Zoological Research ›› 2019, Vol. 40 ›› Issue (6): 506-521.doi: 10.24272/j.issn.2095-8137.2019.063
Special Issue: Tree shrew biology; Animal models
• Articles • Previous Articles Next Articles
Yu Fan1,2,Mao-Sen Ye1,3,Jin-Yan Zhang1,3,Ling Xu1,2,Dan-Dan Yu1,2,Tian-Le Gu1,3,Yu-Lin Yao1,3,Jia-Qi Chen4,Long-Bao Lv4,Ping Zheng2,3,4,5,6,7,Dong-Dong Wu2,6,Guo-Jie Zhang2,6,Yong-Gang Yao1,2,3,4,5()
Received:
2019-07-12
Accepted:
2019-08-09
Online:
2019-11-18
Published:
2019-08-15
Contact:
Yong-Gang Yao
E-mail:yaoyg@mail.kiz.ac.cn
Supported by:
Yu Fan, Mao-Sen Ye, Jin-Yan Zhang, Ling Xu, Dan-Dan Yu, Tian-Le Gu, Yu-Lin Yao, Jia-Qi Chen, Long-Bao Lv, Ping Zheng, Dong-Dong Wu, Guo-Jie Zhang, Yong-Gang Yao. Chromosomal level assembly and population sequencing of the Chinese tree shrew genome.2019.
Zoological Research, 40(6): 506-521.
Table 1
Comparison of Chinese tree shrew assembly quality between assemblies TS_1.0 and TS_2.0"
Version | Item | Contig length (bp) | Scaffold length (bp) | Contig No. | Scaffold No. |
---|---|---|---|---|---|
Short-read assembly (KIZ version 1: TS_1.0) | Total | 2 719 442 484 | 2 861 790 358 | 374 120 | 150 513 |
Max_length | 187 505 | 19 269 909 | – | – | |
>2 000 bp | – | – | 180 802 | 4 525 | |
>100 kb | – | – | 305 | 1 418 | |
N50 | 22 000 | 3 655 608 | 36 335 | 234 | |
N60 | 17 500 | 3 042 664 | 50 199 | 319 | |
N70 | 13 431 | 2 302 651 | 67 915 | 427 | |
N80 | 9 571 | 1 648 848 | 91 810 | 573 | |
Long-read assembly (KIZ version 2: TS_2.0) | Total | 2 667 337 536 | 2 667 507 236 | 3 344 | 1 647 |
Max_length | 16 177 999 | 224 450 918 | – | – | |
>2 000 bp | – | – | 3 344 | 1 647 | |
>100 kb | – | – | 1963 | 281 | |
N50 | 3 217 288 | 104 643 080 | 229 | 10 | |
N60 | 2 462 062 | 94 037 081 | 323 | 13 | |
N70 | 1 641 093 | 71 760 103 | 457 | 16 | |
N80 | 995 871 | 57 328 337 | 664 | 20 |
Figure 1
Assembly, annotation, and nucleotide diversity of Chinese tree shrew genome A: Contig length distribution of long-read assembly (TS_2.0) in comparison with short-read assembly (TS_1.0) (Fan et al., 2013). B: Circos plot showing genome-wide distribution profiles of genes, SNPs, and indels across Chinese tree shrew genome, and values of population genetic parameters (π and Tajima’s D). C: Manhattan plot of nucleotide diversity (π) at gene level based on SNPs located in coding regions of six wild tree shrews. Top 30 genes are shown in plot, with a cut-off π value of 0.025."
