title: Transcriptome dynamics in the asexual cycle of the chordate Botryllus schlosseri.
abstract: BACKGROUND
  We performed an analysis of the transcriptome during the blastogenesis of the chordate Botryllus schlosseri, focusing in particular on genes involved in cell death by apoptosis. The tunicate B. schlosseri is an ascidian forming colonies characterized by the coexistence of three blastogenetic generations: filter-feeding adults, buds on adults, and budlets on buds. Cyclically, adult tissues undergo apoptosis and are progressively resorbed and replaced by their buds originated by asexual reproduction. This is a feature of colonial tunicates, the only known chordates that can reproduce asexually.
  
  
  RESULTS
  Thanks to a newly developed web-based platform ( http://botryllus.cribi.unipd.it ), we compared the transcriptomes of the mid-cycle, the pre-take-over, and the take-over phases of the colonial blastogenetic cycle. The platform is equipped with programs for comparative analysis and allows to select the statistical stringency. We enriched the genome annotation with 11,337 new genes; 581 transcripts were resolved as complete open reading frames, translated in silico into amino acid sequences and then aligned onto the non-redundant sequence database. Significant differentially expressed genes were classified within the gene ontology categories. Among them, we recognized genes involved in apoptosis activation, de-activation, and regulation.
  
  
  CONCLUSIONS
  With the current work, we contributed to the improvement of the first released B. schlosseri genome assembly and offer an overview of the transcriptome changes during the blastogenetic cycle, showing up- and down-regulated genes. These results are important for the comprehension of the events underlying colony growth and regression, cell proliferation, colony homeostasis, and competition among different generations.
authors.affiliation: CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.
authors.forename: Davide
authors.initials: D
authors.lastname: Campagna
authors.affiliation: Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.
authors.forename: Fabio
authors.initials: F
authors.lastname: Gasparini
authors.affiliation: Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.
authors.forename: Nicola
authors.initials: N
authors.lastname: Franchi
authors.affiliation: Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.|Department of Biotechnology, University of Verona, Verona, Italy.
authors.forename: Nicola
authors.initials: N
authors.lastname: Vitulo
authors.affiliation: Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Ballin
authors.affiliation: Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy. lucia.manni@unipd.it.
authors.forename: Lucia
authors.initials: L
authors.lastname: Manni
authors.affiliation: CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.|Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Valle
authors.affiliation: Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.
authors.forename: Loriano
authors.initials: L
authors.lastname: Ballarin
mesh_terms: D000818:Animals; D017209:Apoptosis / Q000235:genetics; D016923:Cell Death; D002874:Chromosome Mapping; D015723:Gene Library; D016678:Genome; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D012100:Reproduction, Asexual / Q000235:genetics*; D059467:Transcriptome; D014561:Urochordata / Q000235:genetics* / Q000254:growth & development
keywords: Apoptosis; Ascidian; Blastogenesis; Differentially expressed genes; RNAseq; Tunicata