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
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Chromosomal level assembly and population sequencing of the Chinese tree shrew genome
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(
)
- 1. Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
2. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming Yunnan 650223, China
3. Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming Yunnan 650204, China
4. Kunming Primate Research Center of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
5. KIZ–CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
6. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
7. Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
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Received:2019-07-12Accepted:2019-08-09Online:2019-11-18Published:2019-08-15 -
Contact:Yong-Gang Yao E-mail:yaoyg@mail.kiz.ac.cn -
Supported by:the National Natural Science Foundation of China(U1402224);Yunnan Province(2015HA038 and 2018FB054);Chinese Academy of Sciences(CAS zsys-02)
Cite this article
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.
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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 |
Table 1
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."
Figure 1
Table 2
Assessment of assembly completeness in Chinese tree shrew using BUSCO"
| Parameter | No. | Percentage (%) |
|---|---|---|
| Complete genes | 3 749 | 91.40 |
| Complete and single-copy genes | 3 696 | 90.10 |
| Complete and duplicated genes | 53 | 1.30 |
| Fragmented genes | 184 | 4.50 |
| Missing genes | 171 | 4.10 |
| Total genes | 4 104 | – |
Table 2
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 3
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 4
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 5
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 6
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 7
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 8
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 9
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 |
Table 10
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 2
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 3
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."
Figure 4
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