- phylogenetic breadth of the underlying OrthoDB data set. - To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.. - The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.. - While the BUSCO completeness level has become a widely used quality measure with similar importance as the N50 measure for assembly contiguity, its informative value is highly dependent on the quality and sampling of the underlying orthology data, which may differ vastly across taxonomic groups. - Currently, multiple represen- tative genomes of the highly diverse and rapidly evolving nematode phylum are still poorly annotated. - To over- come this problem in the case of the nematode model organism Pristionchus pacificus, community-based cura- tions have recently been initiated to improve the quality of gene annotations [3, 4]. - However, further strand-specific RNA-seq and Iso-seq data pointed towards the presence of numerous artificial gene fusions in gene dense regions of the genome [3].. - Here, I make use of the community-curated annota- tions of the P. - pacificus genome to improve the annota- tions of related Pristionchus and other genomes of the family Diplogastridae, which were recently sequenced to study the evolutionary dynamics of novel gene families [9]. - Few exceptions are the ge- nomes of the free-living Oscheius tipulae and the parasitic Haemonchus contortus [18], Dirofilaria immitis [19], Loa loa [20], Brugia malayi [21], and Onchocerca volvulus [22]. - Please note that the most recent updates of the P. - 1) and these do not repre- sent the full range of genomic diversity of the nematode phylum [14, 23]. - To this end, I reannotated nine nematode genomes of the family Diplogastridae including seven other Pristionchus spe- cies, which were sequenced previously as part of a phy- logenomic study to investigate the evolutionary dynamics of novel gene families [9, 26]. - Specifically, pre- dicted open reading frames (ORFs) in assembled RNA- seq transcripts [27] as well as protein sequences of the community-curated P. - gene annotations [9]. - annotation accuracy occurs already within the same nematode family, I reevaluated the BUSCO complete- ness of the gene annotations only inferred from hom- ology data (Fig. - Moreover, the evaluation of the contribu- tion of homology-inferred vs. - The new gene annotations of the nine diplogastrid ge- nomes contain between 19 and 39 thousand gene models that are completely evidence-based as they are either supported by transcriptional evidence or by pro- tein conservation with P. - The third most abundant pattern arises from 204 genes that were not found in any of the. - As mentioned above, an alternative explanation would be that these genes are present but could not be detected by the BUSCO pipeline as the nematode odb10 data set does not represent the full diversity of the nematode phylum [14, 23]. - To further test the possibility of un- detected orthologs, I used a complementary approach to find one-to-one orthologs of the corresponding C. - This revealed that 101 (50%) of these 204 genes have predicted one-to-one orthologs in all diplogastrid genomes, which points to a failure of detection of the BUSCO pipeline (Fig. - Comparison of the bitscores from BLASTP searches between BUSCO genes in C. - Thus, I conclude that the insufficient sample size and phylogenetic breadth of the nematode odb10 data set may cause failures in the ortholog detection by the BUSCO pipeline and that the quality of divergent nematode genomes might therefore be underestimated.. - In this study, I have demonstrated the benefit of the community-curated P. - In this context, community an- notation seems to be one of the most effective methods to increase gene annotation quality beyond what can be achieved using automated pipelines. - For example, in the case of the nine diplogastrid genomes, BUSCO genes that are found in the genome or transcriptome (Add- itional file 1, Tables S1, S2), but not in the final gene an- notations can be taken as candidates to further improve gene annotation quality by manual curation. - In the case of the diplogastrid genomes, the completeness level is likely underestimated by up to 3% (101 out of 3131. - a The left heatmap shows the bitscores for 101 randomly subsampled BUSCO orthologs derived from a BLASTP search of the C. - elegans proteins against annotated protein sets of the ten diplogastrid genomes. - The generation of high quality genomes of further members of the Pristionchus genus may therefore help to characterize and compare the genomic basis of these convergent patterns. - In the case of the nematode model organism Pristionchus pacificus, community-based gene curations have previ- ously been presented as an effective means to lift anno- tation quality above the level of what could be obtained by automated pipelines. - With BUSCO com- pleteness levels between 83 and 86%, the reannotated Pristionchus genomes are more complete than most other members of the nematode phylum. - Third, the insufficient sample size and phylogenetic breadth of the BUSCO and OrthoDB data sets may prohibit the detec- tion of orthologs and thus cause an underestimation of nematode genome quality.. - These transcribed ORFs were aligned against the respective reference assembly with the help of the exonerate protein2genome program with the following parameter settings: --bestn 2, −-dnawor- dlen 20, and --maxintron 20,000 (version . - 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