Genomic DNA Sequence Data Research Articles

Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data.

A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer. Our study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively assess the role of the Knudson two hit genetic model in SCNA generation in prostate cancer. 64 recurrent regions of loss and gain were detected, of which 28 were novel, including regions of loss with more than 15% frequency at Chr4p15.2-p15.1 (15.53%), Chr6q27 (16.50%) and Chr18q12.3 (17.48%). Comprehensive mutation screens of genes, lincRNA encoding sequences, control regions and conserved domains within SCNAs demonstrated that a two-hit genetic model was supported in only a minor proportion of recurrent SCNA losses examined (15/40). We found that recurrent breakpoints and regions of inversion often occur within Knudson model SCNAs, leading to the identification of ZNF292 as a target gene for the deletion at 6q14.3-q15 and NKX3.1 as a two-hit target at 8p21.3-p21.2. The importance of alterations of lincRNA sequences was illustrated by the identification of a novel mutational hotspot at the KCCAT42, FENDRR, CAT1886 and STCAT2 loci at the 16q23.1-q24.3 loss. Our data confirm that the burden of SCNAs is predictive of biochemical recurrence, define nine individual regions that are associated with relapse, and highlight the possible importance of ion channel and G-protein coupled-receptor (GPCR) pathways in cancer development. We concluded that a two-hit genetic model accounts for about one third of SCNA indicating that mechanisms, such haploinsufficiency and epigenetic inactivation, account for the remaining SCNA losses.

A phylogeny of Southern Hemisphere whelks (Gastropoda: Buccinulidae) and concordance with the fossil record

Under current marine snail taxonomy, the majority of whelks from the Southern Hemisphere (Buccinulidae) are hypothesised to represent a monophyletic clade that has evolved independently from Northern Hemisphere taxa (Buccinidae). Phylogenetic analysis of mitochondrial genomic and nuclear ribosomal DNA sequence data indicates that Southern Hemisphere taxa are not monophyletic, and results suggest that dispersal across the equator has occurred in both directions. New Zealand buccinulid whelks, noted for their high endemic diversity, are also found to not be monophyletic. Using independent fossil calibrations, estimated genetic divergence dates show remarkable concordance with the fossil record of the Penion and Kelletia. The divergence dates and the geographic distribution of the genera through time implies that some benthic marine snails are capable of dispersal over long distances, despite varied developmental strategies. Phylogenetic results also indicate that one species, P. benthicolus belongs in Antarctoneptunea.

Abstract 2631: Restrictions on access to systemic therapy limit the application of whole genome sequencing in clinical care

Abstract Background: Whole genome analyses have the potential to identify the full landscape of activating and inactivating genomic abnormalities at work within cancers, and can thus be used to provide rationales for selection of treatment agents or clinical trials in a broad range of patients. Patients & Methods: Eligible patients (pts) with metastatic cancers were recruited within a general oncology practice across the province of B.C., Canada. Each pt underwent a fresh tumor biopsy and a blood sample and had comprehensive DNA (80X) and RNA sequencing. In-depth bioinformatic analyses were preformed to identify genomic changes that may be cancer “drivers” or therapeutically actionable targets. Aberrant pathways were matched to drug databases and manual literature reviews undertaken to identify drugs or clinical trials of potential utility for the individual pt. Results: Between July 2012 - Oct 2015: 380 pts (358 adult + 22 peds) consented; 227 have completed whole DNA and RNA sequencing and analysis to date (remainder ongoing). For this analysis, data is available on 160 pts. Genome bioinformaticians assessed the genomic data to be potentially druggable in all cases. Medical Oncologists assessed this data to be directly clinically actionable in 135 (84%); the difference being that clinicians did not agree that some putative “druggable” drivers (such as p53) or pathways with no current drugs available (MMP, AURA, WNT) were “actionable”. Of the 135 cases, 58 (43%) pts received therapy based directly on this genomic information; 6 on a phase 1 clinical trial. The most common reasons for 77 pts defined as actionable but who have not received genomically-informed therapy were: drug only available on a clinical trial but trial not available to pt - 22 (26%); drug approved but not available off label - 18 (23%); pt presently on first-line therapy that is working - 14 (18%); or death/too unwell 13 (17%). The limited availability of clinical trials was primarily because of highly restrictive trials entry criteria, primarily limiting patients to one primary tumour type or narrowly defined biomarker entry criteria. The most commonly mutated cancer genes identified by the genome analysts were: p53 as the predominant driver in 42%; APC in 16%; KRAS and PI3KCA mutations in 14%. Going forward it is essential to distinguish what driver mutations might be clinically actionable from those that are still only theoretically druggable; and similarly learn to distinguish which targets are actionable but not truly drivers. Conclusions: Genomic DNA and RNA sequencing data were found to be clinically actionable in 84% of pts with advanced cancers in a population cancer care setting. However, the ability to act on this information is limited by the restrictive nature of clinical trials and the lack of accessibility of off-label drugs despite an identified biomarker. As genome sequencing becomes integrated into cancer management these drug access issues need to be addressed. Citation Format: Janessa J. Laskin, Yaoqing Shen, Daniel Renouf, Martin Jones, Howard Lim, Alexandra Fok, Cheryl Ho, Balvir Deol, Karen A. Gelmon, Stephen Chia, Richard Moore, Andrew Mungall, Stephen Yip, Steven Jones, Marco Marra. Restrictions on access to systemic therapy limit the application of whole genome sequencing in clinical care. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2631.

Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data.

High throughput sequencing has facilitated a precipitous drop in the cost of genomic sequencing, prompting predictions of a revolution in medicine via genetic personalization of diagnostic and therapeutic strategies. There are significant barriers to realizing this goal that are related to the difficult task of interpreting personal genetic variation. A comprehensive, widely accessible application for interpretation of whole genome sequence data is needed. Here, we present a series of methods for identification of genetic variants and genotypes with clinical associations, phasing genetic data and using Mendelian inheritance for quality control, and providing predictive genetic information about risk for rare disease phenotypes and response to pharmacological therapy in single individuals and father-mother-child trios. We demonstrate application of these methods for disease and drug response prognostication in whole genome sequence data from twelve unrelated adults, and for disease gene discovery in one father-mother-child trio with apparently simplex congenital ventricular arrhythmia. In doing so we identify clinically actionable inherited disease risk and drug response genotypes in pre-symptomatic individuals. We also nominate a new candidate gene in congenital arrhythmia, ATP2B4, and provide experimental evidence of a regulatory role for variants discovered using this framework.

Contralateral breast cancer can represent a metastatic spread of the first primary tumor: determination of clonal relationship between contralateral breast cancers using next-generation whole genome sequencing.

IntroductionBy convention, a contralateral breast cancer (CBC) is treated as a new primary tumor, independent of the first cancer (BC1). Although there have been indications that the second tumor (BC2) sometimes may represent a metastatic spread of BC1, this has never been conclusively shown. We sought to apply next-generation sequencing to determine a “genetic barcode” for each tumor and reveal the clonal relationship of CBCs.MethodsTen CBC patients with detailed clinical information and available fresh frozen tumor tissue were studied. Using low-coverage whole genome DNA-sequencing data for each tumor, chromosomal rearrangements were enumerated and copy number profiles were generated. Comparisons between tumors provided an estimate of clonal relatedness for tumor pairs within individual patients.ResultsBetween 15–256 rearrangements were detected in each tumor (median 87). For one patient, 76 % (68 out of 90) of the rearrangements were shared between BC1 and BC2, highly consistent with what has been seen for true primary-metastasis pairs (>50 %) and thus confirming a common clonal origin of the two tumors. For most of the remaining cases, BC1 and BC2 had similarly low overlap as unmatched randomized pairs of tumors from different individuals, suggesting the CBC to represent a new independent primary tumor.ConclusionUsing rearrangement fingerprinting, we show for the first time with certainty that a contralateral BC2 can represent a metastatic spread of BC1. Given the poor prognosis of a generalized disease compared to a new primary tumor, these women need to be identified at diagnosis of CBC for appropriate determination of treatment. Our approach generates a promising new method to assess clonal relationship between tumors. Additional studies are required to confirm the frequency of CBCs representing metastatic events.Electronic supplementary materialThe online version of this article (doi:10.1186/s13058-015-0608-x) contains supplementary material, which is available to authorized users.

