From left: Boon-Hui TAY, Sumanty TOHARI, Vydianathan RAVI, Tarang MEHTA, Michelle LIAN, Alice TAY and Alison LEE
Tarang K. Mehta1,2,*, Vydianathan Ravi1,*, Shinichi Yamasaki3, Alison P. Lee1, Michelle M. Lian1, Boon-Hui Tay1, Sumanty Tohari1, Seiji Yanai4, Alice Tay1, Sydney Brenner1,3 and Byrappa Venkatesh1,2.
1 - Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673.
2 - Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
3 - Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
4 - Department of Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa
* contributed equally to this work.
Published online in Proc. Natl. Acad. Sci. USA on 16 September 2013.
To read the article, click here.
Japanese Lamprey Genome Project Website: http://jlampreygenome.imcb.a-star.edu.sg
Cyclostomes, comprising jawless vertebrates such as lampreys and hagfishes, are the sister group of living jawed vertebrates (gnathostomes) and hence an important group for understanding the origin and diversity of vertebrates. In vertebrates and other metazoans, Hox genes determine cell fate along the anterior-posterior axis of embryos and are implicated in driving morphological diversity. Invertebrates contain a single Hox cluster (either intact or fragmented) whereas elephant shark, coelacanth and tetrapods contain four Hox clusters owing to two rounds of whole-genome duplication (‘1R’ and ‘2R’) during early vertebrate evolution. By contrast, most teleost fishes contain up to eight Hox clusters due to an additional ‘teleost-specific’ genome duplication event. By sequencing BAC clones and the whole genome, here we provide evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum). This suggests that the lamprey lineage has experienced an additional genome duplication after 1R and 2R. The relative age of lamprey and human paralogs supports this hypothesis. Compared to gnathostome Hox clusters, lamprey Hox clusters are unusually large. Several conserved noncoding elements (CNEs) were predicted in the Hox clusters of lamprey, elephant shark and human. Transgenic zebrafish assay indicated the potential of CNEs to function as enhancers. Interestingly, CNEs in individual lamprey Hox clusters are frequently conserved in multiple Hox clusters in elephant shark and human, implying a many-to-many orthology relationship between lamprey and gnathostome Hox clusters. Such a relationship suggests that the first two rounds of genome duplication may have occurred independently in the lamprey and gnathostome lineages.
Figure legend: Hox clusters in the Japanese lamprey genome. Sequencing of the lamprey genome has revealed that lampreys contain more than six Hox clusters, compared to four Hox clusters in elephant shark and tetrapods. This suggests that lampreys have experienced an additional round of whole genome duplication compared to elephant shark and tetrapods. Since phylogenetic analyses were inconclusive in establishing one-to-one orthology relationship between the lamprey Hox clusters and tetrapod HoxA, HoxB, HoxC and HoxD clusters, lamprey Hox clusters have been designated as Hoxα to Hoxθ. The lack of one-to-one orthology between the lamprey and tetrapod Hox clusters suggests that the duplication of lamprey and tetrapod Hox clusters occurred independently after the divergence of the lamprey and tetrapod lineages.
For more information on Byrappa VENKATESH’s laboratory, please click here.