shangshanzhizhe / Crickets_Genome_Annotation

Gennome annotation scripts for the crickets Gryllus bimaculatus and Laupala kohalensis.

Crickets Genome Annotation

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• Scripts author: Guillem Ylla
• Article: "Insights into the genomic evolution of insects from cricket genomes"
• Genome database: https://gbimaculatusgenome.rc.fas.harvard.edu

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This repository includes:

1. Compilation of scripts used for the de novo annotating the genomes of the crickets:
   • Gryllus bimaculatus
   • Laupala kohalensis
2. The Analysis directory contains the scripts used to analyze these genomes and generate the results shown publication.
3. The Annotation_files direcotry contains the annotations (gff3 files) for G. bimaculatus and L. kohalensis

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• The genome annotation pipeline involves:

  • Repeat masking with RepeatMasker using a custom repear library generated by combining 5 different tools.
  • Protein coding genes annotation based on MAKER2 pipeline.
  • Functional annotation based on InterProscan and Blast, and creation of a SQL database.

• Pipeline based on the multiple online sources. Most relevant resources used:

  • MAKER tutorial
  • MAKER tutorial to create custom repeat libaries
  • Daren Card pipline for annotating the Boa constrictor genome (https://gist.github.com/darencard/bb1001ac1532dd4225b030cf0cd61ce2)

• The annotation pipline used in both crickets is very similar. If you would like to use it for any other species, I recommend you to check the G. bimaculatus one, since the scripts are better explained.

• Schematic representation of the G. bimaculatus genoem annotation:

• Please cite:

Ylla, G., Nakamura, T., Itoh, T. et al. Insights into the genomic evolution of insects from cricket genomes. Commun Biol 4, 733 (2021). https://doi.org/10.1038/s42003-021-02197-9