The Complete Plastid Genome Sequence of the Haptophyte Emiliania huxleyi: a Comparison to Other Plastid Genomes

The complete nucleotide sequence of the plastid genome of thehaptophyte Emiliania huxleyi has been determined. E. huxleyiis the most abundant coccolithophorid and has a key role inthe carbon cycle. It is also implicated in the production ofdimethylsulphide (DMS), which is involved in cloud nucleationand may affect the global climate. Here, we report the plastidgenome sequence of this ecologically and economically importantspecies and compare its gene content and arrangement to otherknown plastid genomes. The genome is circular and consists of105,309 bp with an inverted repeat of 4,841 bp. In terms ofboth genome size and gene content E. huxleyi cpDNA is substantiallysmaller than any other from the red plastid lineage. The geneticinformation is densely packed, with 86.8% of the genome specifying110 identified protein-coding genes, 9 open reading frames,28 different tRNAs, and 3 rRNAs. A detailed comparison to otherplastid genomes, based on gene content, gene function, and genecluster analysis is discussed. These analyses suggest a closerelationship of the E. huxleyi cpDNA to the chlorophyll c-containingplastids from heterokonts and cryptophytes, and they supportthe origin of the chromophyte plastids from the red algal lineage.     

Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida

In this study, we fully sequenced the circular plastid genome of a brown alga, Undaria pinnatifida. The genome is 130,383 base pairs (bp) in size; it contains a large single-copy (LSC, 76,598 bp) and a small single-copy region (SSC, 42,977 bp), separated by two inverted repeats (IRa and IRb: 5,404 bp). The genome contains 139 protein-coding, 28 tRNA, and 6 rRNA genes; none of these genes contains introns. Organization and gene contents of the U. pinnatifida plastid genome were similar to those of Saccharina japonica. There is a co-linear relationship between the plastid genome of U. pinnatifida and that of three previously sequenced large brown algal species. Phylogenetic analyses of 43 taxa based on 23 plastid protein-coding genes grouped all plastids into a red or green lineage. In the large brown algae branch, U. pinnatifida and S. japonica formed a sister clade with much closer relationship to Ectocarpus siliculosus than to Fucus vesiculosus. For the first time, the start codon ATT was identified in the plastid genome of large brown algae, in the atpA gene of U. pinnatifida. In addition, we found a gene-length change induced by a 3-bp repetitive DNA in ycf35 and ilvB genes of the U. pinnatifida plastid genome.     

Complete Genome Sequence of Borrelia afzelii K78 and Comparative Genome Analysis

The main Borrelia species causing Lyme borreliosis in Europe and Asia are Borrelia afzelii, B. garinii, B. burgdorferi and B. bavariensis. This is in contrast to the United States, where infections are exclusively caused by B. burgdorferi. Until to date the genome sequences of four B. afzelii strains, of which only two include the numerous plasmids, are available. In order to further assess the genetic diversity of B. afzelii, the most common species in Europe, responsible for the large variety of clinical manifestations of Lyme borreliosis, we have determined the full genome sequence of the B. afzelii strain K78, a clinical isolate from Austria. The K78 genome contains a linear chromosome (905,949 bp) and 13 plasmids (8 linear and 5 circular) together presenting 1,309 open reading frames of which 496 are located on plasmids. With the exception of lp28-8, all linear replicons in their full length including their telomeres have been sequenced. The comparison with the genomes of the four other B. afzelii strains, ACA-1, PKo, HLJ01 and Tom3107, as well as the one of B. burgdorferi strain B31, confirmed a high degree of conservation within the linear chromosome of B. afzelii, whereas plasmid encoded genes showed a much larger diversity. Since some plasmids present in B. burgdorferi are missing in the B. afzelii genomes, the corresponding virulence factors of B. burgdorferi are found in B. afzelii on other unrelated plasmids. In addition, we have identified a species specific region in the circular plasmid, cp26, which could be used for species determination. Different non-coding RNAs have been located on the B. afzelii K78 genome, which have not previously been annotated in any of the published Borrelia genomes.     

