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Here, we report the genome sequence of Tenacibaculum mesophilum strain ECR, which was isolated from the river/ocean interface at Trunk River in Falmouth, Massachusetts. The isolation and sequencing were performed as part of the 2016 and 2018 Microbial Diversity courses at the Marine Biological Laboratory in Woods Hole, Massachusetts.

An anaerobic methanotroph (ANME-2d) can perform nitrate-driven anaerobic oxidation of methane through reverse methanogenesis, using nitrate as the terminal electron acceptor, and nitrite produced by ANME-2d is reduced to dinitrogen gas through a syntrophic relationship with an anaerobic ammonium-oxidizing bacterium. Anaerobic link for carbon and nitrogen cycles Microbes capable of the anaerobic oxidation of methane (AOM) are important for controlling the flux of methane from anoxic marine sediments. Recent work has demonstrated AOM coupled to sulphate reduction in a consortium of ANME (anaerobic methanotrophic archaea) and sulphate-reducing bacteria, and coupled to nitrite reduction in consortia enriched with the bacterium Candidatus Methylomirabilis oxyfera and the novel ANME-2d lineage. Here Gene Tyson and colleagues show that a novel ANME-2d archaeon, which they name Candidatus Methanoperedens nitroreducens, is able to performing nitrate-driven AOM without a partner organism via reverse methanogenesis with nitrate as the terminal electron acceptor, using genes for nitrate reduction that have been laterally transferred from a bacterial donor. The authors speculate that ANME- 2d or Methanoperedenaceae lineage may have a pivotal role in linking the global carbon and nitrogen cycles in anoxic environments. Anaerobic oxidation of methane (AOM) is critical for controlling the flux of methane from anoxic environments. AOM coupled to iron.sup.1, manganese.sup.1 and sulphate.sup.2 reduction have been demonstrated in consortia containing anaerobic methanotrophic (ANME) archaea. More recently it has been shown that the bacterium Candidatus'Methylomirabilis oxyfera' can couple AOM to nitrite reduction through an intra-aerobic methane oxidation pathway.sup.3. Bioreactors capable of AOM coupled to denitrification have resulted in the enrichment of 'M. oxyfera' and a novel ANME lineage, ANME-2d.sup.4,5. However, as 'M. oxyfera' can independently couple AOM to denitrification, the role of ANME-2d in the process is unresolved. Here, a bioreactor fed with nitrate, ammonium and methane was dominated by a single ANME-2d population performing nitrate-driven AOM. Metagenomic, single-cell genomic and metatranscriptomic analyses combined with bioreactor performance and .sup.13C- and .sup.15N-labelling experiments show that ANME-2d is capable of independent AOM through reverse methanogenesis using nitrate as the terminal electron acceptor. Comparative analyses reveal that the genes for nitrate reduction were transferred laterally from a bacterial donor, suggesting selection for this novel process within ANME-2d. Nitrite produced by ANME-2d is reduced to dinitrogen gas through a syntrophic relationship with an anaerobic ammonium-oxidizing bacterium, effectively outcompeting 'M. oxyfera' in the system. We propose the name Candidatus 'Methanoperedens nitroreducens' for the ANME-2d population and the family Candidatus'Methanoperedenaceae' for the ANME-2d lineage. We predict that 'M. nitroreducens' and other members of the 'Methanoperedenaceae' have an important role in linking the global carbon and nitrogen cycles in anoxic environments., Author(s): Mohamed F. Haroon [sup.1] , Shihu Hu [sup.2] , Ying Shi [sup.2] , Michael Imelfort [sup.1] [sup.2] , Jurg Keller [sup.2] , Philip Hugenholtz [sup.1] [sup.3] , Zhiguo Yuan [...]

