AUTHOR=Bates Helen J. , Pike Jamie , Price R. Jordan , Jenkins Sascha , Connell John , Legg Andrew , Armitage Andrew , Harrison Richard J. , Clarkson John P. 

TITLE=Comparative genomics and transcriptomics reveal differences in effector complement and expression between races of Fusarium oxysporum f.sp. lactucae

JOURNAL=Frontiers in Plant Science

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1415534

DOI=10.3389/fpls.2024.1415534

ISSN=1664-462X

ABSTRACT=<p>This study presents the first genome and transcriptome analyses for <italic>Fusarium oxysporum</italic> f. sp. <italic>lactucae</italic> (Fola) which causes Fusarium wilt disease of lettuce. Long-read genome sequencing of three race 1 (Fola1) and three race 4 (Fola4) isolates revealed key differences in putative effector complement between races and with other <italic>F. oxysporum</italic> ff. spp. following <italic>mimp</italic>-based bioinformatic analyses. Notably, homologues of <italic>Secreted in Xylem</italic> (<italic>SIX</italic>) genes, also present in many other <italic>F. oxysporum</italic> ff. spp, were identified in Fola, with both <italic>SIX9</italic> and <italic>SIX14</italic> (multiple copies with sequence variants) present in both Fola1 and Fola4. All Fola4 isolates also contained an additional single copy of <italic>SIX8</italic>. RNAseq of lettuce following infection with Fola1 and Fola4 isolates identified highly expressed effectors, some of which were homologues of those reported in other <italic>F. oxysporum</italic> ff. spp. including several in <italic>F. oxysporum</italic> f. sp. <italic>apii</italic>. Although <italic>SIX8</italic>, <italic>SIX9</italic> and <italic>SIX14</italic> were all highly expressed in Fola4, of the two <italic>SIX</italic> genes present in Fola1, only <italic>SIX9</italic> was expressed as further analysis revealed that <italic>SIX14</italic> gene copies were disrupted by insertion of a transposable element. Two variants of Fola4 were also identified based on different genome and effector-based analyses. This included two different <italic>SIX8</italic> sequence variants which were divergently transcribed from a shared promoter with either <italic>PSE1</italic> or <italic>PSL1</italic> respectively. In addition, there was evidence of two independent instances of HCT in the different Fola4 variants. The involvement of helitrons in Fola genome rearrangement and gene expression is discussed.</p>