生物多样性 ›› 2018, Vol. 26 ›› Issue (5): 445-456. DOI: 10.17520/biods.2018058
所属专题: 传粉生物学; 物种形成与系统进化; 昆虫多样性与生态功能
收稿日期:
2018-02-15
接受日期:
2018-05-11
出版日期:
2018-05-20
发布日期:
2018-09-11
通讯作者:
周欣
作者简介:
# 共同第一作者
基金资助:
Dandan Lang1,2, Min Tang1,3, Xin Zhou1,3,*()
Received:
2018-02-15
Accepted:
2018-05-11
Online:
2018-05-20
Published:
2018-09-11
Contact:
Zhou Xin
About author:
# Co-first authors
摘要:
传粉者是重要的生态功能提供者, 在维持稳定的生态系统和高效的农业生产力中发挥着重要作用。因此, 传粉网络的构建和监测工作对评价生态系统平衡和调控农业生产至关重要。该工作的基础就是通过对传粉者及植物的物种鉴定构建其相关性。传统的形态学物种鉴定对分类学专家的专业知识、时间和经验都提出较高的要求。DNA条形码和高通量测序技术(high-throughput sequencing, HTS)的发展及其在传粉网络研究中的应用, 提供了高效、准确鉴定传粉者与植物的方法, 大大提高了传粉网络构建的效率。本文阐述了传粉网络研究相关的研究方法和技术进展, 并提出利用高通量测序技术结合无PCR扩增(PCR-free)的“超级条形码”技术, 有望实现以更高的灵敏度和分辨率对混合物种样品进行定性及相对定量的监测。该方法的有效性已在其他生物多样性研究中得以验证, 在传粉网络研究中虽处于初始阶段, 但应用前景广阔。
郎丹丹, 唐敏, 周欣 (2018) 传粉网络构建的定性定量分子研究: 应用与展望. 生物多样性, 26, 445-456. DOI: 10.17520/biods.2018058.
Dandan Lang,Min Tang,Xin Zhou (2018) Qualitative and quantitative molecular construction of plant-pollinator network: Application and prospective. Biodiversity Science, 26, 445-456. DOI: 10.17520/biods.2018058.
图1 传粉网络构建流程及混合花粉组成分析方法比较。图中蓝色框和绿色框中内容分别为形态学与宏条形码方法, 橙色框中内容为宏基因组方法。底部黑色网络为真实传粉网络模型, 蓝、绿和橙色网络模型分别代表经对应方法分析可能得到的网络结构。由于各种方法都有其局限性, 所得网络均与真实网络存在一定差异。宏条形码和宏基因组技术可解决孢粉学种内形态差异的问题, 但仍存在部分近缘种难以区分的情况。相对于宏条形码技术, 宏基因组技术可避免PCR带来的物种偏倚性, 提高相对丰度的准确率。
Fig. 1 Construction of pollination network and comparison of analysis methods of mixed pollen composition. The contents of the blue and the green boxes refer to morphological and molecular methods, respectively. The content in the orange box is the PCR-free genome-skimming (metagenomics) approach proposed in this paper. The black network model at the bottom represents the real pollination network, and the blue, green and orange network models represent network structures constructed by the corresponding methods. Due to the limitations of various methods, the constructed networks are potentially deviated from the real network. Metabarcoding and metagenomic techniques can alleviate issues caused by intra-specific morphological variations; but some closely related species remain difficult to differentiate. Compared to metabarcoding, the metagenomic technology can reduce species bias caused by PCR and improve the accuracy in relative abundance.
