Bult C J, Blake J A, Calvi B R, Cherry J M, DiFrancesco V, Fullem R, Howe K L, Kaufman T, Mungall C, Perrimon N, Shimoyama M, Sternberg P W, Thomas P, Westerfield M, Consorti A G R. 2019. The alliance of genome resources: building a modern data ecosystem for model organism databases. Genetics, 213, 1189–1196.

Chen H, Fang Y, Song W, Shu H, Li X, Ye W, Wang Y, Dong S. 2023. The SET domain protein PsKMT3 regulates histone H3K36 trimethylation and modulates effector gene expression in the soybean pathogen Phytophthora sojae. Molecular Plant Pathology, 24, 346–358.

Chen H, Shu H, Wang L, Zhang F, Li X, Ochola S O, Mao F, Ma H, Ye W, Gu T, Jiang L, Wu Y, Wang Y, Kamoun S, Dong S. 2018. Phytophthora methylomes are modulated by 6mA methyltransferases and associated with adaptive genome regions. Genome Biology, 19, 181.

Danchin A, Ouzounis C, Tokuyasu T, Zucker J D. 2018. No wisdom in the crowd: Genome annotation in the era of big data-current status and future prospects. Microbial Biotechnology, 11, 588–605.

Denton J F, Lugo-Martinez J, Tucker A E, Schrider D R, Warren W C, Hahn M W. 2014. Extensive error in the number of genes inferred from draft genome assemblies. PLoS Computational Biology, 10, e1003998.

Deutekom E S, Vosseberg J, van Dam T J P, Snel B. 2019. Measuring the impact of gene prediction on gene loss estimates in eukaryotes by quantifying falsely inferred absences. PLoS Computational Biology, 15, e1007301.

Dragan M A, Moghul I, Priyam A, Bustos C, Wurm Y. 2016. GeneValidator: Identify problems with protein-coding gene predictions. Bioinformatics, 32, 1559–1561.

Fang Y, Tyler B M. 2016. Efficient disruption and replacement of an effector gene in the oomycete Phytophthora sojae using CRISPR/Cas9. Molecular Plant Pathology, 17, 127–139.

Feng H, Wan C, Zhang Z, Chen H, Li Z, Jiang H, Yin M, Dong S, Dou D, Wang Y, Zheng X, Ye W. 2021. Specific interaction of an RNA-binding protein with the 3´-UTR of its target mRNA is critical to oomycete sexual reproduction. PLoS Pathogens, 17, e1010001.

Gao J, Cao M, Ye W, Li H, Kong L, Zheng X, Wang Y. 2015. PsMPK7, a stress-associated mitogen-activated protein kinase (MAPK) in Phytophthora sojae, is required for stress tolerance, reactive oxygenated species detoxification, cyst germination, sexual reproduction and infection of soybean. Molecular Plant Pathology, 16, 61–70.

Guigo R, Agarwal P, Abril J F, Burset M, Fickett J W. 2000. An assessment of gene prediction accuracy in large DNA sequences. Genome Research, 10, 1631–1642.

Guigo R, Flicek P, Abril J F, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic V B, Birney E, Castelo R, Eyras E, Ucla C, Gingeras T R, Harrow J, Hubbard T, Lewis S E, Reese M G. 2006. EGASP: The human ENCODE genome annotation assessment project. Genome Biology, 7, S2.1–31.

Hadley C. 2003. Righting the wrongs-DNA and protein sequence databases are increasingly useful research tools. But to maximize their potential, the errors in them need to be addressed. EMBO Reports, 4, 829–831.

Van den Hoogen D J, Meijer H J G, Seidl M F, Govers F. 2018. The ancient link between G-protein-coupled receptors and C-terminal phospholipid kinase domains. mBio, 9, e02119-17.

Hua C L, Wang Y L, Zheng X B, Dou D L, Zhang Z G, Govers F, Wang Y C. 2008. A Phytophthora sojae G-protein alpha subunit is involved in chemotaxis to soybean isoflavones. Eukaryotic Cell, 7, 2133–2140.

Li X, Liu Y, Tan X Q, Li D L, Yang X Y, Zhang X, Zhang D Y. 2020. The high-affinity phosphodiesterase is involved in the polarized growth and pathogenicity of. Fungal Biology, 124, 164–173.

McGowan J, Fitzpatrick D A. 2020. Recent advances in oomycete genomics. Advances in Genetics, 105, 175–228.

Meyer C, Scalzitti N, Jeannin-Girardon A, Collet P, Poch O, Thompson J D. 2020. Understanding the causes of errors in eukaryotic protein-coding gene prediction: A case study of primate proteomes. BMC Bioinformatics, 21, 513.

Mohanta T K, Al-Harrasi A. 2021. Fungal genomes: Suffering with functional annotation errors. IMA Fungus, 12, 32.

Qiu M, Li Y, Zhang X, Xuan M, Zhang B, Ye W, Zheng X, Govers F, Wang Y. 2020. G protein alpha subunit suppresses sporangium formation through a serine/threonine protein kinase in Phytophthora sojae. PLoS Pathogens, 16, e1008138.

Qiu M, Tian M, Yong S, Sun Y, Cao J, Li Y, Zhang X, Zhai C, Ye W, Wang M, Wang Y. 2023. Phase-specific transcriptional patterns of the oomycete pathogen Phytophthora sojae unravel genes essential for asexual development and pathogenic processes. PLoS Pathogens, 19, e1011256.

Salzberg S L. 2019. Next-generation genome annotation: We still struggle to get it right. Genome Biology, 20, 92.

Thines M. 2018. Oomycetes. Current Biology, 28, R812-R813.

Tyler B M, Tripathy S, Zhang X, Dehal P, Jiang R H, Aerts A, Arredondo F D, Baxter L, Bensasson D, Beynon J L, Chapman J, Damasceno C M, Dorrance A E, Dou D, Dickerman A W, Dubchak I L, Garbelotto M, Gijzen M, Gordon S G, Govers F, et al. 2006. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science, 313, 1261–1266.

Wang W Z, Xue Z L, Xie L F, Zhou X, Zhang F, Zhang S C, Govers F, Liu X L. 2023. Sterol-sensing domain (SSD)-containing proteins in sterol auxotrophic mediate sterol signaling and play a role in asexual reproduction and pathogenicity. Microbiology Spectrum, 11, e0379722.

Wang Y, Ye W, Wang Y. 2018. Genome-wide identification of long non-coding RNAs suggests a potential association with effector gene transcription in Phytophthora sojae. Molecular Plant Pathology, 19, 2177–2186.

Weis W I, Kobilka B K. 2018. The molecular basis of G protein-coupled receptor activation. Annual Review of Biochemistry, 87, 897–919.

Ye W, Wang X, Tao K, Lu Y, Dai T, Dong S, Dou D, Gijzen M, Wang Y. 2011. Digital gene expression profiling of the Phytophthora sojae transcriptome. Molecular Plant-Microbe Interactions, 24, 1530–1539.

Zerbino D R, Frankish A, Flicek P. 2020. Progress, challenges, and surprises in annotating the human genome. Annual Review of Genomics and Human Genetics, 21, 55–79.

Zhang X, Zhai C, Hua C, Qiu M, Hao Y, Nie P, Ye W, Wang Y. 2016. PsHint1, associated with the G-protein α subunit PsGPA1, is required for the chemotaxis and pathogenicity of Phytophthora sojae. Molecular Plant Pathology, 17, 272–285.