High-Quality de novo Genome Assembly of Huajingxian 74, a Receptor Parent of Single Segment Substitution Lines

doi:10.1016/j.rsci.2020.09.010

Abstract

Fangping Li, Yanhao Gao, Bingqi Wu, Qingpei Cai, Pengling Zhan, Weifeng Yang, Wanxuan Shi, Xiaohua Li, Zifeng Yang, Quanya Tan, Xin Luan, Guiquan Zhang, Shaokui Wang. High-Quality de novo Genome Assembly of Huajingxian 74, a Receptor Parent of Single Segment Substitution Lines[J]. Rice Science, 2021, 28(2): 109-113.

Figures/Tables 14

Fig. 1. Phenotype (A) and phylogeney (B) of HJX74 (Huajingxian 74).Phylogenetic tree constructed by the maximum- likelihood method using coding sequences of single copy lineal homologous genes (the genes were showed in Table S4). Totally 12 species or varieties were used for alignment, 9 of them are cultivated rice (Nipponbare, 93-11, R498, Zhenshan 97, IR64, Minghui 63, Basmati, DomSuid and HJX74) and the other 3 are wild rice (O. meridionalis, O. barthii and O. rufipogon).

Fig. 2. Characteristics of Huajingxian 74 (HJX74) genome and synteny examining, SNPs (single nucleotide polymorphisms) and InDels (Inserts/Deletes) mining, dN/dS comparison with Nipponbare (NPB) and R498. A, Distribution of SNPs and InDels between HJX74 and NPB (the data refer to Table S5).B, Distribution of SNPs and InDels between HJX74 and R498 (the data refer to Table S6).C, dN/dS distribution of different combinations. The vertical lines represent average values of dN/dS.D, Chromosomal synteny among HJX74 and two reference genomes of rice.E, Interactive dot plot between HJX74 and NPB.F, Interactive dot plot between HJX74 and R498. G, Characteristics of the HJX74 genome. Tracks from outside to inside are the 12 chromosomes of HJX74, GC content, long terminal repeat density, and simple sequence repeat density (the data refer to Table S11).

Table S1. Comparison of contigs and scaffolds among Huajingxian 74 (HJX74) and two reference rice genomes (Nipponbare and R498).

Statistics without reference	HJX74 (contig level)	HJX74	Nipponbare	R498
Contigs	155	108	63	14
Contigs ≥ 1 000 bp	155	108	63	14
Contigs ≥ 5 000 bp	141	94	62	14
Contigs ≥ 10 000 bp	135	88	51	14
Contigs ≥ 25 000 bp	126	80	20	14
Contigs ≥ 50 000 bp	109	69	18	14
Largest contig	26 609 203	44 230 994	43 270 923	44 361 539
Total length	399 000 942	398 866 991	375 049 285	390 983 850
Total length ≥1 000 bp	399 000 942	398 866 991	375 049 285	390 983 850
Total length ≥5 000 bp	398 955 832	398 821 873	375 045 049	390 983 850
Total length ≥10 000 bp	398 920 023	398 786 031	374 960 283	390 983 850
Total length ≥25 000 bp	398 753 016	398 632 314	374 514 817	390 983 850
Total length ≥50 000 bp	398 046 761	398 182 493	374 450 782	390 983 850
N50	14 408 600	31 354 834	29 958 434	31 778 392
N75	11 330 867	30 528 296	28 443 022	29 952 003
L50	11	6	6	6
L75	18	9	9	9
GC (%)	43.7	43.7	43.57	43.62
# N’s (Mismatches)	0	5 511	118 258	50 000
# N’s per 100 kbp (Mismatches)	0	1.38	31.53	12.79

Fig. S1. Hi-C interactive heat map.

Table S2. Evaluation of Huangjingxian 74 genome assembly by Benchmarking Universal single-copy ortholog (BUSCO) and Core Eukaryotic Genes Mapping Approach (CEGMA).

Method (Database)	Data
BUSCO	C, 98.3%; S, 97.6%, D, 0.7%; F, 0.3%; M, 1.4%; n, 1440
CEGMA	Complet: 230 (92.74%); Complete + Partial: 235 (94.76%)

Table S3. LTR-TRs assembly index (LAI) of R498, Nipponbare and Huajingxian 74 (HJX74).