Complete Chloroplast Genome Sequence of <Emphasis Type="Italic">Glycine max</Emphasis> and Comparative Analyses with other Legume Genomes

Lack of complete chloroplast genome sequences is still one of the major limitations to extending chloroplast genetic engineering technology to useful crops. Therefore, we sequenced the soybean chloroplast genome and compared it to the other completely sequenced legumes, Lotus and Medicago. The chloroplast genome of Glycine is 152,218 basepairs (bp) in length, including a pair of inverted repeats of 25,574 bp of identical sequence separated by a small single copy region of 17,895 bp and a large single copy region of 83,175 bp. The genome contains 111 unique genes, and 19 of these are duplicated in the inverted repeat (IR). Comparisons of Glycine, Lotus and Medicago confirm the organization of legume chloroplast genomes based on previous studies. Gene content of the three legumes is nearly identical. The rpl22 gene is missing from all three legumes, and Medicago is missing rps16 and one copy of the IR. Gene order in Glycine, Lotus, and Medicago differs from the usual gene order for angiosperm chloroplast genomes by the presence of a single, large inversion of 51 kilobases (kb). Detailed analyses of repeated sequences indicate that many of the Glycine repeats that are located in the intergenic spacer regions and introns occur in the same location in the other legumes and in Arabidopsis, suggesting that they may play some functional role. The presence of small repeats of psbA and rbcL in legumes that have lost one copy of the IR indicate that this loss has only occurred once during the evolutionary history of legumes.     

The Complete Genome Sequence of the Pathogenic Intestinal Spirochete Brachyspira pilosicoli and Comparison with Other Brachyspira Genomes

Background

The anaerobic spirochete Brachyspira pilosicoli colonizes the large intestine of various species of birds and mammals, including humans. It causes “intestinal spirochetosis”, a condition characterized by mild colitis, diarrhea and reduced growth. This study aimed to sequence and analyse the bacterial genome to investigate the genetic basis of its specialized ecology and virulence.

Methodology/Principal Findings

The genome of B. pilosicoli 95/1000 was sequenced, assembled and compared with that of the pathogenic Brachyspira hyodysenteriae and a near-complete sequence of Brachyspira murdochii. The B. pilosicoli genome was circular, composed of 2,586,443 bp with a 27.9 mol% G+C content, and encoded 2,338 genes. The three Brachyspira species shared 1,087 genes and showed evidence of extensive genome rearrangements. Despite minor differences in predicted protein functional groups, the species had many similar features including core metabolic pathways. Genes distinguishing B. pilosicoli from B. hyodysenteriae included those for a previously undescribed bacteriophage that may be useful for genetic manipulation, for a glycine reductase complex allowing use of glycine whilst protecting from oxidative stress, and for aconitase and related enzymes in the incomplete TCA cycle, allowing glutamate synthesis and function of the cycle during oxidative stress. B. pilosicoli had substantially fewer methyl-accepting chemotaxis genes than B. hyodysenteriae and hence these species are likely to have different chemotactic responses that may help to explain their different host range and colonization sites. B. pilosicoli lacked the gene for a new putative hemolysin identified in B. hyodysenteriae WA1. Both B. pilosicoli and B. murdochii lacked the rfbBADC gene cluster found on the B. hyodysenteriae plasmid, and hence were predicted to have different lipooligosaccharide structures. Overall, B. pilosicoli 95/1000 had a variety of genes potentially contributing to virulence.

Conclusions/Significance

The availability of the complete genome sequence of B. pilosicoli 95/1000 will facilitate functional genomics studies aimed at elucidating host-pathogen interactions and virulence.     

Sequence of the Tomato Chloroplast DNA and Evolutionary Comparison of Solanaceous Plastid Genomes

Tomato, Solanum lycopersicum (formerly Lycopersicon esculentum), has long been one of the classical model species of plant genetics. More recently, solanaceous species have become a model of evolutionary genomics, with several EST projects and a tomato genome project having been initiated. As a first contribution toward deciphering the genetic information of tomato, we present here the complete sequence of the tomato chloroplast genome (plastome). The size of this circular genome is 155,461 base pairs (bp), with an average AT content of 62.14%. It contains 114 genes and conserved open reading frames (ycfs). Comparison with the previously sequenced plastid DNAs of Nicotiana tabacum and Atropa belladonna reveals patterns of plastid genome evolution in the Solanaceae family and identifies varying degrees of conservation of individual plastid genes. In addition, we discovered several new sites of RNA editing by cytidine-to-uridine conversion. A detailed comparison of editing patterns in the three solanaceous species highlights the dynamics of RNA editing site evolution in chloroplasts. To assess the level of intraspecific plastome variation in tomato, the plastome of a second tomato cultivar was sequenced. Comparison of the two genotypes (IPA-6, bred in South America, and Ailsa Craig, bred in Europe) revealed no nucleotide differences, suggesting that the plastomes of modern tomato cultivars display very little, if any, sequence variation. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Rüdiger Cerff]     