Glycine-containing flaxseed orbitides.

Five new orbitides, cyclolinopeptides 21-25, were identified in flaxseed oil (Linum usitatissimum) extracts. Their HPLC-ESIMS quasimolecular ion peaks at m/z 1097.7 (21), 1115.6 (22), 1131.6 (23), 1018.6 (24), and 1034.6 (25) [M + H](+) corresponded to the molecular formulae C59H89N10O10, C58H87N10O10S, C58H87N10O11S, C53H80N9O9S, and C53H80N9O10S, respectively. Their structures were elucidated by extensive HPLC-ESIMS/MS analyses, and their presence was confirmed by precursor proteins identified in flax genomic DNA sequence data. The amino acid sequences of these orbitides were confirmed as [1-10-NαC]-GILVPPFFLI, [1-10-NαC]-GMLIPPFFVI, [1-10-NαC]-GOLIPPFFVI, [1-9-NαC]-GMLVFPLFI, and [1-9-NαC]-GOLVFPLFI for cyclolinopeptides 21-25, respectively. Previously reported orbitides, [1-9-NαC]-ILVPPFFLI (1), [1-9-NαC]-MLIPPFFVI (2), [1-9-NαC]-OLIPPFFVI (3), [1-8-NαC]-MLVFPLFI (7), and [1-8-NαC]-OLVFPLFI (8), were also present in flaxseed oil. The precursors of orbitides 21, 22, and 24 also produced orbitides 1, 2, and 7 by alternative cyclization. Cyclolinopeptides 3, 8, 23, and 25 contain MetO (O) and are not directly encoded, but are products of post-translational modification of the Met present in 2, 7, 22, and 24, respectively. Sufficient cyclolinopeptide 23 was isolated for characterization via 1D ((1)H and (13)C) and 2D (NOESY and HMBC) NMR spectroscopy. These compounds have been named as cyclolinopeptides U, V, W, X, and Y for 21, 22, 23, 24, and 25, respectively.

Molecular evolution of drought tolerance and wood strength related candidate genes in loblolly pine (Pinus taeda L.)

AbstractLoblolly pine (Pinus taeda L.) is an intensely studied species that has become a model system for conifers. It is one of the most important commercial crops in the southeastern United States and grows across a vast territory. Due to exposure to this current diverse environment and the fluctuating climatic conditions of the past, it has likely accumulated substantial variation in adaptive trait and wood strength related genes. We merged a set of newly collected and previously published genomic DNA sequence data and analyzed them for departures from neutrality in 32 drought tolerance and wood strength related candidate genes using neutrality tests, such as Tajima’s D, HKA, MK and nonsynonymous to synonymous substitutions ratio (Z-test). Three other major Southern pines closely related to P. taeda (Pinus echinata Mill., P. elliottii Engelm., and P. palustris Mill.) were used as outgroups in interspecific tests. In three loci (4-coumarate: CoA ligase, putative cell-wall protein and trans-cinnamate 4-hydroxylase 2) neutrality was rejected by both intra- and interspecific tests, consistent with purifying selection. Neutrality was also rejected in several other loci (alpha-tubulin, arabinogalactan 4, arabinogalactan 6, cinnamate 4-hydroxylase 1, cinnamoyl CoA reductase, cinnamyl alcohol dehydrogenase, caffeoyl CoA O-methyltransferase 1, early response to drought 3, glycine hydroxymethyltransferase, ABI1 protein phosphatase 2C-like, putative wall-associated protein kinase, and unknown gene ug_2-498); however, these results are difficult to interpret because only one of the tests proved significant. This study contributes to the ongoing discussion about natural selection in putative adaptive genes in loblolly pine. However, unambiguous interpretation of the results often remains problematic.

SNP discovery in nonmodel organisms: strand bias and base-substitution errors reduce conversion rates.

