@article {64,
	title = {Evaluating Topological Conflict in Centipede Phylogeny Using Transcriptomic Data Sets},
	journal = {Molecular Biology and Evolution},
	volume = {31},
	year = {2014},
	month = {2014},
	pages = {1500 - 1513},
	abstract = {<p>Relationships between the five extant orders of centipedes have been considered solved based on morphology. Phylogenies based on samples of up to a few dozen genes have largely been congruent with the morphological tree apart from an alternative placement of one order, the relictual Craterostigmomorpha, consisting of two species in Tasmania and New Zealand. To address this incongruence, novel transcriptomic data were generated to sample all five orders of centipedes and also used as a test case for studying gene-tree incongruence. Maximum likelihood and Bayesian mixture model analyses of a data set composed of 1,934 orthologs with 45\% missing data, as well as the 389 orthologs in the least saturated, stationary quartile, retrieve strong support for a sister-group relationship between Craterostigmomorpha and all other pleurostigmophoran centipedes, of which the latter group is newly named Amalpighiata. The Amalpighiata hypothesis, which shows little gene-tree incongruence and is robust to the influence of among-taxon compositional heterogeneity, implies convergent evolution in several morphological and behavioral characters traditionally used in centipede phylogenetics, such as maternal brood care, but accords with patterns of first appearances in the fossil record.</p>
},
	keywords = {Chilopoda, Illumina, incongruence, molecular dating, Myriapoda, next-generation sequencing, phylogenomics},
	isbn = {0737-4038},
	doi = {https://doi.org/10.1093/molbev/msu108},
	author = {Fern{\'a}ndez, Rosa and Laumer, Christopher E. and Vahtera, Varpu and Libro, Silvia and Kaluziak, Stefan and Sharma, Prashant P. and P{\'e}rez-Porro, Alicia R. and Edgecombe, Gregory D. and Giribet, Gonzalo}
}
@booklet {54,
	title = {Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa},
	howpublished = {Frontiers in ZoologyFrontiers in Zoology},
	volume = {9},
	year = {2012},
	abstract = {Introduction: Traditionally, genomic or transcriptomic data have been restricted to a few model or emerging model organisms, and to a handful of species of medical and/or environmental importance. Next-generation sequencing techniques have the capability of yielding massive amounts of gene sequence data for virtually any species at a modest cost. Here we provide a comparative analysis of de novo assembled transcriptomic data for ten non-model species of previously understudied animal taxa.Results: cDNA libraries of ten species belonging to five animal phyla (2 Annelida [including Sipuncula], 2 Arthropoda, 2 Mollusca, 2 Nemertea, and 2 Porifera) were sequenced in different batches with an Illumina Genome Analyzer II (read length 100 or 150 bp), rendering between ca. 25 and 52 million reads per species. Read thinning, trimming, and de novo assembly were performed under different parameters to optimize output. Between 67,423 and 207,559 contigs were obtained across the ten species, post-optimization. Of those, 9,069 to 25,681 contigs retrieved blast hits against the NCBI non-redundant database, and approximately 50\% of these were assigned with Gene Ontology terms, covering all major categories, and with similar percentages in all species. Local blasts against our datasets, using selected genes from major signaling pathways and housekeeping genes, revealed high efficiency in gene recovery compared to available genomes of closely related species. Intriguingly, our transcriptomic datasets detected multiple paralogues in all phyla and in nearly all gene pathways, including housekeeping genes that are traditionally used in phylogenetic applications for their purported single-copy nature.Conclusions: We generated the first study of comparative transcriptomics across multiple animal phyla (comparing two species per phylum in most cases), established the first Illumina-based transcriptomic datasets for sponge, nemertean, and sipunculan species, and generated a tractable catalogue of annotated genes (or gene fragments) and protein families for ten newly sequenced non-model organisms, some of commercial importance (i.e., Octopus vulgaris). These comprehensive sets of genes can be readily used for phylogenetic analysis, gene expression profiling, developmental analysis, and can also be a powerful resource for gene discovery. The characterization of the transcriptomes of such a diverse array of animal species permitted the comparison of sequencing depth, functional annotation, and efficiency of genomic sampling using the same pipelines, which proved to be similar for all considered species. In addition, the datasets revealed their potential as a resource for paralogue detection, a recurrent concern in various aspects of biological inquiry, including phylogenetics, molecular evolution, development, and cellular biochemistry. {\textcopyright} 2012 Riesgo et al.; licensee BioMed Central Ltd.},
	keywords = {Annelida, Arthropoda, Illumina, Mollusca, Nemertea, next-generation sequencing, Porifera, Sipuncula},
	author = {Riesgo, Ana and Andrade, S{\'o}nia C.S. and Sharma, Prashant P. and Novo, Marta and P{\'e}rez-Porro, Alicia R. and Vahtera, Varpu and Gonz{\'a}lez, Vanessa L. and Kawauchi, Gisele Y. and Giribet, Gonzalo}
}
