Chromosomal evolution in naked catfishes (Bagridae,Siluriformes): A comparative chromosome mapping study

We analyzed the distribution of repetitive DNA sequences on the chromosomes of nine species of the Bagridae from Thailand, i.e., Hemibagrus filamentus; H. nemurus; H. wyckii; H. wyckioides; Mystus atrifasciatus; M. multiradiatus; M. mysticetus; M. bocourti and Pseudomystus siamensis. Two classes of microsatellites and one transposable element (TE) were mapped by fluorescence in situ hybridization. The distribution of the repetitive sequences was comparatively analyzed in view to investigate their contribution in the chromosomal evolution of this fish group. In all species the microsatellites (CA)₁₅ and (GA)₁₅ are abundantly distributed in all chromosomes, usually in the telomeric regions. The retrotransposable element Rex 1 is widely distributed over the whole genome including heterochromatin and euchromatin, but with an unexpected accumulation in one chromosome pair in some species. In fact, some species–specific patterns could be observed considering both microsatellites and TE distribution. The results demonstrated that the compartmentalization of repeated elements is not simply restricted to heterochromatic regions, as it has been postulated in the first concepts of the genomic organization of repetitive elements in genomes. Moreover, the organization of these repeats seems to reflect their intense and specific evolutionary pathway, providing new insights about the chromosomal evolution in the Bagridae.     

Genome sequence of Methyloversatilis universalis FAM5T, a methylotrophic representative of the order Rhodocyclales

Rhodocyclales are representative of versatile bacteria that are able to utilize a wide variety of organic compounds for growth, but only a few strains have been isolated in pure culture thus far. Here we present the genome sequence of Methyloversatilis universalis FAM5(T), the first cultivable methylotrophic member of the order.     

Genome sequence of a novel species, Propionibacterium humerusii

As part of a larger project to sequence multiple clinical isolates of Propionibacterium acnes, we have produced a draft genome sequence of a novel Propionibacterium species that is closely related to, yet distinct (by sequence) from P. acnes. We have tentatively named this new species Propionibacterium humerusii.     

Genome Sequences of Mannheimia haemolytica Serotype A2: Ovine and Bovine Isolates

