Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map

Figures & data

Table 1. Genome assembly statistics of Gloeostereum incarnatum strain GiC-126.

General features		Properties of predicted gene models
Genome size（Mb）	34.52	Nr alignment	13,751
GC content (%)	49.20	KEGG alignment	10,504
Number of contigs	5885	Swissprot alignment	6358
Number of predict gene models	16,895	KOG alignment	5473
Number of exons	30,162	Pfam alignment	4996
Average exon size (bp)	432.54	GO alignment	3244
Number of introns	13,267	PHI alignment	2170
Average introns size (bp)	253.66	CAZy alignment	144

Figure 1. Genome annotations of Gloeostereum incarnatum strains GiC-126 and CCMJ2665.

Table 2. Genomic characteristics of Gloeostereum incarnatum strains GiC-126 and CCMJ2665.

Strain	GiC-126	CCMJ2665
Genome assembly length (Mb)	34.52	38.65
GC content (%)	49.20	49.00
Number of genes	16,895	15,251
Number of scaffolds	1981	20
Number of contig	5885	3609
Genome coverage	176.0x	94.0x
Sequencing technology	Illumina HiSeq	PacBio Sequel
ssembly Method	Velvet v. 1.2	SOAPdenovo v. OCT-2018

Figure 2. Integration of the Gloeostereum incarnatum genome assembly sequence based on genetic linkage map. Left, CCMJ2665 genome assembly sequence (SCAFFOLD) and length (kb); right, GiC-126 genome assembly sequence (scaffold) and length (kb). Number indicated the lengths of the scaffolds (kb). Red numbers and lines indicate the scaffold sequences where an anchoring problem occurred.

Table 3. Integration of the genome assembly sequences of Gloeostereum incarnatum strains GiC-126 and CCMJ2665.

No.	Number of scaffolds	No.	Number of scaffolds
SCAFFOLD1	1046	SCAFFOLD11	41
SCAFFOLD2	4	SCAFFOLD12	38
SCAFFOLD3	42	SCAFFOLD13	10
SCAFFOLD4	59	SCAFFOLD14	30
SCAFFOLD5	70	SCAFFOLD15	27
SCAFFOLD6	51	SCAFFOLD16	12
SCAFFOLD7	92	SCAFFOLD17	14
SCAFFOLD8	40	SCAFFOLD18	5
SCAFFOLD9	66	SCAFFOLD19	1
SCAFFOLD10	16

Table 4. Composition and number of SSR loci in the Gloeostereum incarnatum genome assembly sequence.

SSR type	Repeats																	Total
	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	>20
Mononucleotide	–	–	–	–	–	291	111	62	32	9	7	3	5	5	2	1	7	535
Dinucleotide	–	207	78	52	29	10	12	8	4	3	2	4	2	1	1	–	2	415
Trinucleotide	464	178	87	42	13	13	6	4	4	–	1	–	–	1	–	–	–	813
Tetranucleotide	56	16	6	5	2	–	–	–	–	–	–	–	–	–	–	–	–	85
Pentanucleotide	17	4	3	3	1	1	–	–	–	1	–	–	–	–	–	–	–	30
Hexanucleotide	14	10	1	2	3	3	1	–	–	–	–	–	–	–	–	–	–	34
Total	551	415	175	104	48	318	130	74	40	13	10	7	7	7	3	1	9	1912

Figure 3. Size distribution of SSR loci in the Gloeostereum incarnatum genome assembly sequence.

Figure 4. Electrophoresis of 51 pairs of SSR primers ≥ 30bp.

Figure 5. Gene ontology (GO) classification of SSR-containing genes in the Gloeostereum incarnatum genome assembly sequence.

Figure 6. KEGG classification of SSR-containing genes in the Gloeostereum incarnatum genome assembly sequence.

Figure 7. Electrophoresis of 25 pairs of SSR primers related to metabolism.

Table 5. Numbers of CAZymes in the two Gloeostereum incarnatum genomes compared with those in other fungi genomes.

