Chinese Journal of Tropical Crops ›› 2020, Vol. 41 ›› Issue (10): 1958-1967.DOI: 10.3969/j.issn.1000-2561.2020.10.003
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Received:
2020-08-05
Revised:
2020-08-27
Online:
2020-10-25
Published:
2020-11-26
CLC Number:
TANG Chaorong. Research Progress on Biology of Rubber Production in Rubber Tree[J]. Chinese Journal of Tropical Crops, 2020, 41(10): 1958-1967.
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URL: http://www.rdzwxb.com/EN/10.3969/j.issn.1000-2561.2020.10.003
指标 Index | 基因组版本(发表刊物/时间)Genome version (Journal name/Publication date) | ||||
---|---|---|---|---|---|
BMC Genomics[ 2013-02-02 | Nature Plants[ 2016-05-23 | Scientific Reports[ 2016-06-24 | Scientific Reports[ 2017-02-02 | Molecular Plant[ 2019-12-12 | |
橡胶品种 | RRIM600 | 热研7-33-97 | RRIM600 | BPM24 | GT1 |
测序方案 | 43× Roche 454, Illumina, SOLiD | 129× Illumina; 4× BAC pool sequence assembly | 134× Illumina; 21× PacBio | 68× Illumina, Roche 454, PacBio; Chicago data | 261× llumina; 104× PacBio; 77× HiC data |
基因组大小 | |||||
估算大小/Gb | 2.15(文献[ | 1.46(17-mer分析) | 2.15(17-mer分析) | ? | 1.56(17-mer分析) |
实际拼接/Gb | 1.12 | 1.37 | 1.55 | 1.26 | 1.47 |
Contig N50/kb | ? | 30.6 | 20.75 | ? | 152.7 |
Scaffold N50 | 2 972 bp | 1.28 Mb | 67.24 kb | 96.83 kb | ? |
基因数目 | 68 955 | 43 792 | 84 440 | 43 868 | 44 187 |
重复序列占比/% | 72.01 | 71.18 | 72.51 | 69.2 | 70.81 |
Tab. 1 Comparison of five Hevea genome assemblies
指标 Index | 基因组版本(发表刊物/时间)Genome version (Journal name/Publication date) | ||||
---|---|---|---|---|---|
BMC Genomics[ 2013-02-02 | Nature Plants[ 2016-05-23 | Scientific Reports[ 2016-06-24 | Scientific Reports[ 2017-02-02 | Molecular Plant[ 2019-12-12 | |
橡胶品种 | RRIM600 | 热研7-33-97 | RRIM600 | BPM24 | GT1 |
测序方案 | 43× Roche 454, Illumina, SOLiD | 129× Illumina; 4× BAC pool sequence assembly | 134× Illumina; 21× PacBio | 68× Illumina, Roche 454, PacBio; Chicago data | 261× llumina; 104× PacBio; 77× HiC data |
基因组大小 | |||||
估算大小/Gb | 2.15(文献[ | 1.46(17-mer分析) | 2.15(17-mer分析) | ? | 1.56(17-mer分析) |
实际拼接/Gb | 1.12 | 1.37 | 1.55 | 1.26 | 1.47 |
Contig N50/kb | ? | 30.6 | 20.75 | ? | 152.7 |
Scaffold N50 | 2 972 bp | 1.28 Mb | 67.24 kb | 96.83 kb | ? |
基因数目 | 68 955 | 43 792 | 84 440 | 43 868 | 44 187 |
重复序列占比/% | 72.01 | 71.18 | 72.51 | 69.2 | 70.81 |
Fig. 1 Rubber biosynthesis and expansion of the REF/SRPP gene family in Hevea (Adopted from Tang et al[6] with modification) A: The rubber biosynthesis pathway and expression profiles (reads per kilobase per million reads mapped; RPKM) of the genes involved in rubber biosynthesis. B: Phylogeny of the REF/SRPP gene family. C: Genomic location of the Hevea REF/SRPP genes. Lx, latex; Bk, bark; Lf, leaf; Rt, root; FF, female flower; MF, male flower.
Fig. 2 Schematic models of the rubber biosynthetic machinery on rubber particles (RPs) (A) and RP formation correlated with the interactions of proteins (B) in the latex of H. brasiliensis (Adopted from Yamashita et al [30])
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