Association mapping currently relies on the identification of genetic markers. Several technologies have been adopted for genetic marker analysis, with single nucleotide polymorphisms (SNPs) being the most popular where a reasonable quantity of genome sequence data are available. We describe several tools we have developed for the discovery, annotation, and visualization of molecular markers for association mapping. These include autoSNPdb for SNP discovery from assembled sequence data; TAGdb for the identification of gene specific paired read Illumina GAII data; CMap3D for the comparison of mapped genetic and physical markers; and BAC and Gene Annotator for the online annotation of genes and genomic sequences. Key words: SNP discovery, association mapping, comparative genomics, second generation genome sequencing. L'analyse d'association repose presentement sur l'identification de marqueurs genetiques. Plusieurs technologies ont ete employees pour l'analyse de marqueurs genetiques, les polymorphismes mononucleeotidiques (SNP) etant les plus populaires la oil une information genomique suffisante etait disponible. Les auteurs decrivent plusieurs outils qu'ils ont deeveloppees pour l'identification, l'annotation et la visualisation des marqueurs moleeculaires pour des fins d'analyse d'association. Ceux-ci incluent autoSNPdb pour l'identification de SNP au sein de donneees de sequence, TAGdb pour l'identification d'etiquettes specifiques d'un gene au sein de collections d'etiquettes de sequence Illumina GAII, CMap3D pour la comparaison de marqueurs genetiques et physiques, et un annotateur de clones BAC et de genes pour effectuer l'annotation automatiseedegenes et de sequences geenomiques. Mots-cles: identification de SNP, analyse d'association, genomique comparee, sequencjage genomique de seconde geeneration., Introduction Association mapping is being driven by changes in technology that permit the discovery of large numbers of genetic variants and the screening for these genetic variations across large populations. [...]

Abstract Background The introduction of second generation sequencing technology has enabled the cost effective sequencing of genomes and the identification of large numbers of genes and gene promoters. However, the assembly of DNA sequences to create a representation of the complete genome sequence remains costly, especially for the larger and more complex plant genomes. Results We have developed an online database, TAGdb, that enables researchers to identify paired read sequences that share identity with a submitted query sequence. These tags can be used to design oligonucleotide primers for the PCR amplification of the region in the target genome. Conclusions The ability to produce large numbers of paired read genome tags using second generation sequencing provides a cost effective method for the identification of genes and promoters in large, complex or orphan species without the need for whole genome assembly.

Nature 500, 567-570(2013); doi:10.1038/nature12375 In this Letter, equation (1) was inadvertently shown incorrectly, with C[O.sub.2] missing from the reaction products. The correct equation (1) is shown below: C[H.sub.4] + 4N[O.sup.-.sub.3] [...]

Molecular surveys of aphotic habitats have indicated the presence of major uncultured lineages phylogenetically classified as members of the Cyanobacteria. One of these lineages has recently been proposed as a nonphotosynthetic sister phylum to the Cyanobacteria, the Melainabacteria, based on recovery of population genomes from human gut and groundwater samples. Here, we expand the phylogenomic representation of the Melainabacteria through sequencing of six diverse population genomes from gut and bioreactor samples supporting the inference that this lineage is nonphotosynthetic, but not the assertion that they are strictly fermentative. We propose that the Melainabacteria is a class within the phylogenetically defined Cyanobacteria based on robust monophyly and shared ancestral traits with photosynthetic representatives. Our findings are consistent with theories that photosynthesis occurred late in the Cyanobacteria and involved extensive lateral gene transfer and extends the recognized functionality of members of this phylum. [ABSTRACT FROM PUBLISHER]

Pongamia pinnata (syn. Millettia pinnata) is a novel, fast-growing arboreal legume that bears prolific quantities of oil-rich seeds suitable for the production of biodiesel and aviation biofuel. Here, we have used Illumina® ,Second Generation DNA Sequencing (2GS)' and a new short-read de novo assembler, SaSSY, to assemble and annotate the Pongamia chloroplast (152,968 bp; cpDNA) and mitochondrial (425,718 bp; mtDNA) genomes. We also show that SaSSY can be used to accurately assemble 2GS data, by re-assembling the Lotus japonicus cpDNA and in the process assemble its mtDNA (380,861 bp). The Pongamia cpDNA contains 77 unique protein-coding genes and is almost 60% gene-dense. It contains a 50 kb inversion common to other legumes, as well as a novel 6.5 kb inversion that is responsible for the non-disruptive, re-orientation of five protein-coding genes. Additionally, two copies of an inverted repeat firmly place the species outside the subclade of the Fabaceae lacking the inverted repeat. The Pongamia and L. japonicus mtDNA contain just 33 and 31 unique proteincoding genes, respectively, and like other angiosperm mtDNA, have expanded intergenic and multiple repeat regions. Through comparative analysis with Vigna radiata we measured the average synonymous and non-synonymous divergence of all three legume mitochondrial (1.59% and 2.40%, respectively) and chloroplast (8.37% and 8.99%, respectively) proteincoding genes. Finally, we explored the relatedness of Pongamia within the Fabaceae and showed the utility of the organellar genome sequences by mapping transcriptomic data to identify up- and down-regulated stress-responsive gene candidates and confirm in silico predicted RNA editing sites. [ABSTRACT FROM AUTHOR]

