Robust Genome Annotation of Petromyzon marinus

Genome annotations were produced using the MAKER^{47 (link)–49 (link)} genome annotation pipeline, which supports re-annotation using pre-existing gene models as input. Previous Petromyzon marinus gene models (WUGSC 7.0/petMar2 assembly)^{50 (link)} were mapped against the new genome assembly into GFF3 format and were used as prior model input to MAKER for re-annotation. Snap^{51 (link)} and Augustus^{52 (link),53 (link)} were also used with MAKER and were trained using the pre-existing lamprey gene models. Additional input to MAKER included previously-published mRNA-seq reads derived from lamprey embryos and testes^{10 (link),12 (link),13 (link)} and assembled using Trinity^{54 (link)}, as well as mRNA-seq reads (NexSeq 75–100 bp paired-end) were derived from whole embryos and dissected heads at Tahara stage 20, as well as dissected embryonic dorsal neural tubes at Tahara stage 18, 20 and 21. The following protein datasets were also used: Ciona intestinalis (sea squirt)^{55 (link)}, Lottia gigantea (limpet)^{56 (link)}, Nematostella vectensis (sea anemone)^{57 (link)}, Takifugu rubripes (pufferfish)^{58 (link)}, Branchiostoma floridae (lancelet)^{59 (link)}, Callorhinchus milii (elephant shark)^{60 (link)}, Xenopus tropicalis (western clawed frog)^{61 (link)}, Drosophila melanogaster (fruit fly)^{62 (link)}, Homo sapiens (human)^{63 (link),64 (link)}, Mus musculus (mouse)^{65 (link)}, Danio rerio (zebrafish)^{66 (link)}, Hydra magnipapillata^{67 (link)}, Trichoplax adhaerens^{68 (link)}, and the Uniprot/Swiss-Prot protein database^{69 (link),70 (link)}. Protein domains were identified in final gene models using the InterProScan domain identification pipeline^{71 (link)–73 (link)}, and putative gene functions were assigned using BLASTP^{74 (link)} identified homology to the Uniprot/Swiss-Prot protein database.

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Smith J.J., Timoshevskaya N., Ye C., Holt C., Keinath M.C., Parker H.J., Cook M.E., Hess J.E., Narum S.R., Lamanna F., Kaessmann H., Timoshevskiy V.A., Waterbury C.K., Saraceno C., Wiedemann L.M., Robb S.M., Baker C., Eichler E.E., Hockman D., Sauka-Spengler T., Yandell M., Krumlauf R., Elgar G, & Amemiya C.T. (2018). The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nature genetics, 50(2), 270-277.

Publication 2017

Branchiostoma floridae Ciona intestinalis Clawed frog Drosophila melanogaster Elephant Embryonic Fruit fly Gene functions Genome Heads Human Hydra Lamprey Lancelet Mouse Mrna Mus musculus Neural tubes Petromyzon marinus Protein Protein domains Pufferfish Sea anemone Sea squirt Shark Takifugu rubripes Trichoplax Zebrafish

Corresponding Organization : University of Kentucky

Other organizations : University of Maryland, College Park, University of Utah, Stowers Institute for Medical Research, Columbia River Inter-Tribal Fish Commission, DKFZ-ZMBH Alliance, Heidelberg University, University of Kansas, University of Washington, Seattle University, Howard Hughes Medical Institute, University of Cape Town, University of Oxford, The Francis Crick Institute, University of California, Merced

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Variable analysis

independent variables

Previous Petromyzon marinus gene models (WUGSC 7.0/petMar2 assembly) used as prior model input to MAKER for re-annotation
Snap and Augustus were also used with MAKER and were trained using the pre-existing lamprey gene models
MRNA-seq reads derived from lamprey embryos and testes, and whole embryos, dissected heads, and dissected embryonic dorsal neural tubes at specific developmental stages
Protein datasets from various organisms (Ciona intestinalis, Lottia gigantea, Nematostella vectensis, Takifugu rubripes, Branchiostoma floridae, Callorhinchus milii, Xenopus tropicalis, Drosophila melanogaster, Homo sapiens, Mus musculus, Danio rerio, Hydra magnipapillata, Trichoplax adhaerens, and Uniprot/Swiss-Prot protein database)

dependent variables

Genome annotations produced using the MAKER genome annotation pipeline

control variables

None explicitly mentioned

controls

Positive control: None mentioned
Negative control: None mentioned

Annotations

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