Complete Genome Sequence and Comparative Genomics of a Novel Myxobacterium Myxococcus hansupus

Myxobacteria, a group of Gram-negative aerobes, belong to the class δ-proteobacteria and order Myxococcales. Unlike anaerobic δ-proteobacteria, they exhibit several unusual physiogenomic properties like gliding motility, desiccation-resistant myxospores and large genomes with high coding density. Here we report a 9.5 Mbp complete genome of Myxococcus hansupus that encodes 7,753 proteins. Phylogenomic and genome-genome distance based analysis suggest that Myxococcus hansupus is a novel member of the genus Myxococcus. Comparative genome analysis with other members of the genus Myxococcus was performed to explore their genome diversity. The variation in number of unique proteins observed across different species is suggestive of diversity at the genus level while the overrepresentation of several Pfam families indicates the extent and mode of genome expansion as compared to non-Myxococcales δ-proteobacteria.     

The Complete Chloroplast Genome of Guadua angustifolia and Comparative Analyses of Neotropical-Paleotropical Bamboos

To elucidate chloroplast genome evolution within neotropical-paleotropical bamboos, we fully characterized the chloroplast genome of the woody bamboo Guadua angustifolia. This genome is 135,331 bp long and comprises of an 82,839-bp large single-copy (LSC) region, a 12,898-bp small single-copy (SSC) region, and a pair of 19,797-bp inverted repeats (IRs). Comparative analyses revealed marked conservation of gene content and sequence evolutionary rates between neotropical and paleotropical woody bamboos. The neotropical herbaceous bamboo Cryptochloa strictiflora differs from woody bamboos in IR/SSC boundaries in that it exhibits slightly contracted IRs and a faster substitution rate. The G. angustifolia chloroplast genome is similar in size to that of neotropical herbaceous bamboos but is ~3 kb smaller than that of paleotropical woody bamboos. Dissimilarities in genome size are correlated with differences in the lengths of intergenic spacers, which are caused by large-fragment insertion and deletion. Phylogenomic analyses of 62 taxa yielded a tree topology identical to that found in preceding studies. Divergence time estimation suggested that most bamboo genera diverged after the Miocene and that speciation events of extant species occurred during or after the Pliocene.     

Complete Genome Sequence of Mycobacterium massiliense

Mycobacterium massiliense is a rapidly growing bacterium associated with opportunistic infections. The genome of a representative isolate (strain GO 06) recovered from wound samples from patients who underwent arthroscopic or laparoscopic surgery was sequenced. To the best of our knowledge, this is the first announcement of the complete genome sequence of an M. massiliense strain.     

Comparative Analysis of the Complete Plastid Genome Sequence of the Red Alga Gracilaria tenuistipitata var. liui Provides Insights into the Evolution of Rhodoplasts and Their Relationship to Other Plastids

We sequenced to completion the circular plastid genome of the red alga Gracilaria tenuistipitata var. liui. This is the first plastid genome sequence from the subclass Florideophycidae (Rhodophyta). The genome is composed of 183,883 bp and contains 238 predicted genes, including a single copy of the ribosomal RNA operon. Comparisons with the plastid genome of Porphyra pupurea reveal strong conservation of gene content and order, but we found major genomic rearrangements and the presence of coding regions that are specific to Gracilaria. Phylogenetic analysis of a data set of 41 concatenated proteins from 23 plastid and two cyanobacterial genomes support red algal plastid monophyly and a specific evolutionary relationship between the Florideophycidae and the Bangiales. Gracilaria maintains a surprisingly ancient gene content in its plastid genome and, together with other Rhodophyta, contains the most complete repertoire of plastid genes known in photosynthetic eukaryotes.Supplementary material () is available for this article.[Reviewing Editor: Dr. W. Ford Doolittle]     

