Francisco Pina-Martins

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

BackgroundThe process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly.ResultsIn Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies.ConclusionsMany current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.

Assemblathon 2: evaluating de novo

BackgroundThe process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly.ResultsIn Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies.ConclusionsMany current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.

concatenator: sequence data matrices handling made easy

concatenator is a simple and user‐friendly software that implements two very useful functions for phylogenetics data analysis. It concatenates NEXUS files of several fragments in a single NEXUS file ready to be used in phylogenetics software, such as paup and mrbayes and it converts FASTA sequence data files to NEXUS and vice‐versa. Additionally, concatenated files can be prepared for partition tests in paup. It is freely available in http://cobig2.fc.ul.pt.

Molecular phylogeny and DNA barcoding in the meadow-spittlebug Philaenus spumarius (Hemiptera, Cercopidae) and its related species

Philaenus spumarius, widely studied for its colour/pattern polymorphism, is a widespread species across the Holartic. The patterns of haplotype divergence at the mitochondrial gene cytochrome oxidase I (COI) found in this study suggest a postglacial western Europe (Iberian and Italian peninsulas to Britain) and a eastern (from Near East to Finland) south-to-north colonization. The haplotypes found in North America are most likely derived from the British haplotypes. The barcode fragment used here allowed the distinction of the species within genus Philaenus and questioned some taxonomic identifications of sequences present in Genbank.

THE EVOLUTION OF CICADA SONGS CONTRASTED WITH THE RELATIONSHIPS INFERRED FROM MITOCHONDRIAL DNA (INSECTA, HEMIPTERA)

ABSTRACT The molecular phylogeny of nine Palaearctic species of cicadas (Hemiptera, Cicadoidea) was inferred using two mitochondrial DNA genes, Cytochrome Oxidase I and II. The two main groups detected, namely species within Tettigetta and Tympanistalna, as well as the two species investigated in the genus Cicada, are robustly supported across the analytical methods. The structure of the song syllables, generated during single tymbal cycles of males of the analysed group of species is remarkably consistent in these two phyletic lines. This reflects the morphology and the mechanics of the tymbal. However the higher level song patterns, which depend on the activity of the central nervous system and have evolved to advertise receptive mates, do not seem to be consistent with either the inferred molecular topology or the basic tymbal cycle. The observed similarities between the molecular phylogeny and the basic tymbal cycles seem to reflect the basic conservative nature of the tymbal structure, while the discrepancy between the former and the calling song pattern is probably related to the high plasticity of the pattern generator in the central nervous system and dependent on species-specific selection.

Conus pennaceus: a phylogenetic analysis of the Mozambican molluscan complex

The genus Conus has over 500 species and is the most species-rich taxon of marine invertebrates. Based on mitochondrial DNA, this study focuses on the phylogenetics of Conus, particularly the pennaceus complex collected along the Mozambican coast. Phylogenetic trees based on both the 16S and the 12S ribosomal genes grossly revealed the same groupings: one that clustered the individuals from the north (Pemba, Nacala and Island of Mozambique), another that grouped the individuals from the central/southern coast (Pomene/Massinga and Inhambane) and a third that assembled the specimens from the central/southern islands (Bazaruto and Inhaca). The 16SrRNA-based trees further distinguished the northern group into a Nacala group and a Pemba+Island of Mozambique group. In all trees, C. p. bazarutensis and C. lohri collected on the central/southern islands grouped separately from the C. p. bazarutensis and C. lohri collected on the central/southern coast, suggesting a genetic similarity between these species. Likewise, C. praelatus revealed greater proximity to C. pennaceus from Pemba. Although different topologies were produced by each gene (low bootstrap support in some nodes), we support the hypothesis of a southward ancestral colonisation pattern, indicated by the 16SrRNA trees. The common ancestor would have shifted from planktonic to non-planktonic larval development and this weak vagility would have promoted the divergence between north and south specimens. Our results suggest that the separation of these groups might have been a relatively recent event, and part of the current morphological variability could be the outcome of phenotypic plasticity and/or ecological adaptation.

