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Article ; Online: MicroRNA annotation of plant genomes - Do it right or not at all.

Taylor, Richard S / Tarver, James E / Foroozani, Alireza / Donoghue, Philip C J

BioEssays : news and reviews in molecular, cellular and developmental biology

2017 Volume 39, Issue 2

Abstract: MicroRNAs are non-coding regulators of gene expression and key factors in development, disease, and targets for bioengineering. Consequently, microRNAs have become essential elements of already burgeoning draft plant genome descriptions where their ... ...

Abstract	MicroRNAs are non-coding regulators of gene expression and key factors in development, disease, and targets for bioengineering. Consequently, microRNAs have become essential elements of already burgeoning draft plant genome descriptions where their annotation is often particularly poor, contributing unduly to the corruption of public databases. Using the Citrus sinensis as an example, we highlight and review common failings of miRNAome annotations. Understanding and exploiting the role of miRNAs in plant biology will be stymied unless the research community acts decisively to improve the accuracy of miRNAome annotations. We encourage genome annotation teams to do it right or not at all.
Language	English
Publishing date	2017-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.201600113
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Article ; Online: Do miRNAs have a deep evolutionary history?

Tarver, James E / Donoghue, Philip C J / Peterson, Kevin J

BioEssays : news and reviews in molecular, cellular and developmental biology

2012 Volume 34, Issue 10, Page(s) 857–866

Abstract: The recent discovery of microRNAs (miRNAs) in unicellular eukaryotes, including miRNAs known previously only from animals or plants, implies that miRNAs have a deep evolutionary history among eukaryotes. This contrasts with the prevailing view that ... ...

Abstract	The recent discovery of microRNAs (miRNAs) in unicellular eukaryotes, including miRNAs known previously only from animals or plants, implies that miRNAs have a deep evolutionary history among eukaryotes. This contrasts with the prevailing view that miRNAs evolved convergently in animals and plants. We re-evaluate the evidence and find that none of the 73 plant and animal miRNAs described from protists meet the required criteria for miRNA annotation and, by implication, animals and plants did not acquire any of their respective miRNA genes from the crown ancestor of eukaryotes. Furthermore, of the 159 novel miRNAs previously identified among the seven species of unicellular protists examined, only 28 from the algae Ectocarpus and Chlamydomonas, meet the criteria for miRNA annotation. Therefore, at present only five groups of eukaryotes are known to possess miRNAs, indicating that miRNAs have evolved independently within eukaryotes through exaptation of their shared inherited RNAi machinery.
MeSH term(s)	Animals ; Base Sequence ; Evolution, Molecular ; Humans ; MicroRNAs/genetics ; MicroRNAs/metabolism ; MicroRNAs/physiology ; Models, Genetic ; Molecular Sequence Annotation ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA Interference ; RNA, Plant/genetics ; RNA, Protozoan/genetics
Chemical Substances	MicroRNAs ; RNA, Plant ; RNA, Protozoan
Language	English
Publishing date	2012-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.201200055
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Article ; Online: The trouble with topology: phylogenies without fossils provide a revisionist perspective of evolutionary history in topological analyses of diversity.

Tarver, James E / Donoghue, Philip C J

Systematic biology

2011 Volume 60, Issue 5, Page(s) 700–712

MeSH term(s)	Alligators and Crocodiles/classification ; Animals ; Biodiversity ; Biological Evolution ; Carnivora/classification ; Extinction, Biological ; Fossils ; Genetic Speciation ; Models, Biological ; Models, Genetic ; Phylogeny ; Time
Language	English
Publishing date	2011-10
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1482572-7
ISSN	1076-836X ; 1063-5157
ISSN (online)	1076-836X
ISSN	1063-5157
DOI	10.1093/sysbio/syr018
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Article ; Online: Rapid Evolution of microRNA Loci in the Brown Algae.

Cock, J Mark / Liu, Fuli / Duan, Delin / Bourdareau, Simon / Lipinska, Agnieszka P / Coelho, Susana M / Tarver, James E

Genome biology and evolution

2017 Volume 9, Issue 3, Page(s) 740–749

Abstract: Stringent searches for microRNAs (miRNAs) have so far only identified these molecules in animals, land plants, chlorophyte green algae, slime molds and brown algae. The identification of miRNAs in brown algae was based on the analysis of a single species, ...

