Genome Annotation and Curation Using MAKER and MAKER‐P

Campbell, Michael S.; Holt, Carson; Moore, Barry; Yandell, Mark

doi:10.1002/0471250953.bi0411s48

Cited by 621 publications

(615 citation statements)

References 24 publications

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“…Average exon and intron sizes were 0.3 kb and 2 kb, respectively, thus placing marbled crayfish gene lengths between those of P. hawaiensis and D. pulex. Gene annotation was performed using the MAKER genome annotation pipeline 29 , which provided important starting points for further analysis. For example, we detected multiple genomic locations for cellulase genes of the GH9 family (Fig.…”

Section: Resultsmentioning

confidence: 99%

Clonal genome evolution and rapid invasive spread of the marbled crayfish

et al. 2018

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The marbled crayfish Procambarus virginalis is a unique freshwater crayfish characterized by very recent speciation and parthenogenetic reproduction. Marbled crayfish also represent an emerging invasive species and have formed wild populations in diverse freshwater habitats. However, our understanding of marbled crayfish biology, evolution and invasive spread has been hampered by the lack of freshwater crayfish genome sequences. We have now established a de novo draft assembly of the marbled crayfish genome. We determined the genome size at approximately 3.5 gigabase pairs and identified >21,000 genes. Further analysis confirmed the close relationship to the genome of the slough crayfish, Procambarusfallax, and also established a triploid AA’B genotype with a high level of heterozygosity. Systematic fieldwork and genotyping demonstrated the rapid expansion of marbled crayfish on Madagascar and established the marbled crayfish as a potent invader of freshwater ecosystems. Furthermore, comparative whole-genome sequencing demonstrated the clonality of the population and their genetic identity with the oldest known stock from the German aquarium trade. Our study closes an important gap in the phylogenetic analysis of animal genomes and uncovers the unique evolutionary history of an emerging invasive species.

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Section: Resultsmentioning

confidence: 99%

Clonal genome evolution and rapid invasive spread of the marbled crayfish

et al. 2018

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“…both an ab initio prediction and an evidence-based alignment. Functional annotation of Maker’s output was done as described in “Support Protocol 3: Assigning putative gene function” of “Genome Annotation and Curation Using MAKER and MAKER-P”[Campbell et al, 2014]. BLAST was used (e-value <0.001) for each predicted gene against the Swiss-Prot release-2016-02 database, where the best hit was used as the putative function of that gene.…”

Section: Methodsmentioning

confidence: 99%

A reference genome of the Chinese hamster based on a hybrid assembly strategy

Rupp

MacDonald

et al. 2018

Biotech & Bioengineering

102

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Accurate and complete genome sequences are essential in biotechnology to facilitate genome-based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short-read based assemblies. Here, we completely resequenced C. griseus using Single Molecule Real Time (SMRT) sequencing and merged this with Illumina-based assemblies. This generated a more contiguous and complete genome assembly than either technology alone, reducing the number of scaffolds by >28-fold, with 90% of the sequence in the 122 longest scaffolds. Most genes are now found in single scaffolds, including up- and downstream regulatory elements, enabling improved study of noncoding regions. With >95% of the gap sequence filled, important CHO cell mutations have been detected in draft assembly gaps. This new assembly will be an invaluable resource for continued basic and pharmaceutical research.

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“…The assembly L50 was 68.1 kb, with the longest contig 312 kb in length. Genome annotation was performed using MAKER (Campbell et al 2014), which takes in ab initio predictions from SNAP (Korf 2004), Augustus (Stanke et al 2006), and GeneMark-ES (Borodovsky and Lomsadze 2011;Ter-Hovhannisyan et al 2008). SNAP and Augustus ab initio parameters were initially run with F. graminearum parameters (https://github.com/hyphaltip/ fungi-gene-prediction-params) followed by parameter training on high-quality predictions from MAKER determined by transcript and protein support (AED better than 0.1).…”

Section: Methodsmentioning

confidence: 99%

PCR Multiplexes DiscriminateFusariumSymbionts of InvasiveEuwallaceaAmbrosia Beetles that Inflict Damage on Numerous Tree Species Throughout the United States

et al. 2017

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Asian Euwallacea ambrosia beetles vector Fusarium mutualists. The ambrosial fusaria are all members of the ambrosia Fusarium clade (AFC) within the Fusarium solani species complex (FSSC). Several EuwallaceaFusarium mutualists have been introduced into nonnative regions and have caused varying degrees of damage to orchard, landscape, and forest trees. Knowledge of symbiont fidelity is limited by current identification methods, which typically requires analysis of DNA sequence data from beetles and the symbionts cultured from their oral mycangia. Here, polymerase chain reaction (PCR)-based diagnostic tools were developed to identify the six Fusarium symbionts of exotic Euwallacea spp. currently known within the United States. Whole-genome sequences were generated for representatives of six AFC species plus F. ambrosium and aligned to the annotated genome of F. euwallaceae. Taxon-specific primer-annealing sites were identified that rapidly distinguish the AFC species currently within the United States. PCR specificity, reliability, and sensitivity were validated using a panel of 72 Fusarium isolates, including 47 reference cultures. Culture-independent multiplex assays accurately identified two AFC fusaria using DNA isolated from heads of their respective beetle partners. The PCR assays were used to show that Euwallacea validus is exclusively associated with AF-4 throughout its sampled range within eastern North America. The rapid assay supports federal and state agency efforts to monitor spread of these invasive pests and mitigate further introductions.Several destructive fungal plant pathogens vectored by exotic bark and ambrosia beetles (Coleoptera: Curculionidae: Scolytinae) have invaded American landscapes and forests within the past century. For example, the redbay ambrosia beetle Xyleborus glabratus (Eichhoff) and its fungal symbiont Raffaelea lauricola T. C. Harr., Fraedrich & Aghayeva are responsible for the death of hundreds of millions of native Lauraceous plants, including avocado (Persea americana), redbay (P. borbonia), and sassafras (Sassafras albidum) (Fraedrich et al. 2008;Ploetz et al. 2013) throughout the coastal southeastern United States. Another group of scolytine beetles, the exotic Euwallacea ambrosia beetles, pose a threat to landscape trees as well as avocado Kasson et al. 2013;Mendel et al. 2012).At least six Euwallacea spp. from Asia have become established within the United States (Cognato et al. 2015;O'Donnell et al. 2015): Euwallacea interjectus (Blandford), E. validus (Eichhoff), E. denticulus (Motschulsky), and three morphologically cryptic species within the E. fornicatus species complex (Eichhoff) (Atkinson 2016;O'Donnell et al. 2015;Storer et al. 2015). Euwallacea spp. are fungus-farming ambrosia beetles that cultivate mutualistic fungi in the genus Fusarium, although this is presently unconfirmed for E. denticulus. Most of these insect species do not cause noticeable economic or ecological damage and, instead, attack and colonize declining and recently killed trees. Howe...

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Genome Annotation and Curation Using MAKER and MAKER‐P

Cited by 621 publications

References 24 publications

Clonal genome evolution and rapid invasive spread of the marbled crayfish

Clonal genome evolution and rapid invasive spread of the marbled crayfish

A reference genome of the Chinese hamster based on a hybrid assembly strategy

PCR Multiplexes DiscriminateFusariumSymbionts of InvasiveEuwallaceaAmbrosia Beetles that Inflict Damage on Numerous Tree Species Throughout the United States

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