Journal
DEVELOPMENTAL BIOLOGY
Volume 452, Issue 1, Pages 8-20Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ydbio.2019.03.015
Keywords
Genome assembly; Genetic mapping; Comparative genomics; Pigmentation; Sex determination; Gene expression analysis
Categories
Funding
- NIH S10 Instrumentation Grants [S10RR029668, S10RR027303]
- NIH [GM66684, HD08070]
- NICHD/NIH [K08-HD42550]
- Basic Science Research Program through the National Research Foundation of Korea - Ministry of Science, ICT and Future Planning [NRF-2016R1C1B2009302]
- UNIST research fund [1.180063, 1.180040]
- Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]
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The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid X. laevis. Here we report a chromosome-scale assembly of the X. tropicalis genome, improving the previously published draft genome assembly through the use of new assembly algorithms, additional sequence data, and the addition of a dense genetic map. The improved genome enables the mapping of specific traits (e.g., the sex locus or Mendelian mutants) and the characterization of chromosome-scale synteny with other tetrapods. We also report an improved annotation of the genome that integrates deep transcriptome sequence from diverse tissues and stages. The exon-intron structures of these genes are highly conserved relative to both X. laevis and human, as are chromosomal linkages (synteny) and local gene order. A network analysis of developmental gene expression will aid future studies.
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