Genome of Mycoplasma haemofelis, unraveling its strategies for survival and persistence

Mycoplasma haemofelis is a mycoplasmal pathogen (hemoplasma) that attaches to the host's erythrocytes. Distributed worldwide, it has a significant impact on the health of cats causing acute disease and, despite treatment, establishing chronic infection. It might also have a role as a zoonotic agent, especially in immunocompromised patients. Whole genome sequencing and analyses of M. haemofelis strain Ohio2 was undertaken as a step toward understanding its survival and persistence. Metabolic pathways are reduced, relying on the host to supply many of the nutrients and metabolites needed for survival. M. haemofelis must import glucose for ATP generation and ribose derivates for RNA/DNA synthesis. Hypoxanthine, adenine, guanine, uracil and CMP are scavenged from the environment to support purine and pyrimidine synthesis. In addition, nicotinamide, amino acids and any vitamins needed for growth, must be acquired from its environment. The core proteome of M. haemofelis contains an abundance of paralogous gene families, corresponding to 70.6% of all the CDSs. This "paralog pool" is a rich source of different antigenic epitopes that can be varied to elude the host's immune system and establish chronic infection. M. haemofelis also appears to be capable of phase variation, which is particularly relevant to the cyclic bacteremia and persistence, characteristics of the infection in the cat. The data generated herein should be of great use for understanding the mechanisms of M. haemofelis infection. Further, it will provide new insights into its pathogenicity and clues needed to formulate media to support the in vitro cultivation of M. haemofelis

Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis

<p>Abstract</p> <p>Background</p> <p>Extensive DNA rearrangement of genic colinearity, as revealed by comparison of orthologous genomic regions, has been shown to be a general concept describing evolutionary dynamics of plant genomes. However, the nature, timing, lineages and adaptation of local genomic rearrangement in closely related species (<it>e.g</it>., within a genus) and haplotype variation of genomic rearrangement within populations have not been well documented.</p> <p>Results</p> <p>We previously identified a hotspot for genic rearrangement and transposon accumulation in the <it>Orp </it>region of Asian rice (<it>Oryza sativa</it>, AA) by comparison with its orthologous region in sorghum. Here, we report the comparative analysis of this region with its orthologous regions in the wild progenitor species (<it>O. nivara</it>, AA) of Asian rice and African rice (<it>O. glaberrima</it>) using the BB genome <it>Oryza </it>species (<it>O. punctata</it>) as an outgroup, and investigation of transposon insertion sites and a segmental inversion event in the AA genomes at the population level. We found that <it>Orp </it>region was primarily and recently expanded in the Asian rice species <it>O. sativa </it>and <it>O. nivara</it>. LTR-retrotransposons shared by the three AA-genomic regions have been fixed in all the 94 varieties that represent different populations of the AA-genome species/subspecies, indicating their adaptive role in genome differentiation. However, LTR-retrotransposons unique to either <it>O. nivara </it>or <it>O. sativa </it>regions exhibited dramatic haplotype variation regarding their presence or absence between or within populations/subpopulations.</p> <p>Conclusions</p> <p>The LTR-retrotransposon insertion hotspot in the <it>Orp </it>region was formed recently, independently and concurrently in different AA-genome species, and that the genic rearrangements detected in different species appear to be differentially triggered by transposable elements. This region is located near the end of the short arm of chromosome 8 and contains a high proportion of LTR-retrotransposons similar to observed in the centromeric region of this same chromosome, and thus may represent a genomic region that has recently switched from euchromatic to heterochromatic states. The haplotype variation of LTR-retrotransposon insertions within this region reveals substantial admixture among various subpopulations as established by molecular markers at the whole genome level, and can be used to develop retrotransposon junction markers for simple and rapid classification of <it>O. sativa </it>germplasm.</p

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs) in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75%) of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR) retrotransposon class of retroelements, with >400 families (>350 newly discovered) contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families) and LINEs (at least 30 families), were observed to contribute 1,991 and ∼35,000 copies, respectively, or a combined ∼1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all) medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to differentially occupy and exploit this genomic diversity

Complete Genome Sequence of Mycoplasma suis and Insights into Its Biology and Adaption to an Erythrocyte Niche

