Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters

Table 2 Differences between the core chromosomes (1-10) of Colletotrichum higginsianum and mini-chromosomes 11 and 12

		Chromosome
Characteristic	1-10 (mean)	11	12
Total length (bp)	4,914,036	646,208	597,935
Number of protein-coding genes	1,438	138	133
Proportion of genes by length (%)	46.0	25.5***	25.4***
Proportion of expressed genes (%)^a	54.1	31.9**	9.8***
Number of transposable element (TE) copies	128	146	63
Proportion of TEs by length (%)	5.9	38.4***	28.0***
G+C (%)	54.5	49.3***	47.2***
Proportion of genes with unknown function (%)	25.7	55.8***	73.7***
Proportion of secreted protein genes (%)	11.2	10.1	7.5
Proportion of effector genes (%) ^b	1.9	5.8**	4.5*

Asterisks indicate data for the mini-chromosomes differ significantly from the mean for chromosomes 1-10 (Fisher’s exact test, *** P <0.001; ** P <0.01; * P <0.05)
^aGenes were considered to be expressed if they showed ≥1% of the expression-level of actin (corresponding to ≥10 TPM), based RNA-Seq data from one in vitro and three in planta samples [13]
^bCandidate secreted effector protein genes included CSEPs predicted from the genome (secreted proteins without homologs outside the genus Colletotrichum) and some ChECs (C. higginsianum effector candidates) previously predicted from the transcriptome [32] that are absent from the new annotation or have BLAST hits to effectors from outside the genus

ISSN: 1471-2164