Single nucleotide polymorphisms (SNPs) have become the marker of choice for genetic studies in organisms of conservation, commercial or biological interest. Most SNP discovery projects in nonmodel organisms apply a strategy for identifying putative SNPs based on filtering rules that account for random sequencing errors. Here, we analyse data used to develop 4723 novel SNPs for the commercially important deep-sea fish, orange roughy (Hoplostethus atlanticus), to assess the impact of not accounting for systematic sequencing errors when filtering identified polymorphisms when discovering SNPs. We used SAMtools to identify polymorphisms in a velvet assembly of genomic DNA sequence data from seven individuals. The resulting set of polymorphisms were filtered to minimize 'bycatch'-polymorphisms caused by sequencing or assembly error. An Illumina Infinium SNP chip was used to genotype a final set of 7714 polymorphisms across 1734 individuals. Five predictors were examined for their effect on the probability of obtaining an assayable SNP: depth of coverage, number of reads that support a variant, polymorphism type (e.g. A/C), strand-bias and Illumina SNP probe design score. Our results indicate that filtering out systematic sequencing errors could substantially improve the efficiency of SNP discovery. We show that BLASTX can be used as an efficient tool to identify single-copy genomic regions in the absence of a reference genome. The results have implications for research aiming to identify assayable SNPs and build SNP genotyping assays for nonmodel organisms.

Structural, Functional, and Taxonomic Diversity of Three PreQ1 Riboswitch Classes

Previously, two riboswitch classes have been identified that sense and respond to the hypermodified nucleobase called prequeuosine1 (preQ1). The enormous expansion of available genomic DNA sequence data creates new opportunities to identify additional representatives of the known riboswitch classes and to discover novel classes. We conducted bioinformatics searches on microbial genomic DNA data sets to discover numerous additional examples belonging to the two previously known riboswitch classes for preQ1 (classes preQ1-I and preQ1-II), including some structural variants that further restrict ligand specificity. Additionally, we discovered a third preQ1-binding riboswitch class (preQ1-III) that is structurally distinct from previously known classes. These findings demonstrate that numerous organisms monitor the concentrations of this modified nucleobase by exploiting one or more riboswitch classes for this widespread compound.

Integrated analysis of whole-genome paired-end and mate-pair sequencing data for identifying genomic structural variations in multiple myeloma.

We present a pipeline to perform integrative analysis of mate-pair (MP) and paired-end (PE) genomic DNA sequencing data. Our pipeline detects structural variations (SVs) by taking aligned sequencing read pairs as input and classifying these reads into properly paired and discordantly paired categories based on their orientation and inferred insert sizes. Recurrent SV was identified from the discordant read pairs. Our pipeline takes into account genomic annotation and genome repetitive element information to increase detection specificity. Application of our pipeline to whole-genome MP and PE sequencing data from three multiple myeloma cell lines (KMS11, MM.1S, and RPMI8226) recovered known SVs, such as heterozygous TRAF3 deletion, as well as a novel experimentally validated SPI1 – ZNF287 inter-chromosomal rearrangement in the RPMI8226 cell line.

Molecular and cellular pathology of very-long-chain acyl-CoA dehydrogenase deficiency

