3.1 Genome sequencing，assembly，and characterizatio...
The assembled genome of hy4 was 33.92Mb，and the total length of the eight largest scaffolds was 29.28Mb(approximately 86.32%of the assembled genome)(Table 1，Figure 3).The longest scaffold of hy4 was～10.0Mb，and N50 was～4.0Mb(Table 1).The whole genome of Cg01 was assembled in 265 scaffolds，with a total length of 55.77Mb(Table 1).The longest scaffold of Cg01 reached 3.5Mb，with N50 of～1.8Mb(Table 1).The average GC content of hy4 was～46.9%，and the ratio of GC sites per 50 kb was 22%～54%，while those of Cg01 were much higher：～53.2%and 37%～59%，respectively(Figure 3).
Table 1 Genomic information for the two HupA-producing endophytes P.polonicum hy4 and C.gloeosporioides Cg01
(https://www.daowen.com)
Figure 3 Genome organization and gene distribution of P.polonicum hy4(A)and C.gloeosporioides Cg01(B)
From the outside inward，the first circle represents the scaffolds.Scaffolds 0～7 represent the longest eight scaffolds of hy4 and Cg01.The second circle indicates the GC content with the ratio of GC sites per 50 kb(hy4：0.22～0.54；Cg01：0.37～0.59).The third circle indicates the gene density with the frequency of sites per 50 kb(deeper color indicates larger numbers；hy4：0～28，Cg01：2～26).
A total of 11，696 and 17，713 protein-coding genes(PCGs)were predicted from the genomes of hy4 and Cg01，respectively.The lengths of PCGs in hy4 ranged from 156 to 19539bp，with an average size of 1637bp.There was a wider range of PCGs lengths in Cg01，from 156 to 31，747bp.Genes were typically with exons，averaging 474bp in hy4 and 504bp in Cg01.The gene density measured as frequency of sites per 50 kb was 0～28 in hy4 and 2～26 in Cg01(Figure 3).
To conduct functional annotation of the gene models，we used the Blastp search(E-value≤1e-5)of the putative PCG sequences against several databases(KEGG，GO，KOG，Pfam，Swiss-Prot，and Refseq).In summary，11，282(96.46%)genes in hy4 and 16，218(91.56%)genes in Cg01 have annotation information(Figure 4)，suggesting high quality of genome assembly and gene prediction.Among these annotated genes in hy4，11240 genes(99.6%)Blastp to Refseq showed an e-value≤1e-5 and 10393 genes(92.1%)had an e-value≤1e-50.In Cg01，16，156(99.6%)genes had an e-value≤1e-5 and 15，193(93.7%)showed e-value≤1e-50.