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中国生物工程杂志

China Biotechnology
China Biotechnology
China Biotechnology  2018, Vol. 38 Issue (7): 21-28    DOI: 10.13523/j.cb.20180704
    
The Analysis of the Low Coverage Haematococcus Pluvialis Draft Genome
Jun CHEN1,2,Hua-jun ZHENG3,**(),Ya-ming LIU1,2,Guo-ping ZHAO3,Song QIN1,**()
1 Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003,China
2 University of Chinese Academy of Sciences, Beijing 101418,China
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Abstract  

The investigation on the genomic study of Haematococcus pluvialis would be significant to explore the origin and evolution of green algae and the stress responses in Haematococcus pluvialis;and promote the development of Haematococcus pluvialis industry. The low-coverage draft genome of Haematococcus pluvialis was constructed by the Illumina Hiseq 2500 platform. The predicted genome size was approximately 547Mb, with the GC content of 59.2% by calculating k-mer distribution. The draft genome contained 11 059 predicted protein-coding genes and the average gene size and CDS were 1 711bp and 681bp; every gene contained 3.2 exons and the size of exon was 353bp in average. The analysis of metabolic pathway indicated that the low-coverage genome contained whole glycolysis, tricarboxylic acid cycle, phosphopentose, purine and pyrimidine synthesis and other basic metabolism pathway.

Key words： Haematococcus pluvialis      Genome sequencing      Gene prediction      Gene functional annotation     
Received: 29 June 2017      Published: 13 August 2018
ZTFLH:  Q78  
Corresponding Authors: Hua-jun ZHENG,Song QIN     E-mail: zhenghj@chgc.sh.cn;sqin@yic.ac.cn
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Jun CHEN
Hua-jun ZHENG
Ya-ming LIU
Guo-ping ZHAO
Song QIN
Cite this article:

Jun CHEN,Hua-jun ZHENG,Ya-ming LIU,Guo-ping ZHAO,Song QIN. The Analysis of the Low Coverage Haematococcus Pluvialis Draft Genome. China Biotechnology, 2018, 38(7): 21-28.

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https://manu60.magtech.com.cn/biotech/10.13523/j.cb.20180704     OR     https://manu60.magtech.com.cn/biotech/Y2018/V38/I7/21

Fig.1 17-mer analysis of genome contigs in H. pluvialis
k-mer Contigs number Size (bp) Ave length (bp) Reads usage(%)
35 113 061 66 423 650 587 24.60
45 118 556 87 506 031 738 30.60
55 63 142 96 909 627 1 534 34.80
65 58 115 101 883 098 1 753 39.10
75 56 423 104 818 003 1 857 42.00
85 58 995 106 127 310 1 798 43.60
95 66 985 105 643 283 1 577 44.40
Table 1 The result of genome assemble with different k-mer value
长度覆盖率(%) 匹配的EST累计数目 累计比例(%)
100 264 26.347
90 495 49.401
80 576 57.485
70 664 66.267
60 727 72.554
50 782 78.043
40 821 81.936
30 849 84.73
20 877 87.524
10 910 90.818
Table 2 Assessment the sequence coverage of H. pluvialis draft genome using known ESTs
匹配基因组 匹配的contig数量 匹配的contig总长度(bp) 比对长度 (bp)
雨生红球藻(Haematococcus pluvialis) 4 964 9 534 797 696 150
莱茵衣藻(Chlamydomonas reinhardtii) 1 977 4 068 934 246 989
团藻(Volvox carteri f. nagariensis) 401 800 015 45 726
多变小球藻(Chlorella variabilis) 347 747 501 3 8375
胶球藻 C-169(Coccomyxa subellipsoidea C-169) 178 352 938 20 464
原壳小球藻(Auxenochlorella protothecoides) 165 316 284 16 626
Table 3 Assessment the sequence coverage of H. pluvialis draft genome using known algal genome sequences updated from NCBI
最佳匹配物种 E-value=10-3 E-value=10-10 E-value=10-20
数目 比例(%) 数目 比例(%) 数目 比例(%)
团藻(Volvox carteri f. nagariensis) 2 148 24.06 1 900 23.57 1 511 21.92
莱茵衣藻(Chlamydomonas reinhardtii) 1 820 20.39 1 618 20.07 1 315 19.08
单针藻(Monoraphidium neglectum) 516 7.49 433 6.28 313 4.54
胶球藻(Coccomyxa subellipsoidea C-169) 262 2.93 225 2.79 163 2.37
多变小球藻(Chlorella variabilis) 172 1.93 143 1.77 90 1.31
原壳小球藻(Auxenochlorella protothecoides) 72 0.81 56 0.69 38 0.55
雨生红球藻(Haematococcus pluvialis) 68 0.76 68 0.84 66 0.96
盐生杜氏藻(Dunaliella salina) 41 0.45 39 0.48 37 0.54
其他 1 260 14.11 1 011 12.54 796 11.55
Table 4 Assessment the sequence coverage of H. pluvialis draft genome using known algal protein sequences
Fig.2 KEGG analysis for predicted proteins of H. pluvialis
Fig.3 KOG analysis for predicted proteins of H. pluvialis
KOG 分类 1.00E-03 1.00E-05 1.00E-10 1.00E-15 1.00E-20 1.00E-25 1.00E-30
Amino acid transport and metabolism 363 343 310 281 245 221 192
Carbohydrate transport and metabolism 334 314 256 213 179 149 129
Cell cycle control, cell division, chromosome partitioning 112 97 70 59 46 35 27
Cell motility 1 1 1 0 0 0 0
Cell wall/membrane/envelope biogenesis 57 50 34 29 17 14 14
Chromatin structure and dynamics 73 67 53 48 43 34 23
Coenzyme transport and metabolism 124 115 101 87 81 71 56
Cytoskeleton 213 179 149 124 107 91 74
Defense mechanisms 21 20 16 6 2 2 2
Energy production and conversion 286 269 243 207 184 162 141
Extracellular structures 49 21 5 2 2 2 2
Function unknown 177 146 103 70 50 38 25
General function prediction 482 410 293 236 196 167 132
Inorganic ion transport and metabolism 231 201 161 126 100 84 64
Intracellular trafficking, secretion, and vesicular transport 220 191 170 139 111 91 79
Lipid transport and metabolism 209 193 159 134 111 88 76
Nuclear structure 16 14 10 7 5 4 3
Nucleotide transport and metabolism 148 141 130 110 97 83 66
Posttranslational modification, protein turnover, chaperones 470 434 364 312 259 218 185
Replication, recombination and repair 152 138 114 100 88 72 58
RNA processing and modification 278 261 229 190 158 130 110
Secondary metabolites biosynthesis, transport and catabolism 227 216 189 156 133 96 71
Signal transduction mechanisms 391 325 253 200 157 117 88
Transcription 240 195 142 109 91 69 57
Translation, ribosomal structure and biogenesis 359 346 308 271 226 198 167
总计 5 233 4 687 3 863 3 216 2 688 2 236 1 841
Table 5 Assessment the KOG analysis for predicted proteins of H. pluvialis under different E-values
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