ArticleBMC genomics2015
An improved genome reference for the African cichlid, Metriaclima zebra.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 82 citations in OpenAlex.
- Bdh1l Gene Expression Is a Potential Molecular Factor in the Evolution of Carotenoid-Based Colour Diversity of Cichlid Fishes.Molecular ecology · 2025Article
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- Turnover of sex chromosomes in the Lake Tanganyika cichlid tribe Tropheini (Teleostei: Cichlidae).Scientific reports · 2024Article
- The evolution and genetic basis of a functionally critical skull bone, the parasphenoid, among Lake Malawi cichlids.Evolutionary journal of the Linnean Society · 2024Article
- Genome assemblies forFrontiers in genetics · 2024Article
- Comparative Genomics Identifies the Evolutionarily Conserved GeneInternational journal of molecular sciences · 2023Article
- PSReliP: an integrated pipeline for analysis and visualization of population structure and relatedness based on genome-wide genetic variant data.BMC bioinformatics · 2023Article
- East African cichlid fishes.EvoDevo · 2023Review
- Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus.BMC genomics · 2022Article
- First characterization of PIWI-interacting RNA clusters in a cichlid fish with a B chromosome.BMC biology · 2022Article
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- The cichlid oral and pharyngeal jaws are evolutionarily and genetically coupled.Nature communications · 2021Article
- Manipulation of the Tyrosinase gene permits improved CRISPR/Cas editing and neural imaging in cichlid fish.Scientific reports · 2021Article
- Origin of a Giant Sex Chromosome.Molecular biology and evolution · 2021Article
- Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika.Scientific reports · 2021Article
- Correspondence of aCGH and long-read genome assembly for detection of copy number differences: A proof-of-concept with cichlid genomes.PloS one · 2021Article
- Weak genetic signal for phenotypic integration implicates developmental processes as major regulators of trait covariation.Molecular ecology · 2021Article
- Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes ofFrontiers in microbiology · 2021Article
- Evolutionary divergence of novel open reading frames in cichlids speciation.Scientific reports · 2020Article
- Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma).BMC genomics · 2020Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundProblems 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 16.5× 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.
resultsOur new assembly closed 68% of the existing gaps and added 90.6 Mbp 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.
conclusionsOur improvements to the M. zebra draft genome suggest that a reasonable investment in long reads could greatly improve many comparable vertebrate draft genome assemblies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.