biostudies-literatureXie YNational Natural Science Foundation of China1040https://www.ebi.ac.uk/biostudies/studies/S-EPMC10607883biostudies-literatureUnknown9(10)Coevolution between the pathogen and host plant drives pathogenic effector diversity. However, the molecular mechanism behind host-specific pathogenesis remains to be explored. Here, we present a 43 Mb whole-genome sequence of <i>Endomelanconiopsis endophytica</i> strain LS29, a host-specific pathogen of the common subtropical tree <i>Castanopsis fissa</i>. We described its genome annotations and identified its effector candidates. By performing temporal transcriptome sequencing of <i>E. endophytica</i> on <i>C. fissa</i> during early infection, we found that <i>E. endophytica</i> repressed other microbes in order to attack the tissue of the host by producing antibiotics earlier than 24 h post-inoculation (hpi). Simultaneously, a variety of effectors were secreted to recognize the host plaJournal of fungi (Basel, Switzerland)Host Recognition and Specific Infection of <i>Endomelanconiopsis endophytica</i> during Early Infection.PMC1060788331830010, 32271608Shi LLi YXie YYu SCheng KfalseHost Recognition and Specific Infection of <i>Endomelanconiopsis endophytica</i> during Early Infection.Coevolution between the pathogen and host plant drives pathogenic effector diversity. However, the molecular mechanism behind host-specific pathogenesis remains to be explored. Here, we present a 43 Mb whole-genome sequence of <i>Endomelanconiopsis endophytica</i> strain LS29, a host-specific pathogen of the common subtropical tree <i>Castanopsis fissa</i>. We described its genome annotations and identified its effector candidates. By performing temporal transcriptome sequencing of <i>E. endophytica</i> on <i>C. fissa</i> during early infection, we found that <i>E. endophytica</i> repressed other microbes in order to attack the tissue of the host by producing antibiotics earlier than 24 h post-inoculation (hpi). Simultaneously, a variety of effectors were secreted to recognize the host pla2023-01-01T00:00:00Z2023 Oct2025-04-04T08:14:59.327Z2025-04-04T08:14:59.327ZS-EPMC106078833788829610.3390/jof9101040