Abstract	Stringent searches for microRNAs (miRNAs) have so far only identified these molecules in animals, land plants, chlorophyte green algae, slime molds and brown algae. The identification of miRNAs in brown algae was based on the analysis of a single species, the filamentous brown alga Ectocarpus sp. Here, we have used deep sequencing of small RNAs and a recently published genome sequence to identify miRNAs in a second brown alga, the kelp Saccharina japonica. S. japonica possesses a large number of miRNAs (117) and these miRNAs are highly diverse, falling into 98 different families. Surprisingly, none of the S. japonica miRNAs share significant sequence similarity with the Ectocarpus sp. miRNAs. However, the miRNA repertoires of the two species share a number of structural and genomic features indicating that they were generated by similar evolutionary processes and therefore probably evolved within the context of a common, ancestral miRNA system. This lack of sequence similarity suggests that miRNAs evolve rapidly in the brown algae (the two species are separated by ∼95 Myr of evolution). The sets of predicted targets of miRNAs in the two species were also very different suggesting that the divergence of the miRNAs may have had significant consequences for miRNA function.
MeSH term(s)	Chlorophyta/genetics ; Evolution, Molecular ; Genome/genetics ; Genomics ; High-Throughput Nucleotide Sequencing ; MicroRNAs/genetics ; Phaeophyceae/genetics
Chemical Substances	MicroRNAs
Language	English
Publishing date	2017-03-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evx038
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Article: Synthesis of gamma,delta-unsaturated and delta,epsilon-unsaturated alpha-amino acids from fragmentation of gamma- and delta-lactones.

Tarver, James E / Joullié, Madeleine M

The Journal of organic chemistry

2004 Volume 69, Issue 3, Page(s) 815–820

Abstract: A noncoded amino acid of cyclomarin A (1) was synthesized in a racemic fashion. The method employs a six-membered ring template to control the relative stereochemistry and introduction of the functional groups. Ultimately, Pd-catalyzed fragmentation of ... ...

Abstract	A noncoded amino acid of cyclomarin A (1) was synthesized in a racemic fashion. The method employs a six-membered ring template to control the relative stereochemistry and introduction of the functional groups. Ultimately, Pd-catalyzed fragmentation of the lactone provided gamma,delta-unsaturated and delta,epsilon-unsaturated alpha-amino acids. A Pd-catalyzed ring opening of a gamma-lactone is also reported.
MeSH term(s)	Amino Acids/chemical synthesis ; Amino Acids/chemistry ; Isomerism ; Lactones/chemistry ; Oligopeptides/chemistry
Chemical Substances	Amino Acids ; Lactones ; Oligopeptides ; cyclomarin A
Language	English
Publishing date	2004-02-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	123490-0
ISSN	1520-6904 ; 0022-3263
ISSN (online)	1520-6904
ISSN	0022-3263
DOI	10.1021/jo035401m
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Article ; Online: Evolutionary history of plant microRNAs.

Taylor, Richard S / Tarver, James E / Hiscock, Simon J / Donoghue, Philip C J

Trends in plant science

2014 Volume 19, Issue 3, Page(s) 175–182

Abstract: microRNAs (miRNAs) are short noncoding regulatory genes that perform important roles in plant development and physiology. With the increasing power of next generation sequencing technologies and the development of bioinformatic tools, there has been a ... ...

