Jouet, A. | bioRxiv Science

bioRxiv2020

Identification of Avramr1 from Phytophthora infestans using long read and cDNA pathogen-enrichment sequencing (PenSeq)

O_LIPotato late blight, caused by the oomycete pathogen Phytophthora infestans, significantly hampers potato production. Recently, a new Resistance to Phytophthora infestans (Rpi) gene, Rpi-amr1, was cloned from a wild Solanum species, Solanum americanum. Identification of the corresponding recognized effector (Avirulence, or Avr) genes from P. infestans is key to elucidating their naturally occurring sequence variation, which in turn informs the potential durability of the cognate late blight resistance. C_LIO_LITo identify the P. infestans effector recognized by Rpi-amr1, we screened available effector libraries and used long read and cDNA pathogen-enrichment sequencing (PenSeq) on four P. infestans isolates to explore the untested effectors. C_LIO_LIBy using SMRT and cDNA PenSeq, we identified 47 highly expressed effectors from P. infestans, including PITG_07569 which triggers a highly specific cell death response when transiently co-expressed with Rpi-amr1 in Nicotiana benthamiana, suggesting that PITG_07569 is Avramr1. C_LIO_LIHere we demonstrate that long read and cDNA PenSeq enables the identification of full-length RxLR effector families, and their expression profile. This study has revealed key insights into the evolution and polymorphism of a complex RxLR effector family that is associated with the recognition by Rpi-amr1. C_LI

genomics↗

bioRxiv2020

A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region

The human- and animal-adapted lineages of the Mycobacterium tuberculosis complex (MTBC) are thought to have clonally expanded from a common progenitor in Africa. However, the molecular events that accompanied this emergence remain largely unknown. Here, we describe two MTBC strains isolated from patients with multidrug-resistant tuberculosis, representing an as-yet-unknown lineage, named Lineage 8 (L8), seemingly restricted to the African Great Lakes region. Using genome-based phylogenetic reconstruction, we show that L8 is a sister clade to the known MTBC lineages. Comparison with other complete mycobacterial genomes indicate that the divergence of L8 preceded the loss of the cobF genome region - involved in the cobalamin/vitamin B12 synthesis - and gene interruptions in a subsequent common ancestor shared by all other known MTBC lineages. This discovery further supports an East African origin for the MTBC and provides additional molecular clues on the ancestral genome reduction associated with adaptation to a pathogenic lifestyle.

microbiology↗