Feb 27, 2023

Public workspaceRepetitive element annotation protocol for the eastern banjo frog V.1

DOI
dx.doi.org/10.17504/protocols.io.bc4niyve
  • Qiye Li1,2,
  • Qunfei Guo1,3,
  • Yang Zhou1,
  • Huishuang Tan1,4,
  • Terry Bertozzi5,6,
  • Yuanzhen Zhu1,7,
  • Ji Li2,8,
  • Stephen Donnellan5,
  • Guojie Zhang2,8,9,10
  • 1BGI-Shenzhen, Shenzhen 518083, China;
  • 2State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
  • 3College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China;
  • 4Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China;
  • 5South Australian Museum, North Terrace, Adelaide 5000, Australia;
  • 6School of Biological Sciences, University of Adelaide, North Terrace, Adelaide 5005, Australia;
  • 7School of Basic Medicine, Qingdao University, Qingdao 266071, China;
  • 8China National Genebank, BGI-Shenzhen, Shenzhen 518120, China;
  • 9Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China;
  • 10Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
Qunfei Guo
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DOI: dx.doi.org/10.17504/protocols.io.bc4niyve
External link: https://doi.org/https://doi.org/10.31229/osf.io/hj7wx
Protocol Citation: Qiye Li, Qunfei Guo, Yang Zhou, Huishuang Tan, Terry Bertozzi, Yuanzhen Zhu, Ji Li, Stephen Donnellan, Guojie Zhang 2023. Repetitive element annotation protocol for the eastern banjo frog. protocols.io https://dx.doi.org/10.17504/protocols.io.bc4niyve
Manuscript citation:
Edmunds SC, Goodman L, Array. GigaByte doi: https://doi.org/10.31229/osf.io/hj7wx
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
Created: February 28, 2020
Last Modified: February 27, 2023
Protocol Integer ID: 33646
Keywords: the eastern banjo frog, repetitive element annotation, homology-based, de novo,
Abstract
This pipeline is the repetitive element annotation by using homology-based, de novo predictions and Tandem Repeats Finder to identify repetitive elements in the Limnodynastes dumerilii dumerilii genome assembly.
The following sub-steps are the process for homology-based predictions to identify repetitive elements in the Limnodynastes dumerilii dumerilii genome assembly.
Identify known repetitive elements by aligning the Limnodynastes dumerilii dumerilii genome sequences against the Repbase-derived RepeatMasker libraries using RepeatMasker (v4.1.0).

Note
Use the parameters "-nolow -norna -no is" when running RepeatMasker.

Identify known repetitive elements by aligning the Limnodynastes dumerilii dumerilii genome sequences against the transposable element protein database using RepeatProteinMask (an application within the RepeatMasker package)

Note
Use the parameters "-noLowSimple -pvalue 0.0001 -engine ncbi" when running RepeatProteinMask.

The following sub-steps are the process for de novo predictions to identify repetitive elements in the Limnodynastes dumerilii dumerilii genome assembly.
Execute RepeatModeler (v2.0, RRID:SCR_015027) on the Limnodynastes dumerilii dumerilii assembly to build a de novo repeat library for this species.
Employ RepeatMasker (v4.1.0) to align the Limnodynastes dumerilii dumerilii genome sequences against the de novo library for repetitive element identification.
Identify tandem repeats in the Limnodynastes dumerilii dumerilii genome assembly by Tandem Repeats Finder (v4.09).

Note
Use the parameters "Match=2 Mismatch=7 Delta=7 PM=80 PI=10 Minscore=50 MaxPeriod=2000" when running Tandem Repeats Finder.