Biology

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Author: search.filters.author.Conte, Matthew A

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    An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags
    (Springer Nature, 2010-04-30) Lee, Bo-Young; Howe, Aimee E; Conte, Matthew A; D'Cotta, Helena; Pepey, Elodie; Baroiller, Jean-Francois; di Palma, Federica; Carleton, Karen L; Kocher, Thomas D
    Large collections of expressed sequence tags (ESTs) are a fundamental resource for analysis of gene expression and annotation of genome sequences. We generated 116,899 ESTs from 17 normalized and two non-normalized cDNA libraries representing 16 tissues from tilapia, a cichlid fish widely used in aquaculture and biological research. The ESTs were assembled into 20,190 contigs and 36,028 singletons for a total of 56,218 unique sequences and a total assembled length of 35,168,415 bp. Over the whole project, a unique sequence was discovered for every 2.079 sequence reads. 17,722 (31.5%) of these unique sequences had significant BLAST hits (e-value < 10-10) to the UniProt database. Normalization of the cDNA pools with double-stranded nuclease allowed us to efficiently sequence a large collection of ESTs. These sequences are an important resource for studies of gene expression, comparative mapping and annotation of the forthcoming tilapia genome sequence.
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    A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs
    (Springer Nature, 2012-06-06) Guyon, Richard; Rakotomanga, Michaelle; Azzouzi, Naoual; Coutanceau, Jean Pierre; Bonillo, Celine; D’Cotta, Helena; Pepey, Elodie; Soler, Lucile; Rodier-Goud, Marguerite; D’Hont, Angelique; Conte, Matthew A; EM van Bers, Nikkie; Penman, David J; Hitte, Christophe; PMA Crooijmans, Richard; Kocher, Thomas D; Ozouf-Costaz, Catherine; Baroiller, Jean Francois; Galibert, Francis
    The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of environments. It is a good model to study evolutionary mechanisms in vertebrates, because of its close relationship to haplochromine cichlids, which have undergone rapid speciation in East Africa. The existing genomic resources for Nile tilapia include a genetic map, BAC end sequences and ESTs, but comparative genome analysis and maps of quantitative trait loci (QTL) are still limited. We have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia and genotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC end sequences, 154 microsatellites and 272 single nucleotide polymorphisms (SNPs). From these, 1296 markers could be associated in 81 RH groups, while 62 were not linked. The total size of the RH map is 34,084 cR3500 and 937,310 kb. It covers 88% of the entire genome with an estimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration to the genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmed that LG16-LG21 are also merged. The orientation and association of RH groups to each chromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55 BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained small orphan groups. Synteny relationships were determined between Nile tilapia, stickleback, medaka and pufferfish. The RH map and associated FISH map provide a valuable gene-ordered resource for gene mapping and QTL studies. All genetic linkage groups with their corresponding RH groups now have a corresponding chromosome which can be identified in the karyotype. Placement of conserved segments indicated that multiple inter-chromosomal rearrangements have occurred between Nile tilapia and the other model fishes. These maps represent a valuable resource for organizing the forthcoming genome sequence of Nile tilapia, and provide a foundation for evolutionary studies of East African cichlid fishes.
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    Evolution of cichlid vision via trans-regulatory divergence
    (Springer Nature, 2012-12-26) O’Quin, Kelly E; Schulte, Jane E; Patel, Zil; Kahn, Nadia; Naseer, Zan; Wang, Helena; Conte, Matthew A; Carleton, Karen L
    Phenotypic evolution may occur through mutations that affect either the structure or expression of protein-coding genes. Although the evolution of color vision has historically been attributed to structural mutations within the opsin genes, recent research has shown that opsin regulatory mutations can also tune photoreceptor sensitivity and color vision. Visual sensitivity in African cichlid fishes varies as a result of the differential expression of seven opsin genes. We crossed cichlid species that express different opsin gene sets and scanned their genome for expression Quantitative Trait Loci (eQTL) responsible for these differences. Our results shed light on the role that different structural, cis-, and trans-regulatory mutations play in the evolution of color vision. We identified 11 eQTL that contribute to the divergent expression of five opsin genes. On three linkage groups, several eQTL formed regulatory “hotspots” associated with the expression of multiple opsins. Importantly, however, the majority of the eQTL we identified (8/11 or 73%) occur on linkage groups located trans to the opsin genes, suggesting that cichlid color vision has evolved primarily via trans-regulatory divergence. By modeling the impact of just two of these trans-regulatory eQTL, we show that opsin regulatory mutations can alter cichlid photoreceptor sensitivity and color vision at least as much as opsin structural mutations can. Combined with previous work, we demonstrate that the evolution of cichlid color vision results from the interplay of structural, cis-, and especially trans-regulatory loci. Although there are numerous examples of structural and cis-regulatory mutations that contribute to phenotypic evolution, our results suggest that trans-regulatory mutations could contribute to phenotypic divergence more commonly than previously expected, especially in systems like color vision, where compensatory changes in the expression of multiple genes are required in order to produce functional phenotypes.
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    Mapping of pigmentation QTL on an anchored genome assembly of the cichlid fish, Metriaclima zebra
    (Springer Nature, 2013-04-27) O’Quin, Claire T; Drilea, Alexi C; Conte, Matthew A; Kocher, Thomas D
    Pigmentation patterns are one of the most recognizable phenotypes across the animal kingdom. They play an important role in camouflage, communication, mate recognition and mate choice. Most progress on understanding the genetics of pigmentation has been achieved via mutational analysis, with relatively little work done to understand variation in natural populations. Pigment patterns vary dramatically among species of cichlid fish from Lake Malawi, and are thought to be important in speciation. In this study, we crossed two species, Metriaclima zebra and M. mbenjii, that differ in several aspects of their body and fin color. We genotyped 798 SNPs in 160 F2 male individuals to construct a linkage map that was used to identify quantitative trait loci (QTL) associated with the pigmentation traits of interest. We also used the linkage map to anchor portions of the M. zebra genome assembly. We constructed a linkage map consisting of 834 markers in 22 linkage groups that spanned over 1,933 cM. QTL analysis detected one QTL each for dorsal fin xanthophores, caudal fin xanthophores, and pelvic fin melanophores. Dorsal fin and caudal fin xanthophores share a QTL on LG12, while pelvic fin melanophores have a QTL on LG11. We used the mapped markers to anchor 66.5% of the M. zebra genome assembly. Within each QTL interval we identified several candidate genes that might play a role in pigment cell development. This is one of a few studies to identify QTL for natural variation in fish pigmentation. The QTL intervals we identified did not contain any pigmentation genes previously identified by mutagenesis studies in other species. We expect that further work on these intervals will identify new genes involved in pigment cell development in natural populations.
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    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.