Mycoplasma suis, the causative agent of porcine infectious anemia, has never been cultured in vitro and mechanisms by which it causes disease are poorly understood. Thus, the objective herein was to use whole genome sequencing and analysis of M. suis to define pathogenicity mechanisms and biochemical pathways. M. suis was harvested from the blood of an experimentally infected pig. Following DNA extraction and construction of a paired end library, whole-genome sequencing was performed using GS-FLX (454) and Titanium chemistry. Reads on paired-end constructs were assembled using GS De Novo Assembler and gaps closed by primer walking; assembly was validated by PFGE. Glimmer and Manatee Annotation Engine were used to predict and annotate protein-coding sequences (CDS). The M. suis genome consists of a single, 742,431 bp chromosome with low G+C content of 31.1%. A total of 844 CDS, 3 single copies, unlinked rRNA genes and 32 tRNAs were identified. Gene homologies and GC skew graph show that M. suis has a typical Mollicutes oriC. The predicted metabolic pathway is concise, showing evidence of adaptation to blood environment. M. suis is a glycolytic species, obtaining energy through sugars fermentation and ATP-synthase. The pentose-phosphate pathway, metabolism of cofactors and vitamins, pyruvate dehydrogenase and NAD+ kinase are missing. Thus, ribose, NADH, NADPH and coenzyme A are possibly essential for its growth. M. suis can generate purines from hypoxanthine, which is secreted by RBCs, and cytidine nucleotides from uracil. Toxins orthologs were not identified. We suggest that M. suis may cause disease by scavenging and competing for host' nutrients, leading to decreased life-span of RBCs. In summary, genome analysis shows that M. suis is dependent on host cell metabolism and this characteristic is likely to be linked to its pathogenicity. The prediction of essential nutrients will aid the development of in vitro cultivation systems

Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome

Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on ∼1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses

Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5A(m).

Sequencing of a contiguous 215-kb interval of Triticum monococcum showed the presence of five genes in the same order as in previously sequenced colinear barley and rice BACs. Gene 2 was in the same orientation in wheat and rice but inverted in barley. Gene density in this region was 1 gene per 43 kb and the ratio of physical to genetic distance was estimated to be 2,700 kb cM(-1). Twenty more-or-less intact retrotransposons were found in the intergenic regions, covering at least 70% of the sequenced region. The insertion times of 11 retrotransposons were less than 5 million years ago and were consistent with their nested structure. Five new families of retro-elements and the first full-length elements for two additional retrotransposon families were discovered in this region. Significantly higher values of GC content were observed for Triticeae BACs compared with rice BACs. Relative enrichment or depletion of certain dinucleotides was observed in the comparison of introns, exons and retrotransposons. A higher proportion of transitions in CG and CNG sites that are targets for cytosine methylation was observed in retrotransposons (76%) than in introns (37%). These results showed that the wheat genome is a complex mixture of different sequence elements, but with general patterns of content and interspersion that are similar to those seen in maize and barley

Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5A(m).

Sequencing of a contiguous 215-kb interval of Triticum monococcum showed the presence of five genes in the same order as in previously sequenced colinear barley and rice BACs. Gene 2 was in the same orientation in wheat and rice but inverted in barley. Gene density in this region was 1 gene per 43 kb and the ratio of physical to genetic distance was estimated to be 2,700 kb cM(-1). Twenty more-or-less intact retrotransposons were found in the intergenic regions, covering at least 70% of the sequenced region. The insertion times of 11 retrotransposons were less than 5 million years ago and were consistent with their nested structure. Five new families of retro-elements and the first full-length elements for two additional retrotransposon families were discovered in this region. Significantly higher values of GC content were observed for Triticeae BACs compared with rice BACs. Relative enrichment or depletion of certain dinucleotides was observed in the comparison of introns, exons and retrotransposons. A higher proportion of transitions in CG and CNG sites that are targets for cytosine methylation was observed in retrotransposons (76%) than in introns (37%). These results showed that the wheat genome is a complex mixture of different sequence elements, but with general patterns of content and interspersion that are similar to those seen in maize and barley