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. 2023 Aug 17;10(9):uhad165.
doi: 10.1093/hr/uhad165. eCollection 2023 Sep.

Benchmarking gene set of gymnosperms for assessing genome and annotation completeness in BUSCO

Jun-Jie Wu  1 , Yu-Wei Han  2 , Chen-Feng Lin  1 , Jing Cai  2 , Yun-Peng Zhao  1
Affiliations

Benchmarking gene set of gymnosperms for assessing genome and annotation completeness in BUSCO

Jun-Jie Wu et al. Hortic Res. .
No abstract available

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Figures

Figure 1
Figure 1
Comparison of the gymnosperm gene set with the embryophyte gene set. a, b Expected and predicted missing values for the input sequence (a) and BUSCOs (b) with different levels of depletion using the gymnosperm (yellow) and Embryophyta (blue) gene sets under genome (rectangle) and protein (circle) modes in BUSCO (version 5.4.7). Solid orange lines indicate the expected missing values. c, d Estimates of mean completeness of the 11 chromosome-level gymnosperm genomes (c) and 204 gymnosperm transcriptomes (d) using the gymnosperm and Embryophyta gene sets. e Species tree inferred from the 1603 gene trees based on the gymnosperm data set using ASTRAL. The rectangles on the species tree represent the gymnosperm genomes used in the gymnosperm gene set. Two heat maps show the proportion of complete and missing BUSCOS using the gymnosperm (GYM) and the Embryophyta (EMB) gene set in BUSCO (version 5.4.7); the color intensity indicates the proportion. Plant silhouettes of Ginkgoidae, Cycadidae, Cupressidae, Gnetidae, and Pinidae were obtained from PhyloPic (http://phylopic.org).
See this image and copyright information in PMC

References

    1. Birks H. Angiosperms versus gymnosperms in the Cretaceous. Proc Natl Acad Sci USA. 2020;117:30879–81 - PMC - PubMed
    1. Condamine FL, Silvestro D, Koppelhus EBet al. . The rise of angiosperms pushed conifers to decline during global cooling. Proc Natl Acad Sci USA. 2020;117:28867–75 - PMC - PubMed
    1. Chen F, Song Y, Li Xet al. . Genome sequences of horticultural plants: past, present, and future. Hortic Res. 2019;6:112 - PMC - PubMed
    1. Yang Y, Ferguson DK, Liu Bet al. . Recent advances on phylogenomics of gymnosperms and a new classification. Plant Divers. 2022;44:340–50 - PMC - PubMed
    1. Manni M, Berkeley MR, Seppey Met al. . BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol. 2021;38:4647–54 - PMC - PubMed