Complete Genome Sequence of Beijerinckia indica subsp. indica

Beijerinckia indica subsp. indica is an aerobic, acidophilic, exopolysaccharide-producing, N₂-fixing soil bacterium. It is a generalist chemoorganotroph that is phylogenetically closely related to facultative and obligate methanotrophs of the genera Methylocella and Methylocapsa. Here we report the full genome sequence of this bacterium.Beijerinckia indica subsp. indica ATCC 9039 is the type strain of the genus Beijerinckia (6), a member of the Rhizobiales order of the Alphaproteobacteria. Beijerinckia spp. are commonly found as free-living bacteria in acidic soils and also in plant rhizosphere and phyllosphere environments (4). Research on Beijerinckia has suffered from chronic taxonomic confusion, with some strains of Sphingomonas and Azotobacter being misidentified in the literature: e.g., a “Beijerinckia” reported to degrade PAH has been reclassified (3). However, some Beijerinckia spp. have received research attention due to their plant growth-promoting properties (7) and for their abundant production of exoheteropolysaccharide with potential biotechnological uses (5).Genomic DNA from Beijerinckia indica subsp. indica was used to create 3-kb, 8-kb, and 40-kb DNA libraries. Sequencing, assembly, and automated annotation were performed at the Joint Genome Institute using standard procedures (U.S. Department of Energy; http://www.jgi.doe.gov/sequencing/strategy.html). The total number of paired-end shotgun Sanger reads in the assembly was 33,870. In addition, Roche 454 sequence data were included into the final assembly. Large Newbler contigs of 454 reads were chopped into 4,975 overlapping fragments of 1,000 bp and entered into the assembly as pseudoreads.The genome of B. indica subsp. indica was 4,170,153 bp. In addition, two plasmids of 181,736 and 66,727 bp were present. There are a total of 3,982 open reading frames (ORFs) predicted using Glimmer, of which 3,784 are predicted protein-coding genes and 2,695 (70%) have been assigned a predicted function. There are 134 pseudogenes, 52 tRNA genes, and three operons each containing 16S, 23S, and 5S rRNA genes. The G+C content is 57.0% (56% and 54% in the plasmids).The bacterium lacks phosphofructokinase, the key enzyme of the Embden-Meyerhof pathway. Instead, it uses the Entner-Doudoroff or pentose phosphate pathway to catabolize sugars, which is typical of free-living Rhizobiales. The majority of the genes involved in N₂ fixation are clustered in two genomic islands (10 kb and 51 kb), with the notable exception of the nifS gene encoding cysteine desulfurase.Beijerinckia indica is a metabolically versatile bacterium capable of growth on a variety of organic acids, sugars, and alcohols (4). In contrast, its close phylogenetic cousins Methylocella and Methylocapsa are highly specialized methanotrophs capable of growth on very few substrates (2). However, the genome size of Beijerinckia indica compared to that of Methylocella silvestris (4.17 versus 4.30 Mbp) and the numbers of predicted protein-encoding genes (3,788 versus 3,917) are remarkably similar. A BLAST analysis indicated that the 57% of the genes in the genome of B. indica have homologues in M. silvestris (stringency threshold expectation value [E] of 1e−50). Some key pathways of one-carbon metabolism (such as the tetrahydromethanopterin and serine pathways of formaldehyde metabolism) that are present in M. silvestris appear to be absent or incomplete in B. indica, which confirms previous experiments showing that the organism is incapable of methylotrophic growth (1). However, an operon encoding a putative propane monooxygenase homologous to soluble propane/methane monooxygenases of Methylocella silvestris BL2 was identified. More in-depth comparison of these genomes will help elucidate what defines their distinct lifestyles.     