This report describes the genome sequences of Mannheimia haemolytica serotype A2 isolated from pneumonic lungs of two different ruminant species, one from Ovis aries, designated ovine (O), and the other from Bos taurus, designated bovine (B).Mannheimia haemolytica is a Gram-negative weakly hemolytic coccobacillus and is the principal bacterial pathogen of respiratory disease in cattle and other domestic and wild ruminants (15, 1, 14). M. haemolytica is a commensal found in the upper respiratory tract of healthy ruminants (6), but in conjunction with certain viral infections and stress factors, this organism multiplies, reaches the lungs, and causes acute fibrinonecrotic pleuropneumonia (16). This disease is commonly known as shipping fever in cattle and costs more than $1 billion annually in economic losses to the U.S. cattle industry alone (2). M. haemolytica produces several virulence factors (3), including leukotoxin (Lkt). Lkt is a member of the RTX (repeats-in-toxin) family of pore-forming exotoxins produced by bacteria, including Actinobacillus actinomycetemcomitans (11), Actinobacillus pleuropneumoniae, (6) and Escherichia coli (18).Of the 12 different serotypes of M. haemolytica that have been identified, serotypes A1 and A2 are the most prevalent worldwide (10, 19). These serotypes colonize the upper respiratory tract of healthy cattle and sheep and are generally (but not exclusively) species specific in their ability to cause pneumonia (10, 19)—serotype A1 being responsible for pneumonia in cattle and serotype A2 being responsible for pneumonia in sheep. The molecular basis for differential susceptibility of sheep and cattle to serotypes A1 and A2 has not been elucidated. The genome of M. haemolytica serotype A1 has been sequenced (9), and the availability of the genome sequence of serotype A2 will facilitate the genomic and proteomic analysis aimed at elucidating the molecular basis for differential species susceptibility. The A2 genomic sequence will provide for the potential identification of additional virulence factors involved in host specificity.High-throughput sequencing was performed via 454 pyrosequencing (12) with an average read length of 300 nucleotides, resulting in approximately 20× coverage for each strain. Quality filtered reads were assembled into contigs by using the Newbler assembler (454 Life Sciences) and produced 82 large contigs (defined as >500 bp) for Bos taurus (bovine [B]) and 14 large contigs for Ovis aries (ovine [O]). The total number of base pairs in large contigs was 2,478,004 for B and 2,584,200 for O, which is in agreement with the published size of the M. haemolytica A1 genome.Contigs were aligned to the genome of serotype A1 by using in-house software. Automated annotation was performed using a protocol similar to the annotation engine service at The Institute for Genomic Research (J. Craig Venter Institute) with some in-house modifications. The protein-coding regions were identified using Glimmer3 (5). BLAST Extend-Repraze was applied to predicted genes to identify truncations due to frameshift mutations or premature stop codons. tRNA and rRNA genes were identified by using tRNAScan-SE (13), and a similarity search was performed using our in-house database. We identified 3,818 protein-coding regions (64% G+C), which is approximately 1,000 more than in the M. haemolytica A1 genome. Homologs between coding regions in A1 and the two A2 strains share 95 to 99% nucleotide identity. Coding regions were annotated using BLASTP (http://blast.ncbi.nlm.nih.gov) with a stringency of 80% identity over 90% lengths. This resulted in fewer genes with assigned function compared to A1 (1,966). The numbers of genes with assigned function were 1,649 (B) and 1,717 (O) with 173 genes unique to O and 57 to B. A large proportion of phage (11.5 and 12.1% for B and O, respectively) and pseudogenes (9.1% and 9.3% for B and O, respectively) were found, indicating the presence of pathogenic islands conducive for lateral gene transfer (for B, COK_0537-COK_0547 and COK_1260-COK_1276; and for O, COI_0076-COI_0079 and COI_1005-COI_1045). In contrast with strain A1, both A2 strains have all secondary metabolism biosynthesis and transport and catabolism pathways, including leukotoxin and fatty acyl coenzyme A (CoA) needed for toxin activation. The first 35 amino acids of the chief virulence factor (Lkt), which is involved in pore formation (4, 7), are 100% identical in O and B. However, LktA of serotype A1 has 51% amino acid substitution in this region but shares 98% overall identity with O and 88% with B, respectively. The host colonization enzyme O-sialoglycoprotein endopeptidase, outer membrane lipoprotein precursor, N-acetyl-hexosamine, dUTP diphosphatase heptosyl transferase, and UDP-glucose 4-epimerase share 98 to 100% identity in all three strains. These are key enzymes involved in lipopolysaccharide (LPS) modification and complex carbohydrate synthesis potentially involved in host cell recognition. We discovered evidence of type III or IV secretion systems in B and O genomes by using a novel computational method (17), which demonstrated homology with conjugal DNA-protein, transfer VirB and pilin (Pilc). However, there is currently no experimental evidence that M. haemolytica possesses systems to chaperone these effector proteins. Collectively, the genomes of B and O are largely in synteny with A1, even though we identified large-scale inversions and rearrangements that will be subsequently confirmed by optical mapping and primer walking.The availability of three M. haemolytica genome sequences will enable a more thorough genome-wide comparison across pathogenic bacteria, especially among RTX toxin-secreting species, and, in conjunction with proteomics, will further enable the design of subunit vaccines.     

Genomic Organization of Repetitive DNA Elements and Its Implications for the Chromosomal Evolution of Channid Fishes (Actinopterygii,Perciformes)

Channid fishes, commonly referred to as “snakeheads”, are currently very important in Asian fishery and aquaculture due to the substantial decline in natural populations because of overexploitation. A large degree of chromosomal variation has been found in this family, mainly through the use of conventional cytogenetic investigations. In this study, we analyzed the karyotype structure and the distribution of 7 repetitive DNA sequences in several Channa species from different Thailand river basins. The aim of this study was to investigate the chromosomal differentiation among species and populations to improve upon the knowledge of its biodiversity and evolutionary history. Rearrangements, such as pericentric inversions, fusions and polyploidization, appear to be important events during the karyotypic evolution of this genus, resulting in the chromosomal diversity observed among the distinct species and even among populations of the same species. In addition, such variability is also increased by the genomic dynamism of repetitive elements, particularly by the differential distribution and accumulation of rDNA sequences on chromosomes. This marked diversity is likely linked to the lifestyle of the snakehead fishes and their population fragmentation, as already identified for other fish species. The karyotypic features highlight the biodiversity of the channid fishes and justify a taxonomic revision of the genus Channa, as well as of the Channidae family as a whole, as some nominal species may actually constitute species complexes.