Comparative genomics of vertebrate Fox cluster loci.

Published onlineComparative StudyJournal ArticleResearch Support, Non-U.S. Gov'tThis is the final version of the article. Available from BioMed Central via the DOI in this record.BACKGROUND: Vertebrate genomes contain numerous duplicate genes, many of which are organised into paralagous regions indicating duplication of linked groups of genes. Comparison of genomic organisation in different lineages can often allow the evolutionary history of such regions to be traced. A classic example of this is the Hox genes, where the presence of a single continuous Hox cluster in amphioxus and four vertebrate clusters has allowed the genomic evolution of this region to be established. Fox transcription factors of the C, F, L1 and Q1 classes are also organised in clusters in both amphioxus and humans. However in contrast to the Hox genes, only two clusters of paralogous Fox genes have so far been identified in the Human genome and the organisation in other vertebrates is unknown. RESULTS: To uncover the evolutionary history of the Fox clusters, we report on the comparative genomics of these loci. We demonstrate two further paralogous regions in the Human genome, and identify orthologous regions in mammalian, chicken, frog and teleost genomes, timing the duplications to before the separation of the actinopterygian and sarcopterygian lineages. An additional Fox class, FoxS, was also found to reside in this duplicated genomic region. CONCLUSION: Comparison of loci identifies the pattern of gene duplication, loss and cluster break up through multiple lineages, and suggests FoxS1 is a likely remnant of Fox cluster duplication.We thank Peter Holland and Dave Ferrier for their discussions on this project and John Mulley for supplying the Amia calva genomic DNA, and for comments on the manuscript. This work was supported by the BBSRC

Eucalyptus spp. pollen transport across Liawenee Moor, on the Central Plateau of Tasmania

Investigation of Eucalyptus spp. pollen transport modes on Liawenee Moor in Tasmania revealed that it is possible to separate woodland areas from areas of moor and heath vegetation. While most Eucalyptus spp. pollen is deposited locally, a relatively small component is distributed across treeless areas, where it behaves in a manner similar to the long-distance transported (LOT) pollen of rainforest and alpine conifer taxa. When deposited into lakes, the Eucalyptus spp. component of the terrestrial pollen is increased compared with local pollen. Knowledge of the percentage Eucalyptus spp. pollen values from extant vegetation communities and the LOT components ofEucalyptus spp. and rainforest-alpine conifer taxa is useful for palaeoecological interpretation of vegetation history from lake sediment cores. Applied to the 8000-year-Iong Camerons Lagoon record, the study confirms the treeless character of Liawenee Moor during the Holocene. The evidence indicates that the moorland has altered from grassy to heath, due to the impacts ofgrazing and burning associated with European pastoral practices, but that the boundaries between the moor and adjacent woodlands have remained stable

Evolution of developmental mechanisms

A report on the joint Spring meeting of the British Society of Developmental Biology and the Genetics Society, York, UK, 20-23 March 2002

Comparative genomics of vertebrate Fox cluster loci

BACKGROUND: Vertebrate genomes contain numerous duplicate genes, many of which are organised into paralagous regions indicating duplication of linked groups of genes. Comparison of genomic organisation in different lineages can often allow the evolutionary history of such regions to be traced. A classic example of this is the Hox genes, where the presence of a single continuous Hox cluster in amphioxus and four vertebrate clusters has allowed the genomic evolution of this region to be established. Fox transcription factors of the C, F, L1 and Q1 classes are also organised in clusters in both amphioxus and humans. However in contrast to the Hox genes, only two clusters of paralogous Fox genes have so far been identified in the Human genome and the organisation in other vertebrates is unknown. RESULTS: To uncover the evolutionary history of the Fox clusters, we report on the comparative genomics of these loci. We demonstrate two further paralogous regions in the Human genome, and identify orthologous regions in mammalian, chicken, frog and teleost genomes, timing the duplications to before the separation of the actinopterygian and sarcopterygian lineages. An additional Fox class, FoxS, was also found to reside in this duplicated genomic region. CONCLUSION: Comparison of loci identifies the pattern of gene duplication, loss and cluster break up through multiple lineages, and suggests FoxS1 is a likely remnant of Fox cluster duplication

Data report: logging while drilling data analysis of Leg 171A, a multivariate statistical approach

In the northern Barbados accretionary wedge, several Deep Sea Drilling Project (DSDP) and Ocean Drilling Program (ODP) legs (DSDP Leg 78 and ODP Legs 110, 156, and 171A) targeted the décollement and the seaward extension of the décollement, the proto-décollement. During Leg 171A, the logging while drilling (LWD) technique was used to determine the physical properties variations along a profile across the deformation front. Because of the unstable borehole conditions in accretionary wedges, LWD is the most effective method for the measurements of physical properties in these poorly consolidated sediments. LWD data are acquired just above the drill bit a few minutes after the formation has been drilled, yielding measurements as close to in situ conditions as possible. The large amount of LWD data and the demand for a quick, objective, and reliable evaluation calls for the application of multivariate statistical methods. The multivariate factor analysis is a method of reducing the amount of logging data while giving them a new integrated meaning with no loss of important information, resulting in factor logs that are helpful tools for further interpretation. The cluster analysis of the two or three most significant factors proved to be a useful and objective method to identify and confirm significant logging units. The main objective of the application of multivariate statistical methods in this study is twofold. First, Leg 171A was a stand-alone logging leg, where no cores were retrieved. The factor analysis was used as an objective tool for a classification of the drilled sequences based on their physical and chemical properties. The new factor logs mirror the basic processes behind the measured geophysical properties and make them easier to interpret. Second, in the succeeding cluster analysis, similar geophysical properties are grouped into one cluster, reflecting one logging unit. These objectively defined logging units can be compared to statistical electrofacies, which are helpful in differentiating lithologic characterizations. In particular for LWD measurements, the multivariate statistical methods of factor and cluster analysis are helpful tools for a fast, reliable, and objective definition of logging units, which should be considered for future legs

Muscle differentiation in a colonial ascidian: organisation, gene expression and evolutionary considerations

Background: Ascidians are tunicates, the taxon recently proposed as sister group to the vertebrates. They possess a chordate-like swimming larva, which metamorphoses into a sessile adult. Several ascidian species form colonies of clonal individuals by asexual reproduction. During their life cycle, ascidians present three muscle types: striated in larval tail, striated in the heart, and unstriated in the adult body-wall. Results: In the colonial ascidian Botryllus schlosseri, we investigated organisation, differentiation and gene expression of muscle beginning from early buds to adults and during zooid regression. We characterised transcripts for troponin T (BsTnT-c), adult muscle-type (BsMA2) and cytoplasmic-type (BsCA1) actins, followed by in situ hybridisation (ISH) on sections to establish the spatio-temporal expression of BsTnT-c and BsMA2 during asexual reproduction and in the larva. Moreover, we characterised actin genomic sequences, which by comparison with other metazoans revealed conserved intron patterns. Conclusion: Integration of data from ISH, phalloidin staining and TEM allowed us to follow the phases of differentiation of the three muscle kinds, which differ in expression pattern of the two transcripts. Moreover, phylogenetic analyses provided evidence for the close relationship between tunicate and vertebrate muscle genes. The characteristics and plasticity of muscles in tunicates are discussed. </p