Table 3
Statistics of Hi-C data for mapping"
Parameter | Hi-C data |
---|---|
Clean data | 705 Gb |
Clean paired-end reads | 2 351 150 069 |
Unmapped paired-end reads | 47 514 976 |
Unmapped paired-end reads rate (%) | 2.02 |
Paired-end reads with singleton | 303 352 692 |
Paired-end reads with singleton rate (%) | 12.9 |
Multi mapped paired-end reads | 443 734 174 |
Multi mapped ratio (%) | 18.87 |
Unique mapped paired-end reads | 1 556 548 227 |
Unique mapped ratio (%) | 66.2 |
Table 4
Pseudo-chromosome sizes and assignment of Hi-C scaffolds"
Pseudo-chromosome | Contig No. | Length (bp) of pseudo-chromosome |
---|---|---|
chr1 | 154 | 224 402 198 |
chr2 | 107 | 187 971 973 |
chr3 | 111 | 137 178 494 |
chr4 | 61 | 121 533 334 |
chr5 | 74 | 120 860 892 |
chr6 | 88 | 117 379 583 |
chr7 | 67 | 108 205 678 |
chr8 | 56 | 108 052 698 |
chr9 | 62 | 104 638 498 |
chr10 | 64 | 101 327 006 |
chr11 | 71 | 97 509 983 |
chr12 | 49 | 94 027 333 |
chr13 | 54 | 92 296 458 |
chr14 | 58 | 89 547 586 |
chr15 | 69 | 71 741 294 |
chr16 | 42 | 69 742 744 |
chr17 | 48 | 66 945 814 |
chr18 | 41 | 63 456 188 |
chr19 | 27 | 57 308 528 |
chr20 | 32 | 54 551 840 |
chr21 | 35 | 49 758 179 |
chr22 | 53 | 52 049 165 |
chr23 | 27 | 43 809 476 |
chr24 | 23 | 42 251 409 |
chr25 | 33 | 41 996 642 |
chr26 | 100 | 30 565 635 |
chr27 | 50 | 25 814 610 |
chr28 | 34 | 26 506 761 |
chr29 | 27 | 22 607 893 |
chr30 | 28 | 21 670 314 |
chrX | 452 | 118 492 391 |
Total anchored | 2 197 | 2 564 200 597 |
Unanchored | 1 616 | 102 561 400 |
Table 5
Assembly quality score value statistics"
Parameter | Long-read assembly (TS_2.0) | Short-read assembly (TS_1.0) |
---|---|---|
Quality value | 28.56 | 26.75 |
Translocation | 2 824 | 6 034 |
Deletion | 3 733 | 12 607 |
Duplication | 142 | 438 |
Inversion | 80 | 99 |
Errors Per 100 Mbp | 253.89 | 718.27 |
HIGH_COV_PE | 12 016 | 66 655 |
HIGH_NORM_COV_PE | 12 415 | 69 902 |
HIGH_OUTIE_PE | 137 | 1 594 |
HIGH_SINGLE_PE | 10 | 151 |
HIGH_SPAN_PE | 1 237 | 32 751 |
LOW_NORM_COV_PE | 536 | 72 38 |
STRECH_PE | 31 741 | 66 763 |
COMPR_PE | 13 818 | 20 437 |
Table 6
Gap closure statistics of the two genome assemblies"
Parameter | Long-read assembly TS_2.0) | Short-read assembly (TS_1.0) |
---|---|---|
Total number of gaps | 1 697 | 223 607 |
Partially closed gap using TS_1.0 | 476 | – |
Partially closed gap using TS_2.0 | – | 0 |
Fully closed gap using TS_1.0 | 39 | – |
Fully closed gap using TS_2.0 | – | 163 220 |
Fully closed gap in genic region | 0 | 65 222 |
Trans-scaffold gaps | 264 | 4 112 |
Table 7
Comparison of transposable elements in Chinese tree shrews between short-read assembly (KIZ version 1: TS_1.0) and long-read assembly (KIZ version 2: TS_2.0)"
Type | Long-read assembly (TS_2.0) | Short-read assembly (TS_1.0) | ||
---|---|---|---|---|
Length (Mp) | % in genome | Length (Mp) | % in genome | |
DNA | 96.8 | 3.6 | 76.6 | 2.7 |
LINE | 553.3 | 20.8 | 295.2 | 10.3 |
SINE | 663.1 | 24.9 | 527.2 | 18.8 |
LTR | 138.0 | 5.2 | 113.1 | 4 |
Other | 0.0005 | 0.0 | 0.06 | 0.002 |
Unknown | 68.0 | 2.6 | 0.9 | 0.03 |
Total | 1 310.5 | 49.1 | 1 001.9 | 35 |
Table 8
Comparison of transposable element subtypes in Chinese tree shrews between short-read assembly (KIZ version 1: TS_1.0) and long-read assembly (KIZ version 2: TS_2.0)"
TE subtype | Long-read assembly (TS_2.0) | Short-read assembly (TS_1.0) | ||
---|---|---|---|---|
Length (Mp) | % in genome | Length (Mp) | % in genome | |
DNA/En-Spm | 7.92 | 0.30 | 4.87 | 0.17 |
DNA/hAT | 34.29 | 1.28 | 33.77 | 1.18 |
