Preliminary Discovery of Repetitive Elements in the Genome
of the Sea Cucumber Holothuria scabra Jaeger, 1833
Delbert Almerick T. Boncan1,2, Iris Diana C. Uy1,
Crimson C. Tayco1, and Arturo O. Lluisma1,3*
1Marine Science Institute, College of Science,
University of the Philippines Diliman, Quezon City 1101 Philippines
2National Institute of Molecular Biology and Biotechnology, College of Science,
University of the Philippines Diliman, Quezon City 1101 Philippines
3Philippine Genome Center, University of the Philippines Diliman,
Quezon City 1101 Philippines
Various classes of repetitive elements exist in the genomes of organisms. Characterizing these genomic elements is important not only because of the potential insights on the biology and evolution of their host's genomes but also because of the potential practical applications that such information might yield. So far, little is known about the types of repetitive elements in the genome of holothurids. In this study, we generated a partial sequence of the genome of the sea cucumber, Holothuria scabra, and searched for tandem and interspersed repetitive elements using various approaches. We conducted the same search on another sea cucumber, Parastichopus parvimensis, using its publicly available genome sequence. The perfect microsatellite profiles of both sea cucumbers show similarities to some known patterns in eukaryotes. The combined perfect and imperfect microsatellite data sets also highlight fundamental microsatellite profile dissimilarities between the two holothurids. This study demonstrates that as much as half of microsatellites in a holothurid genome remain unidentified in perfect repeat scans, and highlights the importance of imperfect repeat-inclusive searches. This study also demonstrates that partial genome sequencing may be used as a cheaper and more efficient alternative to the traditional methods of developing microsatellite markers for H. scabra. On the other hand, combined approach of sequence similarity-based and de novo search of interspersed repeats reveals a diverse subclass/superfamily of transposable elements in the genomes of H. scabra and P. parvimensis. The two species exhibit similar patterns of repeat profiles notwithstanding the disparity in the number of predicted transposable elements. Notably, the major subclass/superfamily identified in the two genomes include DNA/hAT-Blackjack, DNA/hAT-Tip100, DNA/Maverick, RC/Helitron, LINE/L2, LTR/Gypsy, SINE/MIR and SINE/tRNA. The interspersed repeats identified in the study presents the first attempt to survey the transposable elements from the genomes of these two holothurids.
It has long been known that repetitive elements can account for a sizeable fraction of many eukaryotic genomes (Britten and Kohne 1968). Depending on the species, this proportion can vary from a few percent (3% in Saccharomyces cerevisiae, Kim et al. 1998) to a significant amount (e.g. > 80% in maize, Schnable et al. 2009). These repeats are classified as tandem or interspersed repeats based on their sequence characteristics and the mechanism of their generation and replication in the genome. Tandem repeats are comprised by either microsatellites or minisatellites. Microsatellites can exhibit high levels of intraspecific polymorphisms and thus have emerged as popular genetic markers for a wide range of applications in population genetics, conservation biology and evolutionary biology (Goldstein and Schlotterer 1999). On the other hand, interspersed repeats are mainly comprised by transposable elements (TEs) which were initially considered as selfish and junk genetic elements. . . . . read more
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