物种 Species | NCBI序列号 NCBI accession number | 物种 Species | NCBI序列号 NCBI accession number |
---|---|---|---|
Apis andreniformis | KF736157.1 | Bombus lapidarius | KT164641.1 |
Apis cerana | NC_014295.1 | Bombus lucorum | KT164681.1 |
Apis dorsata | KC294229.1 | Bombus pascuorum | KT164630.1 |
Apis florea | NC_021401.1 | Bombus terrestris | KT368150.1 |
Apis mellifera sahariensis | NC_035883.1 | Melipona bicolor | NC_004529.1 |
Apis nigrocincta | KY799147.1 | Melipona scutellaris | NC_026198.1 |
Bombus breviceps | MF478986.1 | Nomada fabriciana | KT164663.1 |
Bombus consobrinus | MF995069.1 | Nomada flava | KT164670.1 |
Bombus hypocrita sapporensis | NC_011923.1 | Nomada flavoguttata | KT164617.1 |
Bombus ignitus | NC_010967.1 | Nomada goodeniana | KT164660.1 |
表1 蜜蜂科20个物种(包括蜜蜂属6个物种)列表及其线粒体基因组NCBI序列号
Table 1 The list of 20 species of Apidae (including six species of Apis) and their mitochondrial genomes’ accession numbers in NCBI
物种 Species | NCBI序列号 NCBI accession number | 物种 Species | NCBI序列号 NCBI accession number |
---|---|---|---|
Apis andreniformis | KF736157.1 | Bombus lapidarius | KT164641.1 |
Apis cerana | NC_014295.1 | Bombus lucorum | KT164681.1 |
Apis dorsata | KC294229.1 | Bombus pascuorum | KT164630.1 |
Apis florea | NC_021401.1 | Bombus terrestris | KT368150.1 |
Apis mellifera sahariensis | NC_035883.1 | Melipona bicolor | NC_004529.1 |
Apis nigrocincta | KY799147.1 | Melipona scutellaris | NC_026198.1 |
Bombus breviceps | MF478986.1 | Nomada fabriciana | KT164663.1 |
Bombus consobrinus | MF995069.1 | Nomada flava | KT164670.1 |
Bombus hypocrita sapporensis | NC_011923.1 | Nomada flavoguttata | KT164617.1 |
Bombus ignitus | NC_010967.1 | Nomada goodeniana | KT164660.1 |
物种 Species | NCBI序列号 NCBI accession number | 物种 Species | NCBI序列号 NCBI accession number |
---|---|---|---|
Anoectochilus emeiensis | NC_033895.1 | Dendrobium parciflorum | NC_035334.1 |
Apostasia odorata | NC_030722.1 | Dendrobium parishii | NC_035339.1 |
Bletilla ochracea | NC_029483.1 | Dendrobium pendulum | NC_029705.1 |
Bletilla striata | NC_028422.1 | Dendrobium primulinum | NC_035321.1 |
Calanthe triplicata | NC_024544.1 | Dendrobium salaccense | NC_035332.1 |
Cattleya crispata | NC_026568.1 | Dendrobium spatella | NC_035333.1 |
Cattleya liliputana | NC_032083.1 | Dendrobium strongylanthum | NC_027691.1 |
Cephalanthera longifolia | NC_030704.1 | Dendrobium wardianum | NC_035329.1 |
Cymbidium aloifolium | NC_021429.1 | Dendrobium wilsonii | NC_035330.1 |
Cymbidium ensifolium | NC_028525.1 | Dendrobium xichouense | NC_035341.1 |
Cymbidium faberi | NC_027743.1 | Elleanthus sodiroi | NC_027266.1 |
Cymbidium goeringii | NC_028524.1 | Epipactis mairei | NC_030705.1 |
Cymbidium kanran | NC_029711.1 | Epipactis veratrifolia | NC_030708.1 |
Cymbidium lancifolium | NC_029712.1 | Erycina pusilla | NC_018114.1 |
Cymbidium macrorhizon | NC_029713.1 | Gastrochilus fuscopunctatus | NC_035830.1 |
Cymbidium mannii | NC_021433.1 | Gastrochilus japonicus | NC_035833.1 |
Cymbidium sinense | NC_021430.1 | Goodyera fumata | NC_026773.1 |
Cymbidium tortisepalum | NC_021431.1 | Goodyera procera | NC_029363.1 |
Cymbidium tracyanum | NC_021432.1 | Goodyera schlechtendaliana | NC_029364.1 |
Cypripedium formosanum | NC_026772.1 | Goodyera velutina | NC_029365.1 |
