDF |

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Section: Discussioncontrasting

confidence: 54%

Peer Review #3 of "ECuADOR—Easy Curation of Angiosperm Duplicated Organellar Regions, a tool for cleaning and curating plastomes assembled from next generation sequencing pipelines (v0.1)"

2020

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“…Because organellar genomic regions are typically analyzed in concatenation (i.e., treated as a single locus), we followed that approach here. However, recent studies have shown that plastid genomes are not free of gene‐tree conflict (e.g., Walker et al., ), suggesting that concatenation approaches may be inappropriate for plastomes, at least in some cases (Gonçalves et al., ). In light of this, multispecies coalescent (MSC) methods have been suggested as an alternative framework for plastome analyses (Gonçalves et al., ), but the appropriateness of this type of approach for plastid data, both theoretically and practically, has not been thoroughly considered.…”

Section: Methodsmentioning

confidence: 99%

Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages

Stull

Soltis

et al. 2020

American J of Botany

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Premise Discordance between nuclear and organellar phylogenies (cytonuclear discordance) is a well‐documented phenomenon at shallow evolutionary levels but has been poorly investigated at deep levels of plant phylogeny. Determining the extent of cytonuclear discordance across major plant lineages is essential not only for elucidating evolutionary processes, but also for evaluating the currently used framework of plant phylogeny, which is largely based on the plastid genome. Methods We present a phylogenomic examination of a major angiosperm clade (Asteridae) based on sequence data from the nuclear, plastid, and mitochondrial genomes as a means of evaluating currently accepted relationships inferred from the plastome and exploring potential sources of genomic conflict in this group. Results We recovered at least five instances of well‐supported cytonuclear discordance concerning the placements of major asterid lineages (i.e., Ericales, Oncothecaceae, Aquifoliales, Cassinopsis, and Icacinaceae). We attribute this conflict to a combination of incomplete lineage sorting and hybridization, the latter supported in part by previously inferred whole‐genome duplications. Conclusions Our results challenge several long‐standing hypotheses of asterid relationships and have implications for morphological character evolution and for the importance of ancient whole‐genome duplications in early asterid evolution. These findings also highlight the value of reevaluating broad‐scale angiosperm and green‐plant phylogeny with nuclear genomic data.

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“…Recent studies have explored gene tree conflicts in plastome-inferred phylogenies and incongruence between gene trees and species trees in plastid genes Gonçalves et al 2019). Gonçalves et al (2019) emphasized the importance of considering variation in phylogenetic signal across plastid genes and the exploration of plastome data to increase accuracy of estimating relationships; they also revealed that phylogenies inferred with multispecies coalescent (MSC) methods are accurate with plastome matrices and should be considered in future phylogenomic investigations. Walker et al (2019) highlighted that most genes are largely uninformative and are unlikely to misguide plant systematics.…”

Section: Phylogenetically Informative Regionsmentioning

confidence: 99%

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Köhler

Reginato

et al. 2020

Preprint

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Chloroplast genomes (plastomes) are frequently treated as highly conserved among land plants. However, many lineages of vascular plants have experienced extensive structural rearrangements, including inversions and modifications to the size and content of genes. Cacti are one of these lineages, containing the smallest plastome known for an obligately photosynthetic angiosperm, including the loss of one copy of the inverted repeat (~25 kb) and the ndh genes suite, but only a few cacti from the subfamily Cactoideae have been sufficiently characterized. Here, we investigated the variation of plastome sequences across the second-major lineage of the Cactaceae, the subfamily Opuntioideae, to address 1) how variable is the content and arrangement of chloroplast genome sequences across the subfamily, and 2) how phylogenetically informative are the plastome sequences for resolving major relationships among the clades of Opuntioideae. Our de novo assembly of the Opuntia quimilo plastome recovered an organelle of 150,347 bp in length with both copies of the inverted repeats and the presence of all the ndh genes suite. An expansion of the large single copy unit and a reduction of the small single copy was observed, including translocations and inversion of genes as well as the putative pseudogenization of numerous loci. Comparative analyses among all clades within Opuntioideae suggested that plastome structure and content vary across taxa of this subfamily, with putative independent losses of the ndh gene suite and pseudogenization of genes across disparate lineages, further demonstrating the dynamic nature of plastomes in Cactaceae. Our plastome dataset was robust in determining relationships among major clades and subclades within Opuntioideae, resolving three tribes with high support: Cylindropuntieae, Tephrocacteae and Opuntieae. A plastome-wide survey for highly informative phylogenetic markers revealed previously unused regions for future use in Sanger-based studies, presenting a valuable dataset with primers designed for continued evolutionary studies across Cactaceae. These results bring new insights into the evolution of plastomes in cacti, suggesting that further analyses should be carried out to address how ecological drivers, physiological constraints and morphological traits of cacti may be related with the common rearrangements in plastomes that have been reported across the family.

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Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes

Cited by 145 publications

References 90 publications

Peer Review #3 of "ECuADOR—Easy Curation of Angiosperm Duplicated Organellar Regions, a tool for cleaning and curating plastomes assembled from next generation sequencing pipelines (v0.1)"

Peer Review #3 of "ECuADOR—Easy Curation of Angiosperm Duplicated Organellar Regions, a tool for cleaning and curating plastomes assembled from next generation sequencing pipelines (v0.1)"

Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

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