Biology
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Item STRUCTURAL EVOLUTION OF AFRICAN CICHLID GENOMES(2018) Conte, Matthew A; Kocher, Thomas D; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)An unanswered question in biology is how the evolution of genome structure supports or accompanies diversification and speciation on different time scales. African cichlid fishes are a well-documented system ideal for studying rapid evolution, due to their phenotypic diversity and high number of speciation events over the last several million years. I generated two de novo genome assemblies of the riverine cichlid Oreochromis niloticus (tilapia) and the Lake Malawi cichlid Metriaclima zebra using high-coverage long-read sequencing data and anchored the assemblies to chromosomes using several genetic and physical maps, to produce two high-quality anchored references. By comparing these chromosome-scale assemblies to integrated recombination, transcriptome, and resequencing data of multiple genera and species, I identified and characterized many large novel genome rearrangement events. These rearrangements included multiple novel sex-determination inversions, several metacentric-acrocentric karyotype differences via centromere assembly and placement, and wide regions of suppressed recombination in genera- and species-level crosses of Lake Malawi cichlids. Karyotype evolution in cichlids was further analyzed with long-read sequencing, specifically revealing the complex structure and content of a highly repetitive supernumerary chromosome present in some but not all individuals of a population across a wide range of eukaryotes, including many cichlid species. These supernumerary "B" chromosomes are shown to be limited to female Lake Malawi cichlids and have a unique evolutionary history with B chromosomes present in Lake Victorian cichlids male and females. This work reveals how structural genomic changes impact a rapidly evolving clade, while providing high-quality resources for the community, a context for previous genetic studies, and a robust platform for future genome research in cichlids.Item An improved genome reference for the African cichlid, Metriaclima zebra(BioMed Central, 2015) Conte, Matthew A.; Kocher, Thomas D.Background: Problems associated with using draft genome assemblies are well documented and have become more pronounced with the use of short read data for de novo genome assembly. We set out to improve the draft genome assembly of the African cichlid fish, Metriaclima zebra, using a set of Pacific Biosciences SMRT sequencing reads corresponding to 16.5x coverage of the genome. Here we characterize the improvements that these long reads allowed us to make to the state-of-the-art draft genome previously assembled from short read data. Results: Our new assembly closed 68 % of the existing gaps and added 90.6Mbp of new non-gap sequence to the existing draft assembly of M. zebra. Comparison of the new assembly to the sequence of several bacterial artificial chromosome clones confirmed the accuracy of the new assembly. The closure of sequence gaps revealed thousands of new exons, allowing significant improvement in gene models. We corrected one known misassembly, and identified and fixed other likely misassemblies. 63.5 Mbp (70 %) of the new sequence was classified as repetitive and the new sequence allowed for the assembly of many more transposable elements. Conclusions: Our improvements to the M. zebra draft genome suggest that a reasonable investment in long reads could greatly improve many comparable vertebrate draft genome assemblies.