Species	GH	GT	CE	PL	AA	CBM	sum	Species	GH	GT	CE	PL	AA	CBM	sum
G. incarnatum Gi-C126	51	31	16	11	30	5	144	G. incarnatum CCMJ2665	203	70	53	24	108	9	467
A. bisporus	159	54	59	10	92	12	386	H. erinaceus	150	66	56	7	88	6	373
A. ostoyae	253	73	86	28	150	25	615	L. bicolor	132	65	35	7	46	6	291
A. cornea	383	84	109	22	155	18	771	L. edodes	229	66	53	8	90	11	457
A. heimuer	301	63	88	19	116	25	612	O. olearius	187	62	54	10	87	7	407
A. subglabra	337	67	98	21	134	20	677	P. ostreatus	209	63	59	23	135	30	519
C. cinereus	175	72	72	13	128	21	481	S. commune	226	73	63	17	81	11	471
F. filiformis	216	75	70	24	96	7	488	T. fuciformis	121	65	50	2	17	4	259
G. lucidum	250	62	57	9	104	6	488	T. mesenterica	67	65	14	2	12	4	164
G. luxurians	302	82	105	13	159	27	688	V. volvacea	201	63	51	28	118	23	484

CAZy Family: GH: glycoside hydrolase; GT: glycosyltransferase; CE: carbohydrate esterases; PL: polysaccharide lyases; AA: auxiliary activities; CBM: carbohydrate-binding modules.

Figure 8. Linkage group of the segregation distortion site. (A) Linkage group with the MAT-A locus. (B) Linkage group before the addition of the MAT-A locus. (C) Linkage group of the segregation distortion site (except LG1).

Table 6. Segregation distortion sites of SSRs in the Gloeostereum incarnatum linkage map after adding the MAT-A locus.

Locus name	Genotype		χ^2 Value	Direction of skewed	Linkage group		scaffold
	A	B			LG	Pos/cM	Pos/cM	Start	End
SSR4	74	40	10.14	A	LG1	43.5	scaffold949	45.227	45.258
SSR583	72	42	7.89	A	LG1	59.9	scaffold1920	104.676	104.687
SSR581	70	44	5.93	A	LG1	64	scaffold1920	99.686	99.697
SSR139	68	46	4.25	A	LG1	67.1	scaffold1920	60.271	60.303
SSR221	68	46	4.25	A	LG1	113.5	scaffold1075	20.503	20.526
SSR171	69	45	5.05	A	LG1	118.5	scaffold1571	249.249	249.272
SSR32	72	42	7.89	A	LG1	140.5	scaffold698	93.528	93.549
SSR301	68	46	4.25	A	LG3	27.8	scaffold681	29.16	29.171
SSR348	68	46	4.25	A	LG4	56.5	scaffold514	416.806	416.823
SSR188	68	46	4.25	A	LG5	50.4	scaffold1367	13.386	13.409
SSR163	69	45	5.05	A	LG5	59.8	scaffold165	155.683	155.7
SSR478	72	42	7.89	A	LG5	64.4	scaffold2154	199.829	199.849
SSR81	72	42	7.89	A	LG5	67	scaffold33	143.301	143.327
SSR470	68	46	4.25	A	LG8	31.6	scaffold2159	40.365	40.385

(A) Skewed toward GiC-126. (B) Skewed toward GiD-15.

Figure 9. Structure of the MAT-A in the GiC-126 genome. (A) Structure of MAT-A. (B) Structures of the mip and beta-fg genes in MAT-A.

Table 7. Genes in the MAT-A in the Gloeostereum incarnatum genome assembly sequence.

No.	Gene	Mating-type locus	Length (bp)
1	HDTF-1 (C12611655)	scaffold353	693
2	HD1-1 (C12616611)	scaffold885	2436
3	HD1-2 (C12616617)	scaffold885	1644
4	mip-1 (C12616608)	scaffold885	864
5	mip-2 (C162616609)	scaffold885	447
6	beta-fg-1 (C12616618)	scaffold885	294
7	beta-fg-2 (C12616619)	scaffold885	510