scholarly journals Evolution of Rosaceae Plastomes Highlights Unique Cerasus Diversification and Independent Origins of Fruiting Cherry

2021 ◽  
Vol 12 ◽  
Author(s):  
Jing Zhang ◽  
Yan Wang ◽  
Tao Chen ◽  
Qing Chen ◽  
Lei Wang ◽  
...  
Keyword(s):  
Single Copy ◽  
Genomic Variation ◽  
Molecular Dating ◽  
Divergent Evolution ◽  
Comparative Genomic ◽  
Evolutionary Patterns ◽  
Protein Coding ◽  
Longmenshan Fault ◽  
Plastid Protein ◽  
Phylogenomic Analyses

Rosaceae comprises numerous types of economically important fruits, ornamentals, and timber. The lack of plastome characteristics has blocked our understanding of the evolution of plastome and plastid genes of Rosaceae crops. Using comparative genomics and phylogenomics, we analyzed 121 Rosaceae plastomes of 54 taxa from 13 genera, predominantly including Cerasus (true cherry) and its relatives. To our knowledge, we generated the first comprehensive map of genomic variation across Rosaceae plastomes. Contraction/expansion of inverted repeat regions and sequence losses of the two single-copy regions underlie large genomic variations in size among Rosaceae plastomes. Plastid protein-coding genes were characterized with a high proportion (over 50%) of synonymous variants and insertion-deletions with multiple triplets. Five photosynthesis-related genes were specially selected in perennial woody trees. Comparative genomic analyses implied divergent evolutionary patterns between pomaceous and drupaceous trees. Across all examined plastomes, unique and divergent evolution was detected in Cerasus plastomes. Phylogenomic analyses and molecular dating highlighted the relatively distant phylogenetic relationship between Cerasus and relatives (Microcerasus, Amygdalus, Prunus, and Armeniaca), which strongly supported treating the monophyletic true cherry group as a separate genus excluding dwarf cherry. High genetic differentiation and distinct phylogenetic relationships implied independent origins and domestication between fruiting cherries, particularly between Prunus pseudocerasus (Cerasus pseudocerasus) and P. avium (C. avium). Well-resolved maternal phylogeny suggested that cultivated P. pseudocerasus originated from Longmenshan Fault zone, the eastern edge of Himalaya-Hengduan Mountains, where it was subjected to frequent genomic introgression between its presumed wild ancestors and relatives.

scholarly journals Phylogenomics and the evolution of hemipteroid insects

2018 ◽  
Vol 115 (50) ◽  
pp. 12775-12780 ◽  
Author(s):  
Kevin P. Johnson ◽  
Christopher H. Dietrich ◽  
Frank Friedrich ◽  
Rolf G. Beutel ◽  
Benjamin Wipfler ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Single Copy ◽  
Molecular Dating ◽  
Protein Coding ◽  
Fossil Calibration ◽  
Large Scale Analysis ◽  
Phylogenetic Framework ◽  
Phylogenomic Analyses

Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid orders (Psocodea, Thysanoptera, and Hemiptera) is strongly supported, as are most relationships among suborders and families. Thysanoptera (thrips) is strongly supported as sister to Hemiptera. However, as in a recent large-scale analysis sampling all insect orders, trees from our data matrices support Psocodea (bark lice and parasitic lice) as the sister group to the holometabolous insects (those with complete metamorphosis). In contrast, four-cluster likelihood mapping of these data does not support this result. A molecular dating analysis using 23 fossil calibration points suggests hemipteroid insects began diversifying before the Carboniferous, over 365 million years ago. We also explore implications for understanding the timing of diversification, the evolution of morphological traits, and the evolution of mitochondrial genome organization. These results provide a phylogenetic framework for future studies of the group.

scholarly journals Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses

2016 ◽  
Author(s):  
Mei Fang Lin ◽  
Wen Hwa Chou ◽  
Marcelo V Kitahara ◽  
Chao Lun Allen Chen ◽  
David John Miller ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Single Copy ◽  
Scleractinian Corals ◽  
Amino Acid Sequences ◽  
Compositional Bias ◽  
Nuclear Markers ◽  
Protein Coding ◽  
Mitochondrial Sequences ◽  
Phylogenomic Analyses ◽  
Close Relatives

Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.

scholarly journals Complete Plastome of Three Korean Asarum (Aristolochiaceae): Confirmation Tripartite Structure within Korean Asarum and Comparative Analyses