Complete Genome Sequence of Anaplasma marginale subsp. centrale

Anaplasma marginale subsp. centrale is a naturally attenuated subtype that has been used as a vaccine for a century. We sequenced the genome of this organism and compared it to those of virulent senso stricto A. marginale strains. The comparison markedly narrows the number of outer membrane protein candidates for development of a safer inactivated vaccine and provides insight into the diversity among strains of senso lato A. marginale.Sir Arnold Theiler described Anaplasma marginale as the “cause of a specific tick-borne disease of cattle” in 1908 (14), providing the first identification of a rickettsial pathogen. Two years later, Theiler isolated a less virulent organism, which he designated A. marginale subtype centrale (15). This naturally attenuated strain has been used as a live vaccine to prevent severe disease due to A. marginale senso stricto strains for 100 years. Understanding the genetic similarities and differences between the vaccine strain and wild-type A. marginale strains will provide clues as to how the vaccine provides protection. To that end, we have sequenced the A. marginale subsp. centrale vaccine strain using a whole-genome shotgun sequencing strategy.Genomic DNA, obtained from Kimron Veterinary institute, was fragmented by hydroshearing and ligated into pSmartLCKan (Lucigen). A total of 10,752 paired-end sequence reads (∼6.5× coverage) were generated. Assembly with Phrap (www.phrap.org) resulted in 148 contigs. Closure was achieved by applying the genome walking method across gap-spanning subclones and genomic DNA amplicons. For polymorphic loci, the most frequently observed subclone sequence was selected.Coding sequences (CDSs) in the single, circular, 1,206,806-bp chromosome were predicted using Glimmer2 and Glimmer3 (4, 5, 12). Annotation was as described previously for A. marginale senso stricto genomes (2, 3). There are 925 predicted CDSs, 19 pseudogenes, 37 tRNA genes, and a single set of rRNA genes in the genome. A. marginale subsp. centrale contains 10 putative genes not found in the closed-core genomes of senso stricto strains (3). Similarly, 18 genes found in senso stricto strains are absent from A. marginale subsp. centrale. This divergence is consistent with the subspecies nomenclature (15), but the findings do not resolve whether these genetic differences warrant classification of the vaccine strain as a distinct species within the genus Anaplasma (6).The ability of live A. marginale subsp. centrale to protect against a diversity of A. marginale strains indicates that epitopes critical for protective immunity are broadly conserved (11). As immunity against A. marginale can be induced by immunization with purified outer membrane protein (OMP) complexes (8-10, 13), identification of OMPs conserved between A. marginale subsp. centrale and senso stricto A. marginale may narrow the vaccine candidate list. A. marginale OMPs cluster predominately into two protein superfamilies, major surface protein 1 (Msp1) and Pfam01617/Msp2 (2). Members of the Msp1 superfamily from senso stricto strains (1, 2) are not well conserved (e.g., Msp1a, Msp1b-1, Msp1b-2, and Mlp2 to Mlp4; 13 to 48% amino acid identity) or are nonexistent (e.g., the products of Msp1b partial genes 1 to 3) in A. marginale subsp. centrale, suggesting that immunity induced by the live vaccine strain is unlikely to be associated with the Msp1 superfamily.Comparative analysis of the Pfam01617/Msp2 superfamily (2, 8) reveals both conservation and diversity. OpAG1 to OpAG3 and Msp4 are generally well conserved, while the family comprising Omp1 to Omp15 found in senso stricto strains (2, 3, 8) is reduced in A. marginale subsp. centrale: genes for the closely related proteins Omp7 to Omp9 are collapsed into a single CDS, and genes for homologs of Omp2, Omp3, Omp6, and Omp15 are missing. The OMP complex capable of inducing protective immunity contains 11 proteins (7, 8). By excluding those without homologs in the vaccine strain and the highly variable Msp2 and Msp3, the number of candidates is narrowed to six: four Msp2 superfamily members (Msp4, Omp1, Omp7, and OpAG2) and two non-superfamily members (AM779/ACIS557 and AM854/ACIS486). The degree of identity among these candidates from the vaccine strain and senso stricto A. marginale strains ranges from 63% (for OpAG2 proteins) to 88% (for Msp4 homologs). While the next steps in vaccine development will require strain analysis for epitope conservation in these candidates and immunization trials to test in vivo efficacy, progress will be accelerated using the minimal candidate list defined by the comparative genomics approach.     

Complete Genome Sequence and Comparative Metabolic Profiling of the Prototypical Enteroaggregative Escherichia coli Strain 042

Background

Escherichia coli can experience a multifaceted life, in some cases acting as a commensal while in other cases causing intestinal and/or extraintestinal disease. Several studies suggest enteroaggregative E. coli are the predominant cause of E. coli-mediated diarrhea in the developed world and are second only to Campylobacter sp. as a cause of bacterial-mediated diarrhea. Furthermore, enteroaggregative E. coli are a predominant cause of persistent diarrhea in the developing world where infection has been associated with malnourishment and growth retardation.

Methods

In this study we determined the complete genomic sequence of E. coli 042, the prototypical member of the enteroaggregative E. coli, which has been shown to cause disease in volunteer studies. We performed genomic and phylogenetic comparisons with other E. coli strains revealing previously uncharacterised virulence factors including a variety of secreted proteins and a capsular polysaccharide biosynthetic locus. In addition, by using Biolog™ Phenotype Microarrays we have provided a full metabolic profiling of E. coli 042 and the non-pathogenic lab strain E. coli K-12. We have highlighted the genetic basis for many of the metabolic differences between E. coli 042 and E. coli K-12.