DNA/TcMar | 52.11 | 1.96 | 26.90 | 0.94 |
LINE/CR1 | 5.57 | 0.21 | 2.00 | 0.07 |
LINE/L1 | 494.51 | 18.54 | 267.29 | 9.34 |
LINE/L2 | 49.48 | 1.86 | 22.04 | 0.77 |
LINE/Penelope | 2.02 | 0.08 | 2.29 | 0.08 |
LTR/ERV1 | 37.66 | 1.41 | 31.77 | 1.11 |
LTR/ERVK | 18.55 | 0.70 | 8.87 | 0.31 |
LTR/ERVL | 78.13 | 2.93 | 68.40 | 2.39 |
LTR/Gypsy | 2.59 | 0.10 | 2.86 | 0.1 |
SINE/Alu | 10.60 | 0.40 | 3.15 | 0.11 |
SINE/B4 | 3.02 | 0.11 | 1.72 | 0.06 |
SINE/MIR | 47.40 | 1.78 | 23.75 | 0.83 |
SINE/tRNA-Lys | 15.04 | 0.56 | 1.14 | 0.04 |
SINE/Tu-III | 404.49 | 15.17 | 410.09 | 14.33 |
Table 9
Comparison of Chinese tree shrew gene annotation between short-read assembly (KIZ version 1: TS_1.0) and long-read assembly (KIZ version 2: TS_2.0)"
Parameter | Long-read assembly (TS_2.0) | Short-read assembly (TS_1.0) |
---|---|---|
Total number of genes | 23 568 | 22 121 |
Complete ORFs | 21 117 | 21 085 |
Annotated genes | 20 811 | 20 225 |
Average mRNA length | 40 114 | 33 712 |
Average CDS length | 1 527 | 1 404 |
Average exon number | 8.86 | 7.54 |
Average exon length | 172 | 186 |
Average intron length | 4 907 | 4 937 |
Table 10
Comparison of Chinese tree shrew gene functional annotation between short-read assembly (KIZ version 1: TS_1.0) and long-read assembly (KIZ version 2: TS_2.0)"
Functional annotation | Short-read assembly (TS_1.0) | Long-read assembly (TS_2.0) | ||
---|---|---|---|---|
No. | Percent (%) | No. | Percent (%) | |
Total | 22 121 | – | 23 568 | – |
InterPro | 17 420 | 78.7 | 17 534 | 74.4 |
KEGG | 16 593 | 75.0 | 16 964 | 72.0 |
Swissprot & TrEMBL | 20 225 | 91.4 | 20 811 | 88.3 |
Unannotated | 1 896 | 8.6 | 2 309 | 11.7 |
Figure 2
Chinese tree shrew and human MHC genes A: Synteny of MHC genes between Chinese tree shrews and humans. HLA class I & II genes are in red, other genes are in black. Tree shrew TS_2.0 assembly and human genome (hg38; https://www.ncbi.nlm.nih.gov/grc/human) were used for comparison. B: Phylogenetic relationship of MHC-class I genes in humans, tree shrews, and mice."
Figure 3
Examples of structural variants in mouse, macaque, tree shrew, and human genomes A: Chinese tree shrews and humans, but not mice, shared a specific genomic structure in the region from MYSM1 to SLC35D1. B: Chinese tree shrews and mice shared a specific genomic structure in the region from PRKAB2 to POLR3GL, which has undergone dramatic changes in humans. GPR89B (G protein-coupled receptor 89B) and NOTCH2NL (notch 2 N-terminal like A) genes, marked in green, were only present in the human genome. These genomes were retrieved from public domains (mouse: GRCm38; https://www.ncbi.nlm.nih.gov/grc/mouse; macaque: rheMac3(Yan et al., 2011); human: hg38; https://www.ncbi.nlm.nih.gov/grc/human) or generated in this study (tree shrew: TS_2.0)."
Figure 4
Overview of updated tree shrew database (TreeshrewDB version 2.0) Inclusion of the high-quality reference genome assembly (TS_2.0) in TreeshrewDB version 2.0 provided a comprehensive update of gene annotation information, genomic variations, population genetic features, and mRNA expressions. Population genetic parameters (including π, Watterson theta estimate (θw) (Watterson, 1975), Tajima’s D (Tajima, 1989), Fu and Li’s D (Fu & Li, 1993), Fu and Li’s F (Fu & Li, 1993), and Fay and Wu’s H (Fay & Wu, 2000)) were estimated based on SNPs located in coding regions in the whole genome sequences of six wild tree shrews. The database is freely accessible at http://www.treeshrewdb.org."
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