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2056
Author(s):  
Mi-Jeong Yoo ◽  
Dong-Pil Jin ◽  
Hyun-Oh Lee ◽  
Chae Eun Lim
Keyword(s):  
Ornamental Plants ◽  
Illumina Miseq ◽  
Single Copy ◽  
Data Set ◽  
Protein Coding ◽  
Morphological Variations ◽  
Oxford Nanopore ◽  
Plastid Protein ◽  
Gene Data ◽  
Small Single Copy

The genus Asarum (Aristolochiaceae) is a well-known resource of medicinal and ornamental plants. However, the taxonomy of Korean Asarum is ambiguous due to their considerable morphological variations. Previously, a unique plastome structure has been reported from this genus. Therefore, we investigated the structural change in the plastomes within three Korean Asarum species and inferred their phylogenetic relationships. The plastome sizes of Asarum species assembled here range from 190,168 to 193,356 bp, which are longer than a typical plastome size (160 kb). This is due to the incorporation and duplication of the small single copy into the inverted repeat, which resulted in a unique tripartite structure. We first verified this unique structure using the Illumina Miseq and Oxford Nanopore MinION platforms. We also investigated the phylogeny of 26 Aristolochiaceae species based on 79 plastid protein-coding genes, which supports the monophyly of Korean Asarum species. Although the 79 plastid protein-coding gene data set showed some limitations in supporting the previous classification, it exhibits its effectiveness in delineating some sections and species. Thus, it can serve as an effective tool for resolving species-level phylogeny in Aristolochiaceae. Last, we evaluated variable sites and simple sequence repeats in the plastome as potential molecular markers for species delimitation.

scholarly journals Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2463 ◽  
Author(s):  
Mei Fang Lin ◽  
Wen Hwa Chou ◽  
Marcelo V. Kitahara ◽  
Chao Lun Allen Chen ◽  
David John Miller ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Single Copy ◽  
Scleractinian Corals ◽  
Amino Acid Sequences ◽  
Compositional Bias ◽  
Nuclear Markers ◽  
Protein Coding ◽  
Mitochondrial Sequences ◽  
Phylogenomic Analyses ◽  
Close Relatives

Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.

scholarly journals PhyloFisher: A phylogenomic package for resolving eukaryotic relationships

PLoS Biology ◽  
2021 ◽  
Vol 19 (8) ◽  
pp. e3001365
Author(s):  
Alexander K. Tice ◽  
David Žihala ◽  
Tomáš Pánek ◽  
Robert E. Jones ◽  
Eric D. Salomaki ◽  
...  
Keyword(s):  
Single Copy ◽  
Protein Coding ◽  
Eukaryotic Diversity ◽  
Protein Coding Genes ◽  
Markov Cluster Algorithm ◽  
Pruning Algorithms ◽  
Phylogenomic Analyses ◽  
Diverse Groups ◽  
Tree Pruning ◽  
Markov Cluster

Phylogenomic analyses of hundreds of protein-coding genes aimed at resolving phylogenetic relationships is now a common practice. However, no software currently exists that includes tools for dataset construction and subsequent analysis with diverse validation strategies to assess robustness. Furthermore, there are no publicly available high-quality curated databases designed to assess deep (>100 million years) relationships in the tree of eukaryotes. To address these issues, we developed an easy-to-use software package, PhyloFisher (https://github.com/TheBrownLab/PhyloFisher), written in Python 3. PhyloFisher includes a manually curated database of 240 protein-coding genes from 304 eukaryotic taxa covering known eukaryotic diversity, a novel tool for ortholog selection, and utilities that will perform diverse analyses required by state-of-the-art phylogenomic investigations. Through phylogenetic reconstructions of the tree of eukaryotes and of the Saccharomycetaceae clade of budding yeasts, we demonstrate the utility of the PhyloFisher workflow and the provided starting database to address phylogenetic questions across a large range of evolutionary time points for diverse groups of organisms. We also demonstrate that undetected paralogy can remain in phylogenomic “single-copy orthogroup” datasets constructed using widely accepted methods such as all vs. all BLAST searches followed by Markov Cluster Algorithm (MCL) clustering and application of automated tree pruning algorithms. Finally, we show how the PhyloFisher workflow helps detect inadvertent paralog inclusions, allowing the user to make more informed decisions regarding orthology assignments, leading to a more accurate final dataset.