BackgroundVery-long-chain acyl-CoA dehydrogenase (VLCAD) deficiency (VLCADD) is diagnosed in the US through newborn screening (NBS). NBS often unequivocally identifies affected individuals, but a growing number of variant patterns can represent mild disease or heterozygous carriers. AimsTo evaluate the validity of standard diagnostic procedures for VLCADD by using functional in vitro tools. MethodsWe retrospectively investigated 13 patient samples referred to our laboratory because of a suspicion of VLCADD but with some uncertainty to the diagnosis. All 13 patients were suspected of having VLCADD either because of abnormal NBS or suggestive clinical findings. ACADVL genomic DNA sequencing data were available for twelve of them. Ten of the patients had an abnormal NBS suggestive of VLCADD, with three samples showing equivocal results. Three exhibited suggestive clinical findings and blood acylcarnitine profile (two of them had a normal NBS and the third one was unscreened). Assay of VLCAD activity and immunoblotting or immunohistologic staining for VLCAD were performed on fibroblasts. Prokaryotic mutagenesis and expression studies were performed for nine uncharacterized ACADVL missense mutations. ResultsVLCAD activity was abnormal in fibroblast cells from 9 patients (8 identified through abnormal NBS, 1 through clinical symptoms). For these 9 patients, immunoblotting/staining showed the variable presence of VLCAD; all but one had two mutated alleles. Two patients with equivocal NBS results (and a heterozygous genotype) and the two patients with normal NBS exhibited normal VLCAD activity and normal VLCAD protein on immunoblotting/staining thus ruling out VLCAD deficiency. Nine pathogenic missense mutations were characterized with prokaryotic expression studies and showed a decrease in enzyme activity and variable stability of VLCAD antigen. ConclusionsThese results emphasize the importance of functional investigation of abnormal NBS or clinical testing suggestive but not diagnostic of VLCADD. A larger prospective study is necessary to better define the clinical and metabolic ramifications of the defects identified in such patients.

Genome-wide identification, evolutionary and expression analyses of putative Fe–S biogenesis genes in rice (Oryza sativa)

Iron-sulfur (Fe-S) proteins are ubiquitous in nature and carry Fe-S clusters (ISCs) as prosthetic groups that are essential in maintaining basic biological processes such as photosynthesis, respiration, nitrogen fixation, and DNA repair. In the present investigation, a comprehensive genome-wide analysis was carried out to find all the genes involved in the formation of ISCs in rice ( Oryza sativa L.) through a systematic EST and genomic DNA sequence data mining. This analysis profiled 44 rice ISC genes (OsISCs) that were identified using in silico analysis. Multiple sequence alignment and phylogenetic analysis revealed that these genes were highly conserved among bacteria, fungi, animals, and plants. EST analysis and RT-PCR assays demonstrated that all OsISCs were active and that the transcript abundance of some OsISCs was tissue specific. The results of this study will assist further investigations to identify and elucidate the structural components involved in the assembly, biogenesis, and regulation of OsISCs. Thus, the outcome of the present study provides basic genomic information for the OsISC and will pave the way for elucidating the precise role of OsISCs in plant growth and development in the future. Also, it may enable us in the future to enhance the crop yield, uptake of Fe, and protection against abiotic and biotic stress.

The bovine genomic DNA sequence data reveal three IGHV subgroups, only one of which is functionally expressed

A comprehensive analysis of cattle shotgun sequencing data reveals 36 immunoglobulin heavy chain variable genes. The previously described bovine subgroup IGHV1 contains 10 functional genes with a conserved promoter including the consensus octamer and several other transcription factor binding sites, intact exons and matching cDNA sequences. Subgroups IGHV2 and IGHV3 consist entirely of pseudogenes. Thus, the bovine germline IGHV repertoire is very limited. The IGHV genes are distributed in mammalian clans I and II, while no clan III genes were detected. Clan-specific PCR of genomic DNA from cattle, sheep, Eurasian elk, white-tailed deer, pig and dolphin indicates highly dynamic evolution of IGHV gene usage within Cetartiodactyla. The bovine germline IGHV repertoire was probably generated by recent duplications of an IGHV1-IGHV2 homology unit. Immunoglobulin heavy chain genes are largely incorrectly assembled in the current cattle genome versions Btau_4.2 and UMD_3.1. FISH experiments confirm an IGHV locus close to terminus of BTA21.

Sequence conservation among orthologous vomeronasal type 1 receptor-like ( ora) genes does not support the differential tuning hypothesis in Salmonidae

Salmon utilize olfactory cues to guide natal stream homing during spawning migrations. Both inorganic and biogenic chemicals have been proposed as odorants that might be used by salmon during homing. In this study, we used genomic DNA sequence data from nine salmonid species to compare nucleotide identities for orthologous main olfactory receptor ( mOR) genes with nucleotide identities for orthologous vomeronasal type 1-like ( ora) receptor genes. We found that orthologs for both classes of olfactory receptor genes ( mORs and Oras) appear to be highly conserved among species. Our findings do not support the differential tuning hypothesis in Salmonidae, which predicts higher sequence conservation for mORs than ora. We did, however, find convincing evidence for site-specific positive selection acting on paralogous main olfactory receptor genes.

