Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences

BACKGROUND

Approximately 11 Mb of finished high quality genomic sequences were sampled from cattle, dog and human to estimate genomic divergences and their regional variation among these lineages.

RESULTS

Optimal three-way multi-species global sequence alignments for 84 cattle clones or loci (each >50 kb of genomic sequence) were constructed using the human and dog genome assemblies as references. Genomic divergences and substitution rates were examined for each clone and for various sequence classes under different functional constraints. Analysis of these alignments revealed that the overall genomic divergences are relatively constant (0.32-0.37 change/site) for pairwise comparisons among cattle, dog and human; however substitution rates vary across genomic regions and among different sequence classes. A neutral mutation rate (2.0-2.2 x 10(-9) change/site/year) was derived from ancestral repetitive sequences, whereas the substitution rate in coding sequences (1.1 x 10(-9) change/site/year) was approximately half of the overall rate (1.9-2.0 x 10(-9) change/site/year). Relative rate tests also indicated that cattle have a significantly faster rate of substitution as compared to dog and that this difference is about 6%.

CONCLUSION

This analysis provides a large-scale and unbiased assessment of genomic divergences and regional variation of substitution rates among cattle, dog and human. It is expected that these data will serve as a baseline for future mammalian molecular evolution studies.

Genome resources and comparative analysis tools for cardiovascular research

Disorders of the cardiovascular system are often caused by the interaction of genetic and environmental factors that jointly contribute to individual susceptibility. Genomic data and bioinformatics tools generated from genome projects, coupled with functional verification, offer novel approaches to study both rare single-gene and complex multigenic cardiovascular diseases. These approaches include gene mapping using genome variation, especially single-nucleotide polymorphisms and comparative genomics within and between species. This chapter illustrates the major genome resources, associated bioinformatics tools, and their potential application in cardiovascular research.

Neutralization and buffering capacity of leaves of sugar maple, largetooth aspen, paper birch and balsam fir

We compared the acidity, the external acid neutralizing capacity and the buffering capacity of leaves of four commercially important tree species, largetooth aspen (Populus grandidentata Michx.), sugar maple (Acer saccharum Marsh.), paper birch (Betula papyrifera Marsh.) and balsam fir (Abies balsamea (L.) Mill), at two sites of contrasting soil fertility in southern Quebec. External acid neutralizing capacity (ENC) of leaves was determined by measuring the change in pH induced by soaking fresh leaves in an acidic solution (pH 4.0) for two hours. The ENC was highest for largetooth aspen (14.3 micro equiv H(+) g(-1)), and lowest for sugar maple and balsam fir (< 5 micro equiv H(+) g(-1)). The buffering capacity index (BCI) was determined by measuring the amount of acid necessary to produce a change of 5 micro equiv H(+) in the leaf homogenate. The BCI ranged from 883 micro equiv H(+) g(-1) for largetooth aspen to less than 105 micro equiv H(+) g(-1) for sugar maple and balsam fir. Leaves of sugar maple and balsam fir had a lower internal pH and a higher percentage of ENC over BCI than paper birch and largetooth aspen. Overall, ENC was correlated with the concentration of all leaf nutrients except Ca, and BCI was correlated with Mg, N and Ca. The site effect was relatively unimportant for all variables.