Abstract	microRNAs (miRNAs) are short noncoding regulatory genes that perform important roles in plant development and physiology. With the increasing power of next generation sequencing technologies and the development of bioinformatic tools, there has been a dramatic increase in the number of studies surveying the miRNAomes of plant species, which has led to an explosion in the number of described miRNAs. Unfortunately, very many of these new discoveries have been incompletely annotated and thus fail to discriminate genuine miRNAs from small interfering RNAs (siRNAs), fragments of longer RNAs, and random sequence. We review the published repertoire of plant miRNAs, discriminating those that have been correctly annotated. We use these data to explore prevailing hypotheses on the tempo and mode of miRNA evolution within the plant kingdom.
MeSH term(s)	Gene Expression Regulation, Plant/genetics ; Gene Expression Regulation, Plant/physiology ; MicroRNAs/genetics ; RNA, Plant/genetics ; RNA, Small Interfering/genetics
Chemical Substances	MicroRNAs ; RNA, Plant ; RNA, Small Interfering
Language	English
Publishing date	2014-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1305448-x
ISSN	1878-4372 ; 1360-1385
ISSN (online)	1878-4372
ISSN	1360-1385
DOI	10.1016/j.tplants.2013.11.008
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Article ; Online: (with research data) Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data.

O'Reilly, Joseph E / Puttick, Mark N / Parry, Luke / Tanner, Alastair R / Tarver, James E / Fleming, James / Pisani, Davide / Donoghue, Philip C J

Biology letters

2016 Volume 12, Issue 4

Abstract: Different analytical methods can yield competing interpretations of evolutionary history and, currently, there is no definitive method for phylogenetic reconstruction using morphological data. Parsimony has been the primary method for analysing ... ...

Abstract	Different analytical methods can yield competing interpretations of evolutionary history and, currently, there is no definitive method for phylogenetic reconstruction using morphological data. Parsimony has been the primary method for analysing morphological data, but there has been a resurgence of interest in the likelihood-based Mk-model. Here, we test the performance of the Bayesian implementation of the Mk-model relative to both equal and implied-weight implementations of parsimony. Using simulated morphological data, we demonstrate that the Mk-model outperforms equal-weights parsimony in terms of topological accuracy, and implied-weights performs the most poorly. However, the Mk-model produces phylogenies that have less resolution than parsimony methods. This difference in the accuracy and precision of parsimony and Bayesian approaches to topology estimation needs to be considered when selecting a method for phylogeny reconstruction.
MeSH term(s)	Bayes Theorem ; Biological Evolution ; Computer Simulation ; Fossils ; Likelihood Functions ; Models, Biological ; Phylogeny
Language	English
Publishing date	2016-04-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2135022-X
ISSN	1744-957X ; 1744-9561
ISSN (online)	1744-957X
ISSN	1744-9561
DOI	10.1098/rsbl.2016.0081
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Zs.A 1364 -Letters-: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss.

Tarver, James E / Taylor, Richard S / Puttick, Mark N / Lloyd, Graeme T / Pett, Walker / Fromm, Bastian / Schirrmeister, Bettina E / Pisani, Davide / Peterson, Kevin J / Donoghue, Philip C J

Genome biology and evolution

2018 Volume 10, Issue 6, Page(s) 1457–1470

Abstract: microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic ... ...

Abstract	microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility of microRNAs has been questioned on evidence of pervasive loss. Here, we show that apparent widespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes. Using a curated data set of animal microRNAomes, we reject the view that miRNA families are never lost, but they are rarely lost (92% are never lost). A small number of families account for a majority of losses (1.7% of families account for >45% losses), and losses are associated with lineages exhibiting phenotypic simplification. Phylogenetic analyses based on the presence/absence of microRNA families among animal lineages, and based on microRNA sequences among Osteichthyes, demonstrate the power of these small data sets in phylogenetic inference. Perceptions of widespread evolutionary loss of microRNA families are due to the uncritical use of public archives corrupted by spurious microRNA annotations, and failure to discriminate false absences that occur because of incomplete microRNAome annotation.
MeSH term(s)	Animals ; Conserved Sequence/genetics ; Evolution, Molecular ; MicroRNAs/genetics ; Molecular Sequence Annotation/methods ; Phenotype ; Phylogeny
Chemical Substances	MicroRNAs
Language	English
Publishing date	2018-05-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evy096
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Article ; Online: Unicellular Origin of the Animal MicroRNA Machinery.