Abstract LB-249: Oncogene-mediated alterations in chromatin conformation

Abstract Emerging evidence suggests that the three-dimensional structure of chromosomes is not random but rather organized into compartments of open and closed chromatin and that this architectural organization plays a major role in gene regulation and genomic aberrations. There is evidence that transcription factors mediate chromatin topology and have been implicated in DNA breaks leading to genomic rearrangement. However, no study, to date, has described a comprehensive, genome-wide characterization of chromatin topological changes, gene regulation, and genomic alterations that can be attributed to oncogenic transcription factors. ETS rearranged prostate cancers, similar to other translocation tumors, represent a common and distinct molecular subclass of PCa based on studies demonstrating characteristic morphologic features, natural history and specific genomic and expression profiles. We hypothesize that ERG mediates specific alterations in chromatin structure that translates into changes in gene expression and genomic alterations in prostate cancer. We used next-generation DNA sequencing and chromosome conformation capture technology (Hi-C) to systematically map long-range chromatin interactions in the prostate cancer genomes of isogenic cell lines that differ in respect to ERG over-expression. Two biological replicate HiC samples were sequenced using five lanes of an Illumina GAIIx flow cell per cell line. After filtering, we obtained a total of roughly 20 million paired end sequence reads that corresponded to intra- and interchromosome interactions per cell line. We validated specific long-range interactions using targeted PCR from 3C libraries and using fluorescent in situ hybridization (FISH). In addition, we performed chromatin-immunoprecipitation with DNA sequencing (ChIPseq) and next generation RNA sequencing (RNA-seq) on the same cell lines to evaluate areas of ERG binding, determine the landscape of histone marks and quantify differential mRNA expression. We identified chromosomal interactions that appear to be dependent on ERG expression and these interactions are associated with ERG binding and changes in gene expression. Finally, we performed an integrative analysis of available whole genome DNA sequencing data (30 x coverage) from 7 prostate cancer samples (Berger et al., Nature 2011) and found associations between mapped genomic rearrangement, ERG binding and cell line specific long range chromosome interactions. Our study indicates, for the first time, that oncogenic transcription factors exert a broad effect on chromatin topology and associated gene regulation, and suggest that chromatin conformation predisposes the genome for later rearrangement events. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-249. doi:10.1158/1538-7445.AM2011-LB-249

Mapping copy number variation by population-scale genome sequencing

SummaryGenomic structural variants (SVs) are abundant in humans, differing from other variation classes in extent, origin, and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (i.e., copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analyzing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.

Editorial

There are some 200 organisms whose genomic sequences have been determined. Roughly 10% of those organisms are insects and this special issue of Insect Molecular Biology marks the publication of the genome sequence of the jewel wasp, Nasonia vitripennis, and its close relatives N. giraulti and N. longicornis. Although the costs and efforts associated with obtaining genomic DNA sequence data continues to decline as new technologies emerge, the value of these data remains high and will continue to do so in the future. Insect Molecular Biology is committed to serving the interests of the insect biological research community and believes there is great value in aggregating related research such as you will find in this special issue on the genome of Nasonia. Although demanding considerable effort from authors, referees, editors and publisher, with adequate planning and leadership special issues can be successfully assembled such that the whole is greater than the sum of its parts and the end product benefits all concerned. We would like to encourage other insect sequencing consortia that are possibly interested in aggregating the research results of their community of genome researchers in order to maximize the impact of their sequencing and analysis efforts to contact us about publication in Insect Molecular Biology. Our experience in publishing special issues devoted to single-organism genomics (honeybee, 2009; Nasonia, 2010; aphid, 2010) will help to ensure it is a successful venture.

