The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes

Embryonic development is arguably the most complex process an organism undergoes during its lifetime, and understanding this complexity is best approached with a systems-level perspective. The sea urchin has become a highly valuable model organism for understanding developmental specification, morphogenesis, and evolution. As a non-chordate deuterostome, the sea urchin occupies an important evolutionary niche between protostomes and vertebrates. Lytechinus variegatus (Lv) is an Atlantic species that has been well studied, and which has provided important insights into signal transduction, patterning, and morphogenetic changes during embryonic and larval development. The Pacific species, Strongylocentrotus purpuratus (Sp), is another well-studied sea urchin, particularly for gene regulatory networks (GRNs) and cis-regulatory analyses. A well-annotated genome and transcriptome for Sp are available, but similar resources have not been developed for Lv. Here, we provide an analysis of the Lv transcriptome at 11 timepoints during embryonic and larval development. Temporal analysis suggests that the gene regulatory networks that underlie specification are well-conserved among sea urchin species. We show that the major transitions in variation of embryonic transcription divide the developmental time series into four distinct, temporally sequential phases. Our work shows that sea urchin development occurs via sequential intervals of relatively stable gene expression states that are punctuated by abrupt transitions.National Science FoundationFirst author draf

Phylogenetic relationships of the geoplaninae genera (Platyhelmintes, Tricladida) as inferred from morphological characters

Este trabalho consiste em uma caracterização morfológica das espécies-tipo da maioria dos gêneros que compõem a subfamília Geoplaninae, e quatro espécies destinadas a servir como grupos externos (Pelmatoplanini, Anzoplanini, Caenoplanini, Bipaliinae). A estudo morfológico das espécies resultou em 69 caracteres morfológicos que foram inseridos em uma matriz de dados e preparados para análise filogenética. Quinze espécies adicionais de outros gêneros de Geoplaninae também foram incluídos na análise. Os resultados corroboram o monofiletismo da subfamília Geoplaninae. De acordo com a hipótese de Meixner, o clado formado pelos gêneros Enterosyringa e Xerapoa, que compartilha características morfológicas com espécies do grupo externo, é o grupo de irmãos de todas as demais espécies de Geoplaninae. Descobrimos que as características anatômicas do aparelho copulador, como a presença e o tipo de papila peniana mostraram possuir muitas reversões e não se mostraram filogeneticamente informativas. Caracteres do sistema muscular podem ser usados de forma mais efetiva para a definição de grupos taxonômicos dentro do Geoplaninae e como indicadores de suas relações evolutivas. Nenhum dos aspectos diagnóstico atuais de da Geoplaninae correspondeu a caracteres autopomórficos em nossa análise. Nossos resultados sugerem que vários gêneros de Geoplaninae representam grupos não naturais, i.e., Geoplana e Notogynaphallia, com alguns caracteres diagnósticos sendo homoplásicos.This work consists of a morphological characterization of the type species of most of the genera that compose Geoplaninae, and four species intended to serve as outgroups (Pelmatoplanini, Anzoplanini, Caenoplanini, Bipaliinae). The morphological study of the species resulted in 69 morphological characters that were entered into a data matrix and prepared for phylogenetic analysis. Fifteen additional species from other Geoplaninae genera were also included in the analysis. The results corroborate the monophyletic status of the subfamily Geoplaninae. According with Meixner\'s hypothesis, the clade formed by Enterosyringa and Xerapoa species, sharing morphological characteristics with outgroup species, is the sister group of all other Geoplaninae species. We found that anatomical features of the copulatory apparatus, such as the presence and type of penis papilla showed many reversions and were not phylogenetically informative. Characters of the muscular system can be used much better for defining taxonomic groups within the Geoplaninae and as indicators of their evolutionary relationships. None of the present diagnostic features of the Geoplaninae formed autapomorphic characters in our analysis. Our results suggest that several genera of Geoplaninae represent unnatural groups, viz., Geoplana and Notogynaphallia, with some diagnostic characters being homoplasic

Panorama de la diversidad de planarias terrestres (Platyhelminthes: Tricladida) de Chile