Cypripedium macranthos | NC_024421.1 | Habenaria pantlingiana | NC_026775.1 |
Dendrobium aphyllum | NC_035322.1 | Habenaria radiata | NC_035834.1 |
Dendrobium brymerianum | NC_035323.1 | Listera fugongensis | NC_030711.1 |
Dendrobium catenatum | NC_024019.1 | Ludisia discolor | NC_030540.1 |
Dendrobium chrysanthum | NC_035336.1 | Masdevallia coccinea | NC_026541.1 |
Dendrobium chrysotoxum | NC_028549.1 | Masdevallia picturata | NC_026777.1 |
Dendrobium crepidatum | NC_035331.1 | Neottia ovate | NC_030712.1 |
Dendrobium denneanum | NC_035324.1 | Neottia pinetorum | NC_030710.1 |
Dendrobium devonianum | NC_035325.1 | Oberonia japonica | NC_035832.1 |
Dendrobium ellipsophyllum | NC_035340.1 | Paphiopedilum armeniacum | NC_026779.1 |
Dendrobium exile | NC_035343.1 | Paphiopedilum niveum | NC_026776.1 |
Dendrobium falconeri | NC_035326.1 | Pelatantheria scolopendrifolia | NC_035829.1 |
Dendrobium fanjingshanense | NC_035344.1 | Phalaenopsis equestris | NC_017609.1 |
Dendrobium fimbriatum | NC_035342.1 | Phragmipedium longifolium | NC_028149.1 |
Dendrobium gratiosissimum | NC_035327.1 | Sobralia callosa | NC_028147.1 |
Dendrobium henryi | NC_035335.1 | Thrixspermum japonicum | NC_035831.1 |
Dendrobium hercoglossum | NC_035328.1 | Vanilla aphylla | NC_035320.1 |
Dendrobium huoshanense | NC_028430.1 | Vanilla planifolia | NC_026778.1 |
Dendrobium jenkinsii | NC_035337.1 | Sobralia aff. bouchei | NC_028209.1 |
Dendrobium lohohense | NC_035338.1 | Phalaenopsis hybrid | NC_025593.1 |
Dendrobium moniliforme | NC_035154.1 | Phalaenopsis aphrodite formosana | NC_007499.1 |
Dendrobium nobile | NC_029456.1 | Oncidium hybrid | NC_014056.1 |
表2 兰科84个物种(包括石斛兰属31个物种)列表及其叶绿体基因组NCBI序列号
Table 2 The list of 84 species of Orchidaceae (including 31 species of Dendrobium) and their chloroplast genomes’ accession numbers in NCBI
物种 Species | NCBI序列号 NCBI accession number | 物种 Species | NCBI序列号 NCBI accession number |
---|---|---|---|
Anoectochilus emeiensis | NC_033895.1 | Dendrobium parciflorum | NC_035334.1 |
Apostasia odorata | NC_030722.1 | Dendrobium parishii | NC_035339.1 |
Bletilla ochracea | NC_029483.1 | Dendrobium pendulum | NC_029705.1 |
Bletilla striata | NC_028422.1 | Dendrobium primulinum | NC_035321.1 |
Calanthe triplicata | NC_024544.1 | Dendrobium salaccense | NC_035332.1 |
Cattleya crispata | NC_026568.1 | Dendrobium spatella | NC_035333.1 |
Cattleya liliputana | NC_032083.1 | Dendrobium strongylanthum | NC_027691.1 |
Cephalanthera longifolia | NC_030704.1 | Dendrobium wardianum | NC_035329.1 |
Cymbidium aloifolium | NC_021429.1 | Dendrobium wilsonii | NC_035330.1 |
Cymbidium ensifolium | NC_028525.1 | Dendrobium xichouense | NC_035341.1 |
Cymbidium faberi | NC_027743.1 | Elleanthus sodiroi | NC_027266.1 |
Cymbidium goeringii | NC_028524.1 | Epipactis mairei | NC_030705.1 |
Cymbidium kanran | NC_029711.1 | Epipactis veratrifolia | NC_030708.1 |
Cymbidium lancifolium | NC_029712.1 | Erycina pusilla | NC_018114.1 |
Cymbidium macrorhizon | NC_029713.1 | Gastrochilus fuscopunctatus | NC_035830.1 |
Cymbidium mannii | NC_021433.1 | Gastrochilus japonicus | NC_035833.1 |
Cymbidium sinense | NC_021430.1 | Goodyera fumata | NC_026773.1 |
Cymbidium tortisepalum | NC_021431.1 | Goodyera procera | NC_029363.1 |