scholarly journals Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses

2016 ◽  
Author(s):  
Mei Fang Lin ◽  
Wen Hwa Chou ◽  
Marcelo V Kitahara ◽  
Chao Lun Allen Chen ◽  
David John Miller ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Single Copy ◽  
Scleractinian Corals ◽  
Amino Acid Sequences ◽  
Compositional Bias ◽  
Nuclear Markers ◽  
Protein Coding ◽  
Mitochondrial Sequences ◽  
Phylogenomic Analyses ◽  
Close Relatives

Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.

scholarly journals Whole genome sequences of 23 species from the Drosophila montium species group (Diptera: Drosophilidae): A resource for testing evolutionary hypotheses

2019 ◽  
Author(s):  
Michael J. Bronski ◽  
Ciera C. Martinez ◽  
Holli A. Weld ◽  
Michael B. Eisen
Keyword(s):  
Large Scale ◽  
Single Copy ◽  
Species Group ◽  
Comparative Genomic ◽  
Regulatory Sequences ◽  
Large Set ◽  
Long Distance ◽  
Protein Coding ◽  
Distance Information ◽  
Repeat Content

AbstractLarge groups of species with well-defined phylogenies are excellent systems for testing evolutionary hypotheses. In this paper, we describe the creation of a comparative genomic resource consisting of 23 genomes from the species-rich Drosophila montium species group, 22 of which are presented here for the first time. The montium group is uniquely positioned for comparative studies. Within the montium clade, evolutionary distances are such that large numbers of sequences can be accurately aligned while also recovering strong signals of divergence; and the distance between the montium group and D. melanogaster is short enough so that orthologous sequence can be readily identified. All genomes were assembled from a single, small-insert library using MaSuRCA, before going through an extensive post-assembly pipeline. Estimated genome sizes within the montium group range from 155 Mb to 223 Mb (mean=196 Mb). The absence of long-distance information during the assembly process resulted in fragmented assemblies, with the scaffold NG50s varying widely based on repeat content and sample heterozygosity (min=18 kb, max=390 kb, mean=74 kb). The total scaffold length for most assemblies is also shorter than the estimated genome size, typically by 5 - 15 %. However, subsequent analysis showed that our assemblies are highly complete. Despite large differences in contiguity, all assemblies contain at least 96 % of known single-copy Dipteran genes (BUSCOs, n=2,799). Similarly, by aligning our assemblies to the D. melanogaster genome and remapping coordinates for a large set of transcriptional enhancers (n=3,457), we showed that each montium assembly contains orthologs for at least 91 % of D. melanogaster enhancers. Importantly, the genic and enhancer contents of our assemblies are comparable to that of far more contiguous Drosophila assemblies. The alignment of our own D. serrata assembly to a previously published PacBio D. serrata assembly also showed that our longest scaffolds (up to 1 Mb) are free of large-scale misassemblies. Our genome assemblies are a valuable resource that can be used to further resolve the montium group phylogeny; study the evolution of protein-coding genes and cis-regulatory sequences; and determine the genetic basis of ecological and behavioral adaptations.

scholarly journals The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6320 ◽  
Author(s):  
Zhen Yang ◽  
Guixi Wang ◽  
Qinghua Ma ◽  
Wenxu Ma ◽  
Lisong Liang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Single Copy ◽  
Molecular Dating ◽  
Phylogenetic Position ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Genome Variation ◽  
Genome Data ◽  
Chloroplast Genomes

Background Previous phylogenetic conclusions on the family Betulaceae were based on either morphological characters or traditional single loci, which may indicate some limitations. The chloroplast genome contains rich polymorphism information, which is very suitable for phylogenetic studies. Thus, we sequenced the chloroplast genome sequences of three Betulaceae species and performed multiple analyses to investigate the genome variation, resolve the phylogenetic relationships, and clarify the divergence history. Methods Chloroplast genomes were sequenced using the high-throughput sequencing. A comparative genomic analysis was conducted to examine the global genome variation and screen the hotspots. Three chloroplast partitions were used to reconstruct the phylogenetic relationships using Maximum Likelihood and Bayesian Inference approaches. Then, molecular dating and biogeographic inferences were conducted based on the whole chloroplast genome data. Results Betulaceae chloroplast genomes consisted of a small single-copy region and a large single copy region, and two copies of inverted repeat regions. Nine hotspots can be used as potential DNA barcodes for species delimitation. Phylogenies strongly supported the division of Betulaceae into two subfamilies: Coryloideae and Betuloideae. The phylogenetic position of Ostryopsis davidiana was controversial among different datasets. The divergence time between subfamily Coryloideae and Betuloideae was about 70.49 Mya, and all six extant genera were inferred to have diverged fully by the middle Oligocene. Betulaceae ancestors were probably originated from the ancient Laurasia. Discussions This research elucidates the potential of chloroplast genome sequences in the application of developing molecular markers, studying evolutionary relationships and historical dynamic of Betulaceae.It also reveals the advantages of using chloroplast genome data to illuminate those phylogenies that have not been well solved yet by traditional approaches in other plants.