Summary The genome of bread wheat ( Triticum aestivum) is predicted to be greater than 16 Gbp in size and consist predominantly of repetitive elements, making the sequencing and assembly of this genome a major challenge. We have reduced genome sequence complexity by isolating chromosome arm 7DS and applied second-generation technology and appropriate algorithmic analysis to sequence and assemble low copy and genic regions of this chromosome arm. The assembly represents approximately 40% of the chromosome arm and all known 7DS genes. Comparison of the 7DS assembly with the sequenced genomes of rice ( Oryza sativa) and Brachypodium distachyon identified large regions of conservation. The syntenic relationship between wheat, B. distachyon and O. sativa, along with available genetic mapping data, has been used to produce an annotated draft 7DS syntenic build, which is publicly available at . Our results suggest that the sequencing of isolated chromosome arms can provide valuable information of the gene content of wheat and is a step towards whole-genome sequencing and variation discovery in this important crop. [ABSTRACT FROM AUTHOR]

The ongoing revolution in DNA sequencing technology now enables the reading of thousands of millions of nucleotide bases in a single instrument run. However, this data quantity is often compromised by poor confidence in the read quality. The identification of genetic polymorphisms from this data is therefore problematic and, combined with the vast quantity of data, poses a major bioinformatics challenge. However, once these difficulties have been addressed, next-generation sequencing will offer a means to identify and characterize the wealth of genetic polymorphisms underlying the vast phenotypic variation in biological systems. We describe the recent advances in next-generation sequencing technology, together with preliminary approaches that can be applied for single nucleotide polymorphism discovery in plant species. [ABSTRACT FROM AUTHOR]

Molecular markers are used to provide the link between genotype and phenotype, for the production of molecular genetic maps and to assess genetic diversity within and between related species. Single nucleotide polymorphisms (SNPs) are the most abundant molecular genetic marker. SNPs can be identified in silico, but care must be taken to ensure that the identified SNPs reflect true genetic variation and are not a result of errors associated with DNA sequencing. The SNP detection method autoSNP has been developed to identify SNPs from sequence data for any species. Confidence in the predicted SNPs is based on sequence redundancy, and haplotype co-segregation scores are calculated for a further independent measure of confidence. We have extended the autoSNP method to produce autoSNPdb, which integrates SNP and gene annotation information with a graphical viewer. We have applied this software to public barley expressed sequences, and the resulting database is available over the Internet. SNPs can be viewed and searched by sequence, functional annotation or predicted synteny with a reference genome, in this case rice. The correlation between SNPs and barley cultivar, expressed tissue type and development stage has been collated for ease of exploration. An average of one SNP per 240 bp was identified, with SNPs more prevalent in the 5′ regions and simple sequence repeat (SSR) flanking sequences. Overall, autoSNPdb can provide a wealth of genetic polymorphism information for any species for which sequence data are available. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented in response to the article which discusses the error-correction of amplicon pyrosequences with the use of the software Acacia.

Metagenomic binning methods that leverage differential population abundances in microbial communities (differential coverage) are emerging as a complementary approach to conventional composition-based binning. Here we introduce GroopM, an automated binning tool that primarily uses differential coverage to obtain high fidelity population genomes from related metagenomes. We demonstrate the effectiveness of GroopM using synthetic and real-world metagenomes, and show that GroopM produces results comparable with more time consuming, labor-intensive methods.

Sequence data is crucial to our understanding of crop growth and development, as differences in DNA sequence are responsible for almost all of the heritable differences between crop varieties and ecotypes. The sequence of a genome is often referred to as the genetic blueprint, and is the foundation for all additional information from the genome to the phenome. The value of DNA sequence is leading to rapid improvements in sequencing technology, increasing throughput, and reducing costs, and technological advances are accelerating with the introduction of novel approaches that are replacing the traditional Sanger-based methods. As genome sequencing becomes cheaper, it will be applied to a greater number of species with increasingly large and complex genomes. This will increase our understanding of how differences in the sequence relate to phenotypic observations, heritable traits, speciation, and evolution. Our understanding of plants will be greatly enhanced by this flow of sequence information, with direct benefit for crop improvement.