Comparative Transcriptomes and EVO-DEVO Studies Depending on Next Generation Sequencing

High throughput technology has prompted the progressive omics studies, including genomics and transcriptomics. We have reviewed the improvement of comparative omic studies, which are attributed to the high throughput measurement of next generation sequencing technology. Comparative genomics have been successfully applied to evolution analysis while comparative transcriptomics are adopted in comparison of expression profile from two subjects by differential expression or differential coexpression, which enables their application in evolutionary developmental biology (EVO-DEVO) studies. EVO-DEVO studies focus on the evolutionary pressure affecting the morphogenesis of development and previous works have been conducted to illustrate the most conserved stages during embryonic development. Old measurements of these studies are based on the morphological similarity from macro view and new technology enables the micro detection of similarity in molecular mechanism. Evolutionary model of embryo development, which includes the “funnel-like” model and the “hourglass” model, has been evaluated by combination of these new comparative transcriptomic methods with prior comparative genomic information. Although the technology has promoted the EVO-DEVO studies into a new era, technological and material limitation still exist and further investigations require more subtle study design and procedure

Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks

Data used for the phylogenetic analysis of Hox and ParaHox genes, including the respective GenBank accession numbers. (DOC 31 kb

Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles

<p>Abstract</p> <p>Background</p> <p>Reptiles are largely under-represented in comparative genomics despite the fact that they are substantially more diverse in many respects than mammals. Given the high divergence of reptiles from classical model species, next-generation sequencing of their transcriptomes is an approach of choice for gene identification and annotation.</p> <p>Results</p> <p>Here, we use 454 technology to sequence the brain transcriptome of four divergent reptilian and one reference avian species: the Nile crocodile, the corn snake, the bearded dragon, the red-eared turtle, and the chicken. Using an in-house pipeline for recursive similarity searches of >3,000,000 reads against multiple databases from 7 reference vertebrates, we compile a reptilian comparative transcriptomics dataset, with homology assignment for 20,000 to 31,000 transcripts per species and a cumulated non-redundant sequence length of 248.6 Mbases. Our approach identifies the majority (87%) of chicken brain transcripts and about 50% of <it>de novo </it>assembled reptilian transcripts. In addition to 57,502 microsatellite loci, we identify thousands of SNP and indel polymorphisms for population genetic and linkage analyses. We also build very large multiple alignments for Sauropsida and mammals (two million residues per species) and perform extensive phylogenetic analyses suggesting that turtles are not basal living reptiles but are rather associated with Archosaurians, hence, potentially answering a long-standing question in the phylogeny of Amniotes.</p> <p>Conclusions</p> <p>The reptilian transcriptome (freely available at <url>http://www.reptilian-transcriptomes.org</url>) should prove a useful new resource as reptiles are becoming important new models for comparative genomics, ecology, and evolutionary developmental genetics.</p

SeaBase : a multispecies transcriptomic resource and platform for gene network inference

Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Integrative and Comparative Biology 54 (2014): 250-263, doi: 10.1093/icb/icu065.Marine and aquatic animals are extraordinarily useful as models for identifying mechanisms of development and evolution, regeneration, resistance to cancer, longevity and symbiosis, among many other areas of research. This is due to the great diversity of these organisms and their wide-ranging capabilities. Genomics tools are essential for taking advantage of these “free lessons” of nature. However, genomics and transcriptomics are challenging in emerging model systems. Here, we present SeaBase, a tool for helping to meet these needs. Specifically, SeaBase provides a platform for sharing and searching transcriptome data. More importantly, SeaBase will support a growing number of tools for inferring gene network mechanisms. The first dataset available on SeaBase is a developmental transcriptome profile of the sea anemone Nematostella vectensis (Anthozoa, Cnidaria). Additional datasets are currently being prepared and we are aiming to expand SeaBase to include user-supplied data for any number of marine and aquatic organisms, thereby supporting many potentially new models for gene network studies.2015-06-0

De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)

<p>Abstract</p> <p>Background</p> <p>Transcriptome sequencing data has become an integral component of modern genetics, genomics and evolutionary biology. However, despite advances in the technologies of DNA sequencing, such data are lacking for many groups of living organisms, in particular, many plant taxa. We present here the results of transcriptome sequencing for two closely related plant species. These species, <it>Fagopyrum esculentum </it>and <it>F. tataricum</it>, belong to the order Caryophyllales - a large group of flowering plants with uncertain evolutionary relationships. <it>F. esculentum </it>(common buckwheat) is also an important food crop. Despite these practical and evolutionary considerations <it>Fagopyrum </it>species have not been the subject of large-scale sequencing projects.</p> <p>Results</p> <p>Normalized cDNA corresponding to genes expressed in flowers and inflorescences of <it>F. esculentum </it>and <it>F. tataricum </it>was sequenced using the 454 pyrosequencing technology. This resulted in 267 (for <it>F. esculentum</it>) and 229 (<it>F. tataricum</it>) thousands of reads with average length of 341-349 nucleotides. <it>De novo </it>assembly of the reads produced about 25 thousands of contigs for each species, with 7.5-8.2× coverage. Comparative analysis of two transcriptomes demonstrated their overall similarity but also revealed genes that are presumably differentially expressed. Among them are retrotransposon genes and genes involved in sugar biosynthesis and metabolism. Thirteen single-copy genes were used for phylogenetic analysis; the resulting trees are largely consistent with those inferred from multigenic plastid datasets. The sister relationships of the Caryophyllales and asterids now gained high support from nuclear gene sequences.</p> <p>Conclusions</p> <p>454 transcriptome sequencing and <it>de novo </it>assembly was performed for two congeneric flowering plant species, <it>F. esculentum </it>and <it>F. tataricum</it>. As a result, a large set of cDNA sequences that represent orthologs of known plant genes as well as potential new genes was generated.</p

