Biodiversity Science ›› 2018, Vol. 26 ›› Issue (5): 445-456.doi: 10.17520/biods.2018058

• Reviews • Previous Article     Next Article

Qualitative and quantitative molecular construction of plant-pollinator network: Application and prospective

Dandan Lang1, 2, Min Tang1, 3, Xin Zhou1, 3, *()   

  1. 1 Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193
    2 College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083
    3 College of Plant Protection, China Agricultural University, Beijing 100193
  • Received:2018-02-15 Accepted:2018-05-11 Online:2018-09-11
  • Zhou Xin
  • About author:

    # Co-first authors

Pollinators serve key ecological functions, ensuring stable ecosystems and high agricultural yields. Hence, assessing ecosystem health and effects of agricultural management would benefit from understanding and monitoring pollination networks, which involves identifications of pollinators and pollinated plants. Classic approaches of morphology-based identification of plants and pollinators can be time-consuming, labor-intensive and costly, and require highly specialized taxonomic expertise. In comparison, DNA barcoding and high-throughput sequencing technologies can provide efficient and accurate identifications of plants and their pollinators, which may facilitate construction of pollination networks. Here we propose using sequencing technologies with a PCR-free genome-skimming work frame, using "super DNA barcode" as a new method to assess plant-pollinator networks. We expect this technique to improve resolution and accuracy of taxonomic identification to help gain quantitative information for bulk samples of pollinators or pollens. Although there are technical challenges to be resolved, the robustness of the new methodology has been validated in relevant biodiversity studies, suggesting promise in constructing pollination networks.

Key words: mitochondria, chloroplast, pollen, metabarcoding, metagenome, PCR-free, quantify

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."

Table 1

The list of 20 species of Apidae (including six species of Apis) and their mitochondrial genomes’ accession numbers in NCBI"

NCBI accession number
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

Fig. 2

The pipeline for P-distance distribution map of mitochondrial and chloroplast genomes"

Table 2

The list of 84 species of Orchidaceae (including 31 species of Dendrobium) and their chloroplast genomes’ accession numbers in NCBI"

NCBI accession number
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

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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