Biodiv Sci ›› 2019, Vol. 27 ›› Issue (5): 526-533. DOI: 10.17520/biods.2018209
• Reviews • Previous Articles Next Articles
Received:
2018-07-30
Accepted:
2018-12-25
Online:
2019-05-20
Published:
2019-05-20
Contact:
Liu Shanlin
Liu Shanlin. DNA barcoding and emerging reference construction and data analysis technologies[J]. Biodiv Sci, 2019, 27(5): 526-533.
标记基因 Marker gene | 目标物种 Targeted group | 数据库 Database |
---|---|---|
16S | 细菌和古细菌 Bacteria and archea ( | 核糖体数据库项目 Ribosomal Database Project ( |
ITS | 真菌( Fungi ( | UNITE ( |
18S | 原生生物 Protist ( | SILVA ( |
matK + rbcL | 植物 Plant ( | 生命条形码数据库 Barcode of Life Data Systems ( |
COI | 动物群( Fauna ( | 核糖体数据库项目 Ribosomal Database Project ( |
Table 1 Marker genes widely used for barcoding
标记基因 Marker gene | 目标物种 Targeted group | 数据库 Database |
---|---|---|
16S | 细菌和古细菌 Bacteria and archea ( | 核糖体数据库项目 Ribosomal Database Project ( |
ITS | 真菌( Fungi ( | UNITE ( |
18S | 原生生物 Protist ( | SILVA ( |
matK + rbcL | 植物 Plant ( | 生命条形码数据库 Barcode of Life Data Systems ( |
COI | 动物群( Fauna ( | 核糖体数据库项目 Ribosomal Database Project ( |
目标序列长度 Targeted region length (bp) | 优势 Advantages | 劣势 Disadvantages | 参考文献 Reference |
---|---|---|---|
~300 | - | 无法处理较长的目标序列; Roche 454平台 Can not work on long fragments; Roche 454 platform | Shokralla et al, 2014 |
~180 | 简单, 易操作, 成本低 Straightforward, easy to operate, cost-efficient | 目标序列偏短, 只能用于物种初筛 Short targeted region; can only be used for species pre-clustering | Meier et al, 2016 |
~650 | 标准DNA条形码全长 Standard full-length COI | 普适性差; 需要多轮PCR过程 Poor universality; multiple rounds of PCR | Shokralla et al, 2015; Cruaud et al, 2017 |
~650 | 易操作, 标准DNA条形码全长 Easy to operate, standard full-length COI | 相对较高的计算资源 Relatively high requirement for computational resources | Liu et al, 2017 |
~650 | 易操作, 标准DNA条形码全长 Easy to operate, standard full-length COI | SMRT平台成本高 High cost of SMRT platform | Hebert et al, 2018 |
~650 | 易操作, 标准DNA条形码全长 Easy to operate, standard full-length COI | 测序平台暂时不够普及 Not a mass production | Yang et al, 2018 |
Table 2 High throughput methods to achieve barcode sequences
目标序列长度 Targeted region length (bp) | 优势 Advantages | 劣势 Disadvantages | 参考文献 Reference |
---|---|---|---|
~300 | - | 无法处理较长的目标序列; Roche 454平台 Can not work on long fragments; Roche 454 platform | Shokralla et al, 2014 |
~180 | 简单, 易操作, 成本低 Straightforward, easy to operate, cost-efficient | 目标序列偏短, 只能用于物种初筛 Short targeted region; can only be used for species pre-clustering | Meier et al, 2016 |
~650 | 标准DNA条形码全长 Standard full-length COI | 普适性差; 需要多轮PCR过程 Poor universality; multiple rounds of PCR | Shokralla et al, 2015; Cruaud et al, 2017 |
~650 | 易操作, 标准DNA条形码全长 Easy to operate, standard full-length COI | 相对较高的计算资源 Relatively high requirement for computational resources | Liu et al, 2017 |
~650 | 易操作, 标准DNA条形码全长 Easy to operate, standard full-length COI | SMRT平台成本高 High cost of SMRT platform | Hebert et al, 2018 |
~650 | 易操作, 标准DNA条形码全长 Easy to operate, standard full-length COI | 测序平台暂时不够普及 Not a mass production | Yang et al, 2018 |
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