Biodiv Sci ›› 2018, Vol. 26 ›› Issue (5): 445-456. DOI: 10.17520/biods.2018058
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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
Dandan Lang,Min Tang,Xin Zhou. Qualitative and quantitative molecular construction of plant-pollinator network: Application and prospective[J]. Biodiv Sci, 2018, 26(5): 445-456.
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 |
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 |
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 |
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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