Conclusion

This study provides a genetic context for the vast amount of experimental and epidemiological data published thus far and provides a template for future diagnostic and intervention strategies.     

Comparative Analysis of Begonia Plastid Genomes and Their Utility for Species-Level Phylogenetics

Recent, rapid radiations make species-level phylogenetics difficult to resolve. We used a multiplexed, high-throughput sequencing approach to identify informative genomic regions to resolve phylogenetic relationships at low taxonomic levels in Begonia from a survey of sixteen species. A long-range PCR method was used to generate draft plastid genomes to provide a strong phylogenetic backbone, identify fast evolving regions and provide informative molecular markers for species-level phylogenetic studies in Begonia.     

科学家完成金小蜂基因组测序

<正>近日,美国罗切斯特大学生物学教授John H.Werren和贝勒医学院基因组测序中心的Stephen Richards领导完成了3种寄生性金小蜂(Nasonia vitripennis,N.giraulti和N.longicornis)的基因组测序。这一成果揭示     

Complete Plastid Genome Sequencing of Four Tilia Species (Malvaceae): A Comparative Analysis and Phylogenetic Implications

Tilia is an ecologically and economically important genus in the family Malvaceae. However, there is no complete plastid genome of Tilia sequenced to date, and the taxonomy of Tilia is difficult owing to frequent hybridization and polyploidization. A well-supported interspecific relationships of this genus is not available due to limited informative sites from the commonly used molecular markers. We report here the complete plastid genome sequences of four Tilia species determined by the Illumina technology. The Tilia plastid genome is 162,653 bp to 162,796 bp in length, encoding 113 unique genes and a total number of 130 genes. The gene order and organization of the Tilia plastid genome exhibits the general structure of angiosperms and is very similar to other published plastid genomes of Malvaceae. As other long-lived tree genera, the sequence divergence among the four Tilia plastid genomes is very low. And we analyzed the nucleotide substitution patterns and the evolution of insertions and deletions in the Tilia plastid genomes. Finally, we build a phylogeny of the four sampled Tilia species with high supports using plastid phylogenomics, suggesting that it is an efficient way to resolve the phylogenetic relationships of this genus.     

Complete Sequence and Comparative Analysis of the Chloroplast Genome of Coconut Palm (Cocos nucifera)

Coconut, a member of the palm family (Arecaceae), is one of the most economically important trees used by mankind. Despite its diverse morphology, coconut is recognized taxonomically as only a single species (Cocos nucifera L.). There are two major coconut varieties, tall and dwarf, the latter of which displays traits resulting from selection by humans. We report here the complete chloroplast (cp) genome of a dwarf coconut plant, and describe the gene content and organization, inverted repeat fluctuations, repeated sequence structure, and occurrence of RNA editing. Phylogenetic relationships of monocots were inferred based on 47 chloroplast protein-coding genes. Potential nodes for events of gene duplication and pseudogenization related to inverted repeat fluctuation were mapped onto the tree using parsimony criteria. We compare our findings with those from other palm species for which complete cp genome sequences are available.     

The Complete Genome Sequence of Methanobrevibacter sp. AbM4

Methanobrevibacter sp. AbM4 was originally isolated from the abomasal contents of a sheep and was chosen as a representative of the Methanobrevibacter wolinii clade for genome sequencing. The AbM4 genome is smaller than that of the rumen methanogen M. ruminantium M1 (2.0 Mb versus 2.93 Mb), encodes fewer open reading frames (ORFs) (1,671 versus 2,217) and has a lower G+C percentage (29% versus 33%). Overall, the composition of the AbM4 genome is very similar to that of M1 suggesting that the methanogenesis pathway and central metabolism of these strains are highly similar, and both organisms are likely to be amenable to inhibition by small molecule inhibitors and vaccine-based methane mitigation technologies targeting these conserved features. The main differences compared to M1 are that AbM4 has a complete coenzyme M biosynthesis pathway and does not contain a prophage or non-ribosomal peptide synthase genes. However, AbM4 has a large CRISPR region and several type I and type II restriction-modification system components. Unusually, DNA-directed RNA polymerase B′ and B′′ subunits of AbM4 are joined, a feature only previously observed in some thermophilic archaea. AbM4 has a much reduced complement of genes encoding adhesin-like proteins which suggests it occupies a ruminal niche different from that of M1.