Cymbidium tracyanum | NC_021432.1 | Goodyera schlechtendaliana | NC_029364.1 |
Cypripedium formosanum | NC_026772.1 | Goodyera velutina | NC_029365.1 |
Cypripedium macranthos | NC_024421.1 | Habenaria pantlingiana | NC_026775.1 |
Dendrobium aphyllum | NC_035322.1 | Habenaria radiata | NC_035834.1 |
Dendrobium brymerianum | NC_035323.1 | Listera fugongensis | NC_030711.1 |
Dendrobium catenatum | NC_024019.1 | Ludisia discolor | NC_030540.1 |
Dendrobium chrysanthum | NC_035336.1 | Masdevallia coccinea | NC_026541.1 |
Dendrobium chrysotoxum | NC_028549.1 | Masdevallia picturata | NC_026777.1 |
Dendrobium crepidatum | NC_035331.1 | Neottia ovate | NC_030712.1 |
Dendrobium denneanum | NC_035324.1 | Neottia pinetorum | NC_030710.1 |
Dendrobium devonianum | NC_035325.1 | Oberonia japonica | NC_035832.1 |
Dendrobium ellipsophyllum | NC_035340.1 | Paphiopedilum armeniacum | NC_026779.1 |
Dendrobium exile | NC_035343.1 | Paphiopedilum niveum | NC_026776.1 |
Dendrobium falconeri | NC_035326.1 | Pelatantheria scolopendrifolia | NC_035829.1 |
Dendrobium fanjingshanense | NC_035344.1 | Phalaenopsis equestris | NC_017609.1 |
Dendrobium fimbriatum | NC_035342.1 | Phragmipedium longifolium | NC_028149.1 |
Dendrobium gratiosissimum | NC_035327.1 | Sobralia callosa | NC_028147.1 |
Dendrobium henryi | NC_035335.1 | Thrixspermum japonicum | NC_035831.1 |
Dendrobium hercoglossum | NC_035328.1 | Vanilla aphylla | NC_035320.1 |
Dendrobium huoshanense | NC_028430.1 | Vanilla planifolia | NC_026778.1 |
Dendrobium jenkinsii | NC_035337.1 | Sobralia aff. bouchei | NC_028209.1 |
Dendrobium lohohense | NC_035338.1 | Phalaenopsis hybrid | NC_025593.1 |
Dendrobium moniliforme | NC_035154.1 | Phalaenopsis aphrodite formosana | NC_007499.1 |
Dendrobium nobile | NC_029456.1 | Oncidium hybrid | NC_014056.1 |
图3 线粒体基因组和叶绿体基因组种间及属间遗传距离图。(a) Apis属内6个物种线粒体基因组上13个蛋白编码基因序列P-distance图; (b) Apidae科内20个物种线粒体基因组上13个蛋白编码基因序列P-diatance图; (c) Dendrobium属内31个物种叶绿体基因组上67个蛋白编码基因序列P-distance图; (d) Orchidaceae科内84个物种叶绿体基因组上67个蛋白编码基因序列P-distance图。图a和b中, 橙色区域为COI条形码序列所在位置, 橙色虚线圆圈表示COI条形码序列P-distance中值; 图c和d中, 橙色区域为matK条形码序列所在位置, 紫色区域为rbcL条形码序列所在位置, 橙色虚线圆圈表示matK条形码序列P-distance中值, 紫色虚线圆圈表示rbcL条形码序列P-distance中值。
Fig. 3 The P-distance map among species and genera of the mitochondrial genomes and the chloroplast genomes. (a) The P-distance map of 13 protein-coding genes in the mitochondrial genomes among six species in Apis; (b) The P-distance map of 13 protein-coding genes in the mitochondrial genomes among 20 species in Apidae; (c) The P-distance map of 67 protein-coding genes in the chloroplast genomes among 31 species in Dendrobium; (d) The P-distance map of 67 protein-coding genes in the chloroplast genomes among 84 species in Orchidaceae. In panels a & b, the orange area is the location of the COI barcode, and the orange dotted circle represents the median value of the COI barcode’s P-distance. In panels c & d, the orange area is the location of the matK barcode, the purple area is the location of the rbcL barcode, and the orange dotted circle represents the median value of the matK barcode’s P-distance, the purple dotted circle represents the median value of the rbcL barcode’s P-distance.
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