Species	Length	Intact	Total	Raw LAI	LAI
R498 (indica)	390 983 850	0.0663	0.2828	23.44	23.94
Nipponbare (japonica)	375 049 285	0.0505	0.2452	20.58	22.59
HJX74 (indica)	398 866 991	0.0656	0.2887	22.73	23.42

Fig. S2. Cumulative sequence length and presence and absence variations (PAVs) distribution.A and B, Comparison of cumulative sequence length of HJX74 and two published reference rice genomes (NPB and R498); C and D, Comparison of PAVs length distribution in HJX74 and two published reference rice genomes (NPB and R498).

Fig. S3. Interactive dot plot of Huajingxian 74 (HJX74) and two reference rice genomes (R498 and Nipponbare, NPB).A to C, Paired comparison of HJX74 and two reference genomes on genome level; D, Comparison of HJX74 and two reference rice genomes on the region of chromosome 6(un, Unique alignment; re, Repetitive alignment; sh, Show repetitive alignment).

Fig. S4. Presence and absence variations (PAVs) types and distribution of some chromosomes with significantly different lengths between Huajingxian 74 (HJX74) and Nipponbare (NPB).A, Chromosome 2; B, Chromosome 3; C, Chromosome10.

Table S7. Clustering of homologous genes of 12 species of rice.

Species	Protein	Cluster	Singleton
Oryza barthii	34 575	24 966	3 223
Oryza meridionalis	29 308	20 721	4 088
Oryza rufipogon	37 062	27 114	2 912
Oryza sativa Nipponbare	35 667	23 642	5 446
Oryza sativa 93-11	37 878	25 644	3 690
Oryza sativa Basmati	41 259	29 417	4 210
Oryza sativa DomSufid	38 329	28 037	3 490
Oryza sativa Minghui 63	83 258	40 508	13 514
Oryza sativa R498	88 169	27 111	33 193
Oryza sativa Zhenshan 97	84 957	40 646	14 163
Oryza sativa Huajingxian 74	46 933	27 202	7 991
Oryza sativa IR64	41 458	23 591	9 810

Table S9. Chromosome lengths of Huajingxian 74 (HJX74), Nipponbare (NPB) and R498.

Chromosome	Length of each chromosome (bp)
Chromosome	HJX74	NPB	R498
1	44 230 993	43 270 923	44 361 539
2	38 415 586	35 937 250	37 764 328
3	39 700 684	36 413 819	39 691 490
4	36 567 208	35 502 694	35 849 732
5	30 862 635	29 958 434	31 237 231
6	31 992 588	31 248 787	32 465 040
7	30 655 926	29 697 621	30 277 827
8	30 528 296	28 443 022	29 952 003
9	24 203 274	23 012 720	24 760 661
10	25 662 364	23 207 287	25 582 588
11	31 354 834	29 021 106	31 778 392
12	27 052 960	27 531 856	26 601 357
Average difference		1.390 Mb	0.07543 Mb

Table S10. Repeat content (LTR-RTs) in Huajingxian 74 (HJX74), R498 and Nipponbare (NPB).

Repeat content	HJX74		R498		NPB
Repeat content	Length (bp)	Percentage of genome (%)	Length (bp)	Percentage of genome (%)	Length (bp)	Percentage of genome (%)
Total	110 814 118	27.78	109 473 086	28.00	90 414 977	24.12
Gypsy	84 080 899	21.08	82 619 222	21.13	64 570 822	17.22
Copia	13 457 780	3.37	12 661 044	3.24	13 948 467	3.72
Unknown	13 275 439	3.33	14 192 820	3.63	11 895 688	3.17

Fig. S5. Online accesible platfrom of HJX74 Genome data.A, Display of platform homepage; B, Platform sequence search (BLAST) function; C, Display of FPtools page and online sequence extraction page; D, Display of genes browsing page.

Fig. S6. Sequence difference in presence and absence variations (PAVs) locus.A, SNP detection in PAVs locus; B, Insertion sites detection in PAVs locus.

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