中国科学数据论文数据样例 2014( 数据样例描述 )

Transkriptio

1 中国科学数据论文数据样例 2014( 数据样例描述 ) 1. DarwinTree 基础数据集 : 面向所有生物的 Gene Mark 数据及其与任意阶元物种分类名称对应的统计数据集 # query # db.query.find({"accession" : "AB008781"}) /* 0 */ { "ACCESSION" : "AB008781", "COMMON_NAME" : "chloroplast Persicaria hydropiper", "DEFINITION" : "Persicaria hydropiper chloroplast rbcl, accd genes for ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, acetyl-coa carboxilase beta subunit, complete and partial cds.", "GENE" : [ "rbcl", "accd" ], "PRODUCT" : [ "ribulose-1,5-bisphosphate carboxylase/oxygenaselarge subunit", "acetyl-coa carboxilase beta subunit" ], "SCIENTIFIC_NAME" : "Persicaria hydropiper",

2 "TAXON_ID" : 27478, "TAXON_LEVEL" : "Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; Caryophyllales; Polygonaceae; Polygonoideae; Persicarieae; Persicaria.", "VERSION" : "AB GI: ", "_id" : , "file" : "/mnt/genbank130419/gbpln1.seq.gz" } #meta # db.meta.find({"accession" : "AB008781"}) /* 0 */ /* 0 */ { "_id" : , "ORIGIN" : "", "DEFINITION" : "Persicaria hydropiper chloroplast rbcl, accd genes for ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, acetyl-coa carboxilase beta subunit, complete and partial cds.", "FEATURES" : [ { "location" : " ", "key" : "source", "key_table" : { "organelle" : "plastid:chloroplast", "db_xref" : "taxon:46901", "mol_type" : "genomic DNA", "organism" : "Persicaria hydropiper" } },

3 { "location" : " ", "key" : "gene", "key_table" : { "gene" : "rbcl" } }, { "location" : " ", "key" : "CDS", "key_table" : { "product" : "ribulose-1,5-bisphosphate carboxylase/oxygenaselarge subunit", "codon_start" : "1", "transl_table" : "11", "db_xref" : "GI: ", "translation" : "MSPQTETKASVGFKAGVKEYKLNYYTPDYEPHAHDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGR CYGIEPVAGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYTKTFQGPPHGIQVERDKLNKYGRPL LGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIFKSQSETGEIKGHYLNATAGTCEEMIKR AVFARELGVPIVMHDYLTGGFTANTTLAHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRLSGGDHVHAGTVVGKL EGEREITLGFVDLLRDDFVEKDRSRGIYFTQPWVSLPGVIPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAAA NRVALEACVQARNEGRDLAREGNEIIRKACKWSPELAAACEVWKEIKFEFQAMDTL", "gene" : "rbcl", "protein_id" : "BAA " } }, { "location" : "1937..>2572", "key" : "gene", "key_table" : { "gene" : "accd" } }, { "location" : "1937..>2572", "key" : "CDS", "key_table" : { "product" : "acetyl-coa carboxilase beta subunit", "codon_start" : "1", "transl_table" : "11", "db_xref" : "GI: ", "translation" : "MEKWWFNSMLYKEELEHRCELSKSMSSLDPIDNTSSRENTSINFTEKNIHSWSNGFSYRNYDLLFGIRDIRNFISDETFLVRDSRG ETYSIYFDIENQIVEIENDHSFWSELQKKFSNYLNSSYVNGSKSGDTHYDLSMYDTQSRLNNHINSCIDSYLHSQMRIENSVLSAS

4 DNYSDIDILDESQTPTNTKGKNKNLGVPKKYRNLWIQCEN", "gene" : "accd", "protein_id" : "BAA " } } ], "REFERENCE" : [ { "JOURNAL" : "Am. J. Bot. (1997) In press", "TITLE" : "Interspecific relationships in Fagopyrum (Polygonaceae) revealed by the nucleotide sequences of the rbcl and accd genes and their intergenic region", "REFERENCE" : "1", "AUTHORS" : "Yasui,Y. and Ohnishi,O." }, { "JOURNAL" : "