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Comparative Study
. 2021 May 7;13(5):evab063.
doi: 10.1093/gbe/evab063.

Comparative Analysis of Annotation Pipelines Using the First Japanese White-Eye (Zosterops japonicus) Genome

Madhvi Venkatraman  1   2 , Robert C Fleischer  1 , Mirian T N Tsuchiya  1   3
Affiliations
Comparative Study

Comparative Analysis of Annotation Pipelines Using the First Japanese White-Eye (Zosterops japonicus) Genome

Madhvi Venkatraman et al. Genome Biol Evol. .

Abstract

Introduced into Hawaii in the early 1900s, the Japanese white-eye or warbling white-eye (Zosterops japonicus) is now the most abundant land bird in the archipelago. Here, we present the first Z. japonicus genome, sequenced from an individual in its invasive range. This genome provides an important resource for future studies in invasion genomics. We annotated the genome using two workflows-standalone AUGUSTUS and BRAKER2. We found that AUGUSTUS was more conservative with gene predictions when compared with BRAKER2. The final number of annotated gene models was similar between the two workflows, but standalone AUGUSTUS had over 70% of gene predictions with Blast2GO annotations versus under 30% using BRAKER2. Additionally, we tested whether using RNA-seq data from 47 samples had a significant impact on annotation quality when compared with data from a single sample, as generating RNA-seq data for genome annotation can be expensive and requires well preserved tissue. We found that more data did not significantly change the number of annotated genes using AUGUSTUS but using BRAKER2 the number increased substantially. The results presented here will aid researchers in annotating draft genomes of nonmodel species as well as those studying invasion success.

Keywords: bird genomics; genome annotation; invasion biology.

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Figures

<sc>Fig</sc>. 1.
Fig. 1.
(A) Visualization of assembly stats (https://github.com/rjchallis/assembly-stats) displaying the scaffold N50 in dark orange, N90 in light orange, GC content in dark blue, and BUSCO results in green. (B) Illustration of Zosterops japonicus. (C) Venn diagram of orthologs identified by Orthofinder comparing AUGUSTUS (workflow 1) and BRAKER (workflow 2) results from both data sets (D1 and D2). http://bioinformatics.psb.ugent.be/webtools/Venn/.
See this image and copyright information in PMC

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