Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes

Background Comparisons between the genomes of the closely related nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal high rates of rearrangement, with a bias towards within-chromosome events. To assess whether this pattern is true of nematodes in general, we have used genome sequence to compare two nematode species that last shared a common ancestor approximately 300 million years ago: the model C. elegans and the filarial parasite Brugia malayi. Results An 83 kb region flanking the gene for Bm-mif-1 (macrophage migration inhibitory factor, a B. malayi homolog of a human cytokine) was sequenced. When compared to the complete genome of C. elegans, evidence for conservation of long-range synteny and microsynteny was found. Potential C. elegans orthologs for II of the 12 protein-coding genes predicted in the B. malayi sequence were identified. Ten of these orthologs were located on chromosome I, with eight clustered in a 2.3 Mb region. While several, relatively local, intrachromosomal rearrangements have occurred, the order, composition, and configuration of two gene clusters, each containing three genes, was conserved. Comparison of B. malayi BAC-end genome survey sequence to C. elegans also revealed a bias towards intrachromosome rearrangements. Conclusions We suggest that intrachromosomal rearrangement is a major force driving chromosomal organization in nematodes, but is constrained by the interdigitation of functional elements of neighboring genes

Warming and glacier recession in the Rakaia valley, Southern Alps of New Zealand, during Heinrich Stadial 1

The termination of the last ice age featured a major reconfiguration of Earthʼs climate and cryosphere, yet the underlying causes of these massive changes continue to be debated. Documenting the spatial and temporal variations of atmospheric temperature during deglaciation can help discriminate among potential drivers. Here, we present a 10Be surface-exposure chronology and glaciological reconstruction of ice recession following the Last Glacial Maximum (LGM) in the Rakaia valley, Southern Alps of New Zealand. Innermost LGM moraines at Big Ben have an age of 17,840 ± 240 yrs, whereas ice-marginal moraines or ice-molded bedrock surfaces at distances up-valley from Big Ben of 12.5 km (Lake Coleridge), ∼25 km (Castle Hill), ∼28 km (Double Hill), ∼43 km (Prospect Hill), and ∼58 km (Reischek knob) have ages of 17,020 ± 70 yrs, 17,100 ± 110 yrs, 16,960 ± 370 yrs, 16,250 ± 340 yrs, and 15,660 ± 160 yrs, respectively. These results indicate extensive recession of the Rakaia glacier, which we attribute primarily to the effects of climatic warming. In conjunction with geomorphological maps and a glaciological reconstruction for the Rakaia valley, we use our chronology to infer timing and magnitude of past atmospheric temperature changes. Compared to an overall temperature rise of ∼4.65 °C between the end of the LGM and the start of the Holocene, the glacier recession between ∼17,840 and ∼15,660 yrs ago is attributable to a net temperature increase of ∼4.0 °C (from −6.25 to −2.25 °C), accounting for ∼86% of the overall warming. Approximately 3.75 °C (∼70%) of the warming occurred between ∼17,840 and ∼16,250 yrs ago, with a further 0.75 °C (∼16%) increase between ∼16,250 and ∼15,660 yrs ago. A sustained southward shift of the Subtropical Front (STF) south of Australia between ∼17,800 and ∼16,000 yrs ago coincides with the warming over the Rakaia valley, and suggests a close link between Southern Ocean frontal boundary positions and southern mid-latitude climate. Most of the deglacial warming in the Southern Alps occurred during the early part of Heinrich Stadial 1 (HS1) of the North Atlantic region. Because the STF is associated with the position of the westerly wind belt, our findings support the concept that a southward shift of Earthʼs wind belts accompanied the early part of HS1 cooling in the North Atlantic, leading to warming and deglaciation in southern middle latitudes

The decaying genome of Mycobacterium leprae.

Everything that we need to know about Mycobacterium leprae, a close relative of the tubercle bacillus, is encrypted in its genome. Inspection of the 3.27 Mb genome sequence of an armadillo-derived Indian isolate of the leprosy bacillus identified 1,605 genes encoding proteins and 50 genes for stable RNA species. Comparison with the genome sequence of Mycobacterium tuberculosis revealed an extreme case of reductive evolution, since less than half of the genome contains functional genes while inactivated or pseudogenes are highly abundant. The level of gene duplication was approximately 34% and, on classification of the proteins into families, the largest functional groups were found to be involved in the metabolism and modification of fatty acids and polyketides, transport of metabolites, cell envelope synthesis and gene regulation. Reductive evolution, gene decay and genome downsizing have eliminated entire metabolic pathways, together with their regulatory circuits and accessory functions, particularly those involved in catabolism. This may explain the unusually long generation time and account for our inability to culture the leprosy bacillus