The aldehyde dehydrogenase (ALDH) gene superfamily of the moss Physcomitrella patens and the algae Chlamydomonas reinhardtii and Ostreococcus tauri

The assembled Physcomitrella patens genome has been released. This provides a unique opportunity to identify and characterize new genes, and to compare moss genes with other plant genes from previously released plant genomes. Aldehyde dehydrogenases (ALDHs) comprise a protein superfamily of NAD(P) -dependent enzymes [EC 1.2.1] found in bacteria, animals and green plants capable of oxidizing a variety of aromatic and aliphatic aldehydes. ALDHs are key enzymes of abiotic stress-tolerance in a variety of organisms. In bryophytes, ALDHs are postulated to play a role in vegetative desiccation-tolerance. Using recently available genomic DNA sequence data, we have identified members of the ALDH gene superfamily in the marine picoeukaryote Ostreococcus tauri, the unicellular green algae Chlamydomonas reinhardtii and the moss Physcomitrella patens. The Arabidopsis thaliana genome has been shown to contain 14 unique ALDH sequences encoding members of nine ALDH protein families. The O. tauri genome contains six unique ALDH sequences encoding members of six ALDH protein families. The C. reinhardtii genome contains eight unique ALDH sequences encoding members of seven ALDH protein families. The P. patens genome contains 20 unique ALDH sequences encoding members of ten ALDH protein families. These three genomes encode members of ten previously identified protein families (ALDH2, ALDH3, ALDH5, ALDH6, ALDH7, ALDH10, ALDH11, ALDH12, ALDH21 and ALDH22) and two novel protein families (ALDH23 and ALDH24). We analyzed a sequence alignment of ALDH deduced amino acid sequences among plants using neighbor-joining and maximum parsimony methods. These analyses demonstrate that 1) at least eight ALDH protein families, as represented in the O. tauri and/or C. reinhardtii genomes were present prior to the evolution of land plants and each of these families have been maintained throughout land plant evolution, 2) novel ALDH families of as yet unknown function have evolved in several lineages of land plants including the mosses and flowering plants and 3) the moss P. patens exhibits a highly expanded set of sequences in three families, ALDH3, ALDH5 and ALDH11.

Polymorphic microsatellite loci for the common marmoset (Callithrix jacchus) designed using a cost‐ and time‐efficient method

We describe a cost- and time-efficient method for designing new microsatellite markers in any species with substantial genomic DNA sequence data available. Using this technique, we report 14 new polymorphic dinucleotide microsatellite loci isolated from the common marmoset. The relative yield of new polymorphisms was higher with less labor than described in previous marmoset studies. Of 20 loci initially evaluated, 14 were polymorphic and amplified reliably (70% success rate). The number of alleles ranged from 3 to 9 with heterozygosity varying from 0.48 to 0.83.

Molecular phylogeny of Pinanga (Palmae) based on internal transcribed spacers (ITS) sequence data

Molecular phylogeny of 52 species of Pinanga (Palmae) were investigated using the internal transcribed spacer (ITS) sequence data of nuclear ribosomal DNA. Polymorphic sequence data were identified in the ITS region of Pinanga, indicating that concerted evolution is not completely homogenizing ITS repeats in the nuclear genome. The strict consensus of Pinanga used in the study showed that the genus is monophyletic. Pinanga rivularis and P. aristata formed the basal clade; followed by P. albescens, P. brevipes, P. veitchii, P. sessilifolia and P. crassipes as sister taxa; and P. disticha, P. watanaiana, and P. pulchella were sister taxa to the clade containing the sampled species of Pinanga used in the study. In general, two major clades were recognized: first, Pinanga from Wallacea, East Malesia and adjacent region clade and second, Pinanga from West Malesia and adjacent region clade. The clade separation was strongly correspond with geographical distribution and it did not support infrageneric classification based on distichous and sprirally triads flower described by Beccari (1886). Conforming phylogenetic tree generated by ITS sequence data and morphological observations appear that habit, size and form of stem, leaf and inflorescence were not useful characters for infrageneric classification of Pinanga. Examination of phylogenetic relationships using combination of morphological characters including pollen morphology, cytological data, nuclear genome size and DNA sequence data are necessary for providing a more accurate picture of phylogenetic relationships and affords the opportunity to garner insights into evolutionary process of Pinanga.