Identifying signatures of natural selection in cork oak (Quercus suber L.) genes through SNP analysis

Cork oak (Quercus suber L.) is an evergreen tree species endemic to the western Mediterranean Basin with a major economical, social and ecological relevance, associated with cork extraction and exploitation. In the last years, cork oak stands have been facing a significant decline, which may be aggravated by the climate changes that are predicted to occur within cork oak distribution range during this century. Under this scenario, the assessment of adaptive genetic variation is essential to understand how cork oak may cope with these threats and to delineate strategies for the management of its genetic resources. In this study, six candidate genes possibly significant for environmental adaptation were analysed in cork oak populations from its entire distribution range. Signatures of natural selection were investigated using population genetic statistics and environmental association tests under alternative scenarios of population genetic structure. Signals of balancing selection were detected in the putative non-expressor of pathogenesis-related gene 1 (NPR1), involved in plant defence response against pathogens, in auxin response factor 16 (ARF16), a gene implicated in root development, in RAN3, also involved in developmental processes, and in glutamine synthetase nodule isozyme (GS), involved in nitrogen fixation. Furthermore, for ARF16, a class I heat shock protein (sHSP) and GS, associations were found between SNP allele and haplotype frequencies and several spatial and climatic variables, suggesting that these genes may have a role on cork oak local adaptation. In this study, the first steps were taken into gathering information on cork oak adaptation to environmental conditions.

4Pipe4 – A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information

BackgroundNext-generation sequencing datasets are becoming more frequent, and their use in population studies is becoming widespread. For non-model species, without a reference genome, it is possible from a panel of individuals to identify a set of SNPs that can be used for further population genotyping. However the lack of a reference genome to which the sequenced data could be compared makes the finding of SNPs more troublesome. Additionally when the data sources (strains) are not identified (e.g. in datasets of pooled individuals), the problem of finding reliable variation in these datasets can become much more difficult due to the lack of specialized software for this specific task.ResultsHere we describe 4Pipe4, a 454 data analysis pipeline particularly focused on SNP detection when no reference or strain information is available. It uses a command line interface to automatically call other programs, parse their outputs and summarize the results. The variation detection routine is built-in in the program itself. Despite being optimized for SNP mining in 454 EST data, it is flexible enough to automate the analysis of genomic data or even data from other NGS technologies. 4Pipe4 will output several HTML formatted reports with metrics on many of the most common assembly values, as well as on all the variation found. There is also a module available for finding putative SSRs in the analysed datasets.ConclusionsThis program can be especially useful for researchers that have 454 datasets of a panel of pooled individuals and want to discover and characterize SNPs for subsequent individual genotyping with customized genotyping arrays. In comparison with other SNP detection approaches, 4Pipe4 showed the best validation ratio, retrieving a smaller number of SNPs but with a considerably lower false positive rate than other methods.4Pipe4’s source code is available at https://github.com/StuntsPT/4Pipe4.

Structure_threader: an improved method for automation and parallelization of programs structure, fastStructure and MavericK on multicore CPU systems

Structure_threader is a program to parallelize multiple runs of genetic clustering software that does not make use of multithreading technology (structure, fastStructure and MavericK) on multicore computers. Our approach was benchmarked across multiple systems and displayed great speed improvements relative to the single‐threaded implementation, scaling very close to linearly with the number of physical cores used. Structure_threader was compared to previous software written for the same task—ParallelStructure and StrAuto and was proven to be the faster (up to 25% faster) wrapper under all tested scenarios. Furthermore, Structure_threader can perform several automatic and convenient operations, assisting the user in assessing the most biologically likely value of ‘K’ via implementations such as the “Evanno,” or “Thermodynamic Integration” tests and automatically draw the “meanQ” plots (static or interactive) for each value of K (or even combined plots). Structure_threader is written in python 3 and licensed under the GPLv3. It can be downloaded free of charge at https://github.com/StuntsPT/Structure_threader.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species - eScholarship

BackgroundThe process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly.ResultsIn Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies.ConclusionsMany current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.