Approximately 25 species of terrestrial planarians are known from Chile, collected in a few localities between the Atacama (28° S) and Aisén (46° S) regions, only three of them taxonomically well known. From the remaining species, the available morphological information is insufficient for taxonomic or phylogenetic purposes, or presents synonymy problems. Recent surveys carried out in this country have found more specimens of probably unknown species to science. Reviewing the type material of the described species, together with collecting in other regions not yet explored for this purpose, and building a team of taxonomists, are necessary steps to approach such an unknown and diverse group of flatworms.De Chile se conocen 25 especies nominales de planarias terrestres, procedentes de unas pocas localidades situadas entre las regiones de Atacama (28° S) y de Aisén (46° S); sólo tres de ellas taxonómicamente bien conocidas. De las restantes especies se dispone de información morfológica insuficiente con fines taxonómicos o filogenéticos, o presentan problemas de sinonimia. En muestreos recientes realizados en el país se han recolectado más especímenes de especies probablemente aún no conocidas por la ciencia. La acción conjunta del examen del material tipo de las especies descritas, del muestreo en otras regiones aún no exploradas con esta finalidad y de la formación de un cuerpo de taxónomos son pasos necesarios para abordar este grupo de vermes tan diverso y desconocido

The complete mitochondrial genome of the pentastomid Linguatula arctica (Pentastomida) from reindeer (Rangifer tarandus) in Northern Norway

Here, we present the first complete mitochondrial genome of the pentastomid Linguatula arctica collected from the nasal passages of a reindeer (Rangifer tarandus) in Norway. The full length mitochondrial genome of L. arctica, which measures 14,789 bp in length, contains 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. A clear A + T bias is observed in the mitogenome of L. arctica with an overall base composition of 32.6% A, 27.5% T, 32.8% C, and 7,1% G., and a GC content of 39.9%. The gene arrangement is identical to that of previously described pentastomid mitogenomes.publishedVersio

LTR retroelements are intrinsic components of transcriptional networks in frogs

BACKGROUND: LTR retroelements (LTR REs) constitute a major group of transposable elements widely distributed in eukaryotic genomes. Through their own mechanism of retrotranscription LTR REs enrich the genomic landscape by providing genetic variability, thus contributing to genome structure and organization. Nonetheless, transcriptomic activity of LTR REs still remains an obscure domain within cell, developmental, and organism biology. RESULTS: Here we present a first comparative analysis of LTR REs for anuran amphibians based on a full depth coverage transcriptome of the European pool frog, Pelophylax lessonae, the genome of the African clawed frog, Silurana tropicalis (release v7.1), and additional transcriptomes of S. tropicalis and Cyclorana alboguttata. We identified over 1000 copies of LTR REs from all four families (Bel/Pao, Ty1/Copia, Ty3/Gypsy, Retroviridae) in the genome of S. tropicalis and discovered transcripts of several of these elements in all RNA-seq datasets analyzed. Elements of the Ty3/Gypsy family were most active, especially Amn-san elements, which accounted for approximately 0.27% of the genome in Silurana. Some elements exhibited tissue specific expression patterns, for example Hydra1.1 and MuERV-like elements in Pelophylax. In S. tropicalis considerable transcription of LTR REs was observed during embryogenesis as soon as the embryonic genome became activated, i.e. at midblastula transition. In the course of embryonic development the spectrum of transcribed LTR REs changed; during gastrulation and neurulation MuERV-like and SnRV like retroviruses were abundantly transcribed while during organogenesis transcripts of the XEN1 retroviruses became much more active. CONCLUSIONS: The differential expression of LTR REs during embryogenesis in concert with their tissue-specificity and the protein domains they encode are evidence for the functional roles these elements play as integrative parts of complex regulatory networks. Our results support the meanwhile widely accepted concept that retroelements are not simple “junk DNA” or “harmful genomic parasites” but essential components of the transcriptomic machinery in vertebrates

Improving draft genome contiguity with reference-derived in silico mate-pair libraries

Background: Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available. Findings: In order to improve genome contiguity, we have developed Cross-Species Scaffolding - a new pipeline that imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico. Conclusions: We show how genome assembly metrics and gene prediction dramatically improve with our pipeline by assembling two primate genomes solely based on ~30x coverage of shotgun sequencing data

Improving draft genome contiguity with reference-derived in silico mate-pair libraries

Background: Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available. Findings: In order to improve genome contiguity, we have developed Cross-Species Scaffolding - a new pipeline that imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico. Conclusions: We show how genome assembly metrics and gene prediction dramatically improve with our pipeline by assembling two primate genomes solely based on ~30x coverage of shotgun sequencing data