The Capsaspora genome reveals a complex unicellular prehistory of animals
Hiroshi Suga,Zehua Chen,Alex de Mendoza,Arnau Sebé-Pedrós,Matthew Brown,Eric Kramer,Martin Carr,Pierre Kerner,Michel Vervoort,Núria Sánchez-Pons,Guifré Torruella,Romain Derelle,Gerard Manning,B. Franz Lang,Carsten Russ,Brian J. Haas,Andrew J. Roger,Chad Nusbaum,Iñaki Ruiz-Trillo,Iñaki Ruiz-Trillo,Iñaki Ruiz-Trillo +20 more
TLDR
It is proposed that the acquisition of these metazoan-specific developmental systems and the co-option of pre-existing genes drove the evolutionary transition from unicellular protists to metazoans.Abstract:
To reconstruct the evolutionary origin of multicellular animals from their unicellular ancestors, the genome sequences of diverse unicellular relatives are essential. However, only the genome of the choanoflagellate Monosiga brevicollis has been reported to date. Here we completely sequence the genome of the filasterean Capsaspora owczarzaki, the closest known unicellular relative of metazoans besides choanoflagellates. Analyses of this genome alter our understanding of the molecular complexity of metazoans’ unicellular ancestors showing that they had a richer repertoire of proteins involved in cell adhesion and transcriptional regulation than previously inferred only with the choanoflagellate genome. Some of these proteins were secondarily lost in choanoflagellates. In contrast, most intercellular signalling systems controlling development evolved later concomitant with the emergence of the first metazoans. We propose that the acquisition of these metazoan-specific developmental systems and the co-option of pre-existing genes drove the evolutionary transition from unicellular protists to metazoans. Unicellular ancestors of metazoans can provide significant insights into the origin of multicellularity. Suga et al. present the first complete genome of the filasterean Capsaspora owczarzakiand suggest an evolutionary mechanism for the transition from unicellular protists to metazoans.read more
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Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments
Brian J. Haas,Steven L. Salzberg,Wei Zhu,Mihaela Pertea,Jonathan E. Allen,Joshua Orvis,Owen White,C R Buell,Jennifer R. Wortman +8 more
TL;DR: The experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
Journal ArticleDOI
A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data
Joseph W. Spatafora,Ying Chang,Gerald L. Benny,Katy Lazarus,Matthew E. Smith,Mary L. Berbee,Gregory Bonito,Nicolas Corradi,Igor V. Grigoriev,Andrii P. Gryganskyi,Timothy Y. James,Kerry O'Donnell,Robert W. Roberson,Thomas N. Taylor,Jessie K. Uehling,Rytas Vilgalys,Merlin M. White,Jason E. Stajich +17 more
TL;DR: It is demonstrated that zygomycetes comprise two major clades that form a paraphyletic grade, and the phyla Mucoromycota and ZoopagomyCota are circumscribed.
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Evolution by gene loss
Ricard Albalat,Cristian Cañestro +1 more
TL;DR: These questions are addressed, and insights are discussed from genomic studies of gene loss in populations and their relevance in evolutionary biology and biomedicine.
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BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database
TL;DR: The BRAKER2 pipeline as mentioned in this paper generates and integrates external protein support into the iterative process of training and gene prediction by GeneMark-EP+ and AUGUSTUS, and it is favorably compared with other pipelines, e.g. MAKER2, in terms of accuracy and performance.
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