Emerging model spedies driven by transciptomics

This work is focused on 'emerging model species', i.e. question-driven model species which have sufficient molecular resources to investigate a specific phenomenon in molecular biology, developmental biology, molecular ecology and evolution or related molecular fields. This thesis shows how transcriptomic data can be generated, analyzed, and used to investigate such phenomena of interest even in species lacking a reference genome. The initial ButterflyBase resource has proven to be useful to researchers of species without a reference genome but is limited to the Lepidoptera and supports only the older Sanger sequencing technologies. Thanks to Next Generation Sequencing, transcriptome sequencing is more cost effective but the bottleneck of transcriptomic projects is now the bioinformatic analysis and data mining/dissemination. Therefore, this work continues with presenting novel and innovative approaches which effectively overcome this bottleneck. The est2assembly software produces deeply annotated reference transcriptomes stored in the Chado database. The Drupal Bioinformatic Server Framework and genes4all provide species-neutral and an innovative approach in building standardized online databases and associated web services. All public insect mRNA data were analyzed with est2assembly and genes4all to produce the InsectaCentral. With InsectaCentral, a powerful resource is now available to assist molecular biology in any question-driven model insect species. The software presented here was developed according to specifications of the General Model Organism Database (GMOD) community. All software specifications are species-neutral and can be seamlessly deployed to assist any research community. Further through a case studies chapter, it becomes apparent that the transcriptomic approach is more cost-effective than a genomic approach and therefore sequence-driven evolutionary biology will benefit faster with this field

Gene discovery in the horned beetle Onthophagus taurus

<p>Abstract</p> <p>Background</p> <p>Horned beetles, in particular in the genus <it>Onthophagus</it>, are important models for studies on sexual selection, biological radiations, the origin of novel traits, developmental plasticity, biocontrol, conservation, and forensic biology. Despite their growing prominence as models for studying both basic and applied questions in biology, little genomic or transcriptomic data are available for this genus. We used massively parallel pyrosequencing (Roche 454-FLX platform) to produce a comprehensive EST dataset for the horned beetle <it>Onthophagus taurus</it>. To maximize sequence diversity, we pooled RNA extracted from a normalized library encompassing diverse developmental stages and both sexes.</p> <p>Results</p> <p>We used 454 pyrosequencing to sequence ESTs from all post-embryonic stages of <it>O. taurus. </it>Approximately 1.36 million reads assembled into 50,080 non-redundant sequences encompassing a total of 26.5 Mbp. The non-redundant sequences match over half of the genes in <it>Tribolium castaneum</it>, the most closely related species with a sequenced genome. Analyses of Gene Ontology annotations and biochemical pathways indicate that the <it>O. taurus </it>sequences reflect a wide and representative sampling of biological functions and biochemical processes. An analysis of sequence polymorphisms revealed that SNP frequency was negatively related to overall expression level and the number of tissue types in which a given gene is expressed. The most variable genes were enriched for a limited number of GO annotations whereas the least variable genes were enriched for a wide range of GO terms directly related to fitness.</p> <p>Conclusions</p> <p>This study provides the first large-scale EST database for horned beetles, a much-needed resource for advancing the study of these organisms. Furthermore, we identified instances of gene duplications and alternative splicing, useful for future study of gene regulation, and a large number of SNP markers that could be used in population-genetic studies of <it>O. taurus </it>and possibly other horned beetles.</p

The developmental origins of heterodonty and acrodonty as revealed by reptile dentitions

Despite the exceptional diversity and central role of dentitions in vertebrate evolution, many aspects of tooth characters remain unknown. Here, we exploit the large array of dental phenotypes in acrodontan lizards, including EDA mutants showing the first vertebrate example of positional transformation in tooth identity, to assess the developmental origins and evolutionary patterning of tooth types and heterodonty. We reveal that pleurodont versus acrodont dentition can be determined by a simple mechanism, where modulation of tooth size through EDA signaling has major consequences on dental formula, thereby providing a new flexible tooth patterning model. Furthermore, such implication of morphoregulation in tooth evolution allows predicting the dental patterns characterizing extant and fossil lepidosaurian taxa at large scale. Together, the origins and diversification of tooth types, long a focus of multiple research fields, can now be approached through evo-devo approaches, highlighting the importance of underexplored dental features for illuminating major evolutionary patterns.Peer reviewe