An EPIC journey to locate single-copy nuclear markers in sea anemones

Order Acipenseriformes contains 27 extant species distributed across the northern hemisphere, including so-called “living fossil” species of garfish and sturgeons. Previous studies have focused on their mitochondrial genetics and have rarely used nuclear genetic data, leaving questions as to their phylogenetic relationships. This study aimed to utilize a bioinformatics approach to screen for candidate single-copy nuclear genes, using transcriptomic data from sturgeon species and genomic data from the spotted gar, Lepisosteus oculatus. We utilized nested polymerase chain reaction (PCR) and degenerate primers to identify nuclear protein-coding (NPC) gene markers to determine phylogenetic relationships among the Acipenseriformes. We identified 193 nuclear single-copy genes, selected from 1850 candidate genes with at least one exon larger than 700 bp. Forty-three of these genes were used for primer design and development of 30 NPC markers, which were sequenced for at least 14 Acipenseriformes species. Twenty-seven NPC markers were found completely in 16 species. Gene trees according to Bayesian inference (BI) and maximum likelihood (ML) were calculated based on the 30 NPC markers (20,946 bp total). Both gene and species trees produced very similar topologies. A molecular clock model estimated the divergence time between sturgeon and paddlefish at 204.1 Mya, approximately 10% later than previous estimates based on cytochrome b data (184.4 Mya). The successful development and application of NPC markers provides a new perspective and insight for the phylogenetic relationships of Acipenseriformes. Furthermore, the newly developed nuclear markers may be useful in further studies on the conservation, evolution, and genomic biology of this group.

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Phylogenetic Signal in Mitochondrial and Nuclear Markers in Sea Anemones (Cnidaria, Actiniaria)

Integrative and Comparative Biology ◽

10.1093/icb/icq081 ◽

2010 ◽

Vol 50 (3) ◽

pp. 371-388 ◽

Cited By ~ 27

Author(s):

M. Daly ◽

L. C. Gusmao ◽

A. J. Reft ◽

E. Rodriguez

Keyword(s):

Phylogenetic Signal ◽

Sea Anemones ◽

Nuclear Markers ◽

Mitochondrial And Nuclear Markers

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Transcriptome-Mining for Single-Copy Nuclear Markers in Ferns

PLoS ONE ◽

10.1371/journal.pone.0076957 ◽

2013 ◽

Vol 8 (10) ◽

pp. e76957 ◽

Cited By ~ 39

Author(s):

Carl J. Rothfels ◽

Anders Larsson ◽

Fay-Wei Li ◽

Erin M. Sigel ◽

Layne Huiet ◽

...

Keyword(s):

Single Copy ◽

Nuclear Markers

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

10.7287/peerj.preprints.2151 ◽

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.

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

PeerJ ◽

10.7717/peerj.2463 ◽

2016 ◽

Vol 4 ◽

pp. e2463 ◽

Cited By ~ 11

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.

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Multiple species of wild tree peonies gave rise to the ‘king of flowers’, Paeonia suffruticosa Andrews

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2014.1687 ◽

2014 ◽

Vol 281 (1797) ◽

pp. 20141687 ◽

Cited By ~ 32

Author(s):

Shi-Liang Zhou ◽

Xin-Hui Zou ◽

Zhi-Qin Zhou ◽

Jing Liu ◽

Chao Xu ◽

...

Keyword(s):

Wild Species ◽

Parental Species ◽

Phylogenetic Analyses ◽

Single Copy ◽

Rna Seq ◽

Nuclear Markers ◽

Homoploid Hybridization ◽

Wild Tree ◽

Traditional Cultivars ◽

Multiple Species

The origin of cultivated tree peonies, known as the ‘king of flowers' in China for more than 1000 years, has attracted considerable interest, but remained unsolved. Here, we conducted phylogenetic analyses of explicitly sampled traditional cultivars of tree peonies and all wild species from the shrubby section Moutan of the genus Paeonia based on sequences of 14 fast-evolved chloroplast regions and 25 presumably single-copy nuclear markers identified from RNA-seq data. The phylogeny of the wild species inferred from the nuclear markers was fully resolved and largely congruent with morphology and classification. The incongruence between the nuclear and chloroplast trees suggested that there had been gene flow between the wild species. The comparison of nuclear and chloroplast phylogenies including cultivars showed that the cultivated tree peonies originated from homoploid hybridization among five wild species. Since the origin, thousands of cultivated varieties have spread worldwide, whereas four parental species are currently endangered or on the verge of extinction. The documentation of extensive homoploid hybridization involved in tree peony domestication provides new insights into the mechanisms underlying the origins of garden ornamentals and the way of preserving natural genetic resources through domestication.

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

10.7287/peerj.preprints.2151v1 ◽

2016 ◽

Cited By ~ 1

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.

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Identification and characterization of anonymous nuclear markers for the double-striped cockroach, Blattella bisignata

Bulletin of Entomological Research ◽

10.1017/s0007485312000375 ◽

2012 ◽

Vol 103 (1) ◽

pp. 29-35 ◽

Cited By ~ 1

Author(s):

Q.-P. Ren ◽

Z. Fan ◽

X.-M. Zhou ◽

G.-F. Jiang ◽

Y.-T. Wang ◽

...

Keyword(s):

Southwest China ◽

Genomic Library ◽

Southern China ◽

Average Length ◽

Single Copy ◽

Small Scale ◽

Nuclear Markers ◽

Representative Species ◽

Identification And Characterization

AbstractDuring the last decade, multilocus analysis has gradually become a powerful tool for the studies of population genetics and phylogeography. The double-striped cockroach, Blattella bisignata, is endemic to southeast Asia, and there is currently little genetic information available for the species. We chose it as the target species to investigate a biodiversity hotspot in southwest China. Here, we report the identification and characterization of 11 single-copy anonymous nuclear markers with an average length of 378bp. These loci, isolated from a genomic library of B. bisignata, can amplify in two additional Blattella species (B. germanica and B. lituricollis). While testing these markers in representative species of Blattellidae, Blattidae and Epilampridae, some of them can cross-amplify successfully. After sequencing 30 individuals collected from southern China per locus, we found relatively high variability (approximately 3.6 SNPs per 100bp). Finally, a small-scale study was also performed to show that these markers do indeed fulfill the expectations as phylogeographic markers.

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Standardized nuclear markers advance metazoan taxonomy

10.1101/2021.05.07.443120 ◽

2021 ◽

Author(s):

Lars Dietz ◽

Jonas Eberle ◽

Christoph Mayer ◽

Sandra Kukowka ◽

Claudia Bohacz ◽

...

Keyword(s):

Animal Species ◽

Mitochondrial Gene ◽

Single Copy ◽

Dna Barcodes ◽

Science And Society ◽

Nuclear Markers ◽

Closely Related Species ◽

Universal Approach ◽

Fundamental Units ◽

Better Than

Species are the fundamental units of life and their recognition is essential for science and society. DNA barcoding, the use of a single and often mitochondrial gene, has been increasingly employed as a universal approach for the identification of animal species. However, this approach faces several challenges. Here, we demonstrate with empirical data from a number of metazoan animal lineages that multiple nuclear-encoded markers, so called universal single-copy orthologs (USCOs) performs much better than the single barcode gene to discriminate closely related species. Overcoming the general shortcomings of mitochondrial DNA barcodes, USCOs also accurately assign samples to higher taxonomic levels. These loci thus provide a powerful and unifying framework for species delimitation which considerably improves the DNA-based inference of animal species.

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