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Developmental Biology: Genomics Special Issue

Update on Developmental Biology special Xenopus genome issue.

The submission of the X. laevis genome manuscript has been delayed, so as to optimize the chromosome scale assembly.  We have pushed back the deadline for submission of manuscripts, which use or enrich the genomics of Xenopus or other amphibians, to the end of October.  People can take advantage of this delay to further hone their ideas, or discuss them at the MBL PI meeting.


If you have ideas, or plans for manuscripts that exploit either the X. tropicalis, the X. laevis, or indeed other amphibian genomes, then Developmental Biology would be very happy to consider them.

Please send a paragraph on your plans to Richard Harland, then the journal can further plan this special issue.  If you are doing some whole genome analysis that may not be covered in the X. laevis genome paper, let Richard know and he would be happy to share plans for the main manuscript with you.


We prefer that people use the new assembly of record for Xenopus laevis (version 9.1).  This is now available, along with annotation, on the Xenbase server, in both browser and downloadable formats.  The assembly is a chromosome scale reassembly of version 7.1, so any analysis you have previously done should in principle be able to be “lifted over” to the new coordinates.  However, we will accept alignments to the 7.1 assembly.


The X. laevis 9.1 assembly improves on previous version by capturing >90% of the assembled sequence into 18 pseudomolecules representing the 18 chromosomes of X. laevis. These have been named based off of their orthology to X. tropicalis and unique evolutionary history. The v7.2 assembly was improved by Dovetail, using their proprietary Chicago reads followed by Hi-C data to measure DNA-DNA interactions and assemble scaffolds large enough to be ordered/oriented by BAC-FISH and synteny to X. tropicalis. Regions with important genes that were affected by gaps were replaced by high quality BAC sequences.


A new X. tropicalis assembly is also available at Xenbase.


The new X. tropicalis v9.0 assembly improves on previous versions by utilizing Dovetail’s Chicago reads to reorient small segments of X. tropicalis chromosomes whose orientation could not be discerned by the genetic map. Additional extrachromosomal sequence has been assigned to chromosomes. Improvements to the X. laevis transcriptome, which is used as a sister taxon, have also improved models in the X. tropicalis genome.


Please contact:


Richard Harland
Editor, Developmental Biology
harland@berkeley.edu
University of California, Berkeley
Department of Molecular & Cell Biology
142 Life Sciences Addition #3200
Berkeley, CA 94720-3200

 

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Developmental Biology is planning a special issue to follow the publication of the Xenopus laevis genome paper (soon to be submitted). 

If you have ideas, or plans for manuscripts that exploit either the X. tropicalis, the X. laevis, or indeed other amphibian genomes, then Developmental Biology would be very happy to consider them. 

Please send a paragraph on your plans to Dr. Richard Harland, then the journal can plan what kind of scope this special issue might have.  If you are doing some whole genome analysis that may not be covered in the X. laevis genome paper, let Dr. Harland know and he would be happy to share their plans for the manuscript with you.

Please contact:

Richard Harland
Editor, Developmental Biology
Department Co-Chair and C.H. Li Distinguished Professor of Genetics, Genomics and Development
harland@berkeley.edu
University of California, Berkeley
Department of Molecular & Cell Biology
142 Life Sciences Addition #3200
Berkeley, CA 94720-3200

Last Updated: 2015-08-31

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