Genome assembly and transcriptome profiling of the woodland strawberry (<i>Fragaria vesca</i>) 'Ruegen'

Xue Li; Shuang Liu; Junxiang Zhang; Zhihong Zhang; Xue Li; Shuang Liu; Junxiang Zhang; Zhihong Zhang

doi:10.48130/frures-0025-0022

Figures (5) Tables (3)

Figure 1.
Circular visualization of 'Ruegen' genome. The circular diagram displays (from inner to outer rings): (1) chromosomal homologous relationships; (2) GC content distribution (100-kb windows); (3) GC skew patterns (100-kb windows); (4) gene density (100-kb windows).
Figure 2.
Hi-C assembly chromosome interaction heatmap. chr1−chr7 represents chromosome groups 1−7. The horizontal and vertical axes represent the order of each bin on the corresponding chromosome group.
Figure 3.
Comparative distribution of gene structural elements in 'Ruegen', 'CFRA2339', 'Hawaii 4', and 'Yellow Wonder'. (a) Gene length distribution (bp), showing the percentage of genes in each size bin. (b) CDS length distribution (bp). (c) Exon length distribution (bp). (d) Intron length distribution (bp).
Figure 4.
Heat map of expression levels of EBGs during fruit development in 'Ruegen' (RG) and 'YanLi' (YL). (a) Five EBGs show divergent expression patterns between 'Yanli' (YL) and RG while maintaining consistent allelic expression within YL. (b) F3'H and FLS exhibiting expression patterns concordant with specific YL alleles. The color scale represents log₁₀(FPKM + 0.0001) normalized expression values.
Figure 5.
Heat map of expression levels of LBGs during fruit development in 'Ruegen' (RG) and 'YanLi' (YL). (a) ANS, TT19, and MYB1 show divergent expression patterns between 'Yanli' (YL) and RG while maintaining consistent allelic expression within YL. (b) The expression pattern of AHA10 gene is similar in YL and RG. (c) Four RG LBGs exhibiting expression patterns concordant with specific YL alleles. The color scale represents log₁₀(FPKM + 0.0001) normalized expression values.

Assembly feature	Number
Scaffold number	50
Scaffold length	221,321,825
Scaffold N50 (bp)	33,167,685
Scaffold N90 (bp)	23,655,317
Scaffold max (bp)	40,042,862
Gap total length (bp)	3,010
Contig number	142
Contig length (bp)	221,318,815
Contig N50 (bp)	8,351,392
Contig N90 (bp)	1,040,108
Contig max (bp)	18,184,794
GC content (%)	38.48

Table 1.

Statistical information on genome assembly.

	Description	Reference databases	Number	Percent (%)
Total			36,071
	Annotated		31,377	86.99
		InterPro	23,870	66.18
		GO	16,366	45.37
		KEGG_ALL	30,574	84.76
		KEGG_KO	10,674	29.59
		Swissprot	19,054	52.82
		TrEMBL	30,140	83.56
		TF	1,736	4.81
		Pfam	23,481	65.10
		NR	30,947	85.79
		KOG	23,055	63.92
	Unannotated		4,694	13.01

Table 2.

Functional annotation statistics results.

	RepBase TEs		TE proteins		De novo		Combined TEs
	Length (bp)	% in genome	Length (bp)	% in genome	Length (bp)	% in genome	Length (bp)	% in genome
DNA	22,861,785	10.33	4,802,499	2.17	19,895,368	8.99	29,624,293	13.39
LINE	2,837,652	1.28	1,789,441	0.81	3,417,282	1.54	4,676,541	2.11
SINE	10,031	0	0	0	8,265	0	18,296	0.01
LTR	26,068,846	11.78	9,354,199	4.23	22,028,459	9.95	35,119,957	15.87
Satellite	352,115	0.16	0	0	257,026	0.12	549,061	0.25
Simple_repeat	0	0	0	0	274,771	0.12	274,771	0.12
Other	299	0	747	0	0	0	1,046	0
Unknown	393,519	0.18	18,210	0.01	10,928,536	4.94	11,128,498	5.03
Total	51,904,045	23.45	15,956,836	7.21	56,499,821	25.53	79,971,177	36.13

Table 3.

Statistics of the repeated sequences.