2.3　Sequencing and assembly

The genomes of P.polonicum hy4 and C.gloeosporioides Cg01 were sequenced with Illumina HiSeq 2000，using a whole-genome shotgun-sequencing strategy.Three sequencing libraries were constructed for P.polonicum hy4，with insert sizes of 170bp，750bp，and 5kb.Four libraries were for C.gloeosporioides Cg01，with insert sizes of 170bp，300bp，500bp，and 5 kb.Clean reads were assembled using ALLPATHS-LG to construct scaffolds(Gnerre et al.，2011).The Whole Genome Shotgun projects have been deposited at DDBJ/ENA/GenBank under the accession QPIC00000000(P.polonicum hy4)and QRFY00000000(C.gloeosporioides Cg01).The versions described in this paper are version QPIC01000000 and QRFY01000000，respectively.(https://www.daowen.com)

The RNA sequencing was performed with an Illumina HiSeq 4000 and 125bp pairedend reads were generated.Clean reads were obtained by removing reads containing adapter，reads containing ploy-N and low quality reads from raw data.Top Hat v2.0.12 was used to align the clean reads to the reference genomes(Trapnell et al.，2009).Cufflinks(Trapnell et al.，2010)was then used to calculate the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced(FPKM).