scholarly journals Complete Chloroplast Genome Sequence of Chinese Lacquer Tree (Toxicodendron vernicifluum, Anacardiaceae) and Its Phylogenetic Significance

2020 ◽  
Vol 2020 ◽  
pp. 1-13 ◽  
Author(s):  
Lu Wang ◽  
Na He ◽  
Yao Li ◽  
Yanming Fang ◽  
Feilong Zhang
Keyword(s):  
Phylogenetic Analyses ◽  
Single Copy ◽  
Evolutionary Patterns ◽  
Closely Related Species ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genome Sequence ◽  
Cp Genome ◽  
Rna Genes ◽  
Toxicodendron Vernicifluum

Chinese lacquer tree (Toxicodendron vernicifluum) is an important commercial arbor species widely cultivated in East Asia for producing highly durable lacquer. Here, we sequenced and analyzed the complete chloroplast (cp) genome of T. vernicifluum and reconstructed the phylogeny of Sapindales based on 52 cp genomes of six families. The plastome of T. vernicifluum is 159,571 bp in length, including a pair of inverted repeats (IRs) of 26,511 bp, separated by a large single-copy (LSC) region of 87,475 bp and a small single-copy (SSC) region of 19,074 bp. A total of 126 genes were identified, of which 81 are protein-coding genes, 37 are transfer RNA genes, and eight are ribosomal RNA genes. Forty-nine mononucleotide microsatellites, one dinucleotide microsatellite, two complex microsatellites, and 49 long repeats were determined. Structural differences such as inversion variation in LSC and gene loss in IR were detected across cp genomes of the six genera in Anacardiaceae. Phylogenetic analyses revealed that the genus Toxicodendron is closely related to Pistacia and Rhus. The phylogenetic relationships of the six families in Sapindales were well resolved. Overall, this study providing complete cp genome resources will be beneficial for determining potential molecular markers and evolutionary patterns of T. vernicifluum and its closely related species.

scholarly journals Phylogenomic Analyses of Hepatica Species and Comparative Analyses Within Tribe Anemoneae (Ranunculaceae)

2021 ◽  
Vol 12 ◽  
Author(s):  
Kyu Tae Park ◽  
SeonJoo Park
Keyword(s):  
Phylogenetic Analyses ◽  
Single Copy ◽  
Rrna Genes ◽  
Large Single Copy ◽  
Protein Coding ◽  
Comparative Analyses ◽  
Phylogenomic Analyses ◽  
Small Genus ◽  
Small Single Copy ◽  
Large Single Copy Region

Hepatica is a small genus of Ranunculaceae with medicinal and horticultural value. We characterized nine complete chloroplast (cp) genomes of Hepatica, which ranged from 159,549 to 161,081 bp in length and had a typical quadripartite structure with a large single-copy region (LSC; 80,270–81,249 bp), a small single-copy region (SSC; 17,029–17,838 bp), and two copies of inverted repeat (IR; 31,008–31,100 bp). The cp genomes of Hepatica possess 76 protein-coding genes (PCGs), 29 tRNAs, and four rRNA genes. Comparative analyses revealed a conserved ca. 5-kb IR expansion in Hepatica and other Anemoneae; moreover, multiple inversion events occurred in Hepatica and its relatives. Analyses of selection pressure (dN/dS) showed that most of the PCGs are highly conserved except for rpl20 and rpl22 in Hepatica falconeri, Hepatica americana, and Hepatica acutiloba. Two genes (rps16 and infA) were identified as pseudogenes in Hepatica. In contrast, rpl32 gene was completely lost. The phylogenetic analyses based on 76 PCGs resolved the phylogeny of Hepatica and its related genera. Non-monophyly of Anemone s.l. indicates that Hepatica should be reclassified as an independent genus. In addition, Hepatica nobilis var. japonica is not closely related to H. nobilis.

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