Bråte, Jon / Neumann, Ralf S / Fromm, Bastian / Haraldsen, Arthur A B / Tarver, James E / Suga, Hiroshi / Donoghue, Philip C J / Peterson, Kevin J / Ruiz-Trillo, Iñaki / Grini, Paul E / Shalchian-Tabrizi, Kamran

Current biology : CB

2018 Volume 28, Issue 20, Page(s) 3288–3295.e5

Abstract: The emergence of multicellular animals was associated with an increase in phenotypic complexity and with the acquisition of spatial cell differentiation and embryonic development. Paradoxically, this phenotypic transition was not paralleled by major ... ...

Abstract	The emergence of multicellular animals was associated with an increase in phenotypic complexity and with the acquisition of spatial cell differentiation and embryonic development. Paradoxically, this phenotypic transition was not paralleled by major changes in the underlying developmental toolkit and regulatory networks. In fact, most of these systems are ancient, established already in the unicellular ancestors of animals [1-5]. In contrast, the Microprocessor protein machinery, which is essential for microRNA (miRNA) biogenesis in animals, as well as the miRNA genes themselves produced by this Microprocessor, have not been identified outside of the animal kingdom [6]. Hence, the Microprocessor, with the key proteins Pasha and Drosha, is regarded as an animal innovation [7-9]. Here, we challenge this evolutionary scenario by investigating unicellular sister lineages of animals through genomic and transcriptomic analyses. We identify in Ichthyosporea both Drosha and Pasha (DGCR8 in vertebrates), indicating that the Microprocessor complex evolved long before the last common ancestor of animals, consistent with a pre-metazoan origin of most of the animal developmental gene elements. Through small RNA sequencing, we also discovered expressed bona fide miRNA genes in several species of the ichthyosporeans harboring the Microprocessor. A deep, pre-metazoan origin of the Microprocessor and miRNAs comply with a view that the origin of multicellular animals was not directly linked to the innovation of these key regulatory components.
MeSH term(s)	Animals ; Base Sequence ; Evolution, Molecular ; Mesomycetozoea/genetics ; Mesomycetozoea/metabolism ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Phylogeny
Chemical Substances	MicroRNAs
Language	English
Publishing date	2018-10-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2018.08.018
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Article ; Online: microRNAs and the evolution of complex multicellularity: identification of a large, diverse complement of microRNAs in the brown alga Ectocarpus.

Tarver, James E / Cormier, Alexandre / Pinzón, Natalia / Taylor, Richard S / Carré, Wilfrid / Strittmatter, Martina / Seitz, Hervé / Coelho, Susana M / Cock, J Mark

Nucleic acids research

2015 Volume 43, Issue 13, Page(s) 6384–6398

Abstract: There is currently convincing evidence that microRNAs have evolved independently in at least six different eukaryotic lineages: animals, land plants, chlorophyte green algae, demosponges, slime molds and brown algae. MicroRNAs from different lineages are ...

Abstract	There is currently convincing evidence that microRNAs have evolved independently in at least six different eukaryotic lineages: animals, land plants, chlorophyte green algae, demosponges, slime molds and brown algae. MicroRNAs from different lineages are not homologous but some structural features are strongly conserved across the eukaryotic tree allowing the application of stringent criteria to identify novel microRNA loci. A large set of 63 microRNA families was identified in the brown alga Ectocarpus based on mapping of RNA-seq data and nine microRNAs were confirmed by northern blotting. The Ectocarpus microRNAs are highly diverse at the sequence level with few multi-gene families, and do not tend to occur in clusters but exhibit some highly conserved structural features such as the presence of a uracil at the first residue. No homologues of Ectocarpus microRNAs were found in other stramenopile genomes indicating that they emerged late in stramenopile evolution and are perhaps specific to the brown algae. The large number of microRNA loci in Ectocarpus is consistent with the developmental complexity of many brown algal species and supports a proposed link between the emergence and expansion of microRNA regulatory systems and the evolution of complex multicellularity.
MeSH term(s)	Evolution, Molecular ; Genetic Loci ; Genetic Variation ; Genome ; MicroRNAs/chemistry ; MicroRNAs/classification ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Phaeophyceae/genetics ; Phaeophyceae/metabolism ; Polymerase Chain Reaction ; Sequence Analysis, RNA
Chemical Substances	MicroRNAs
Language	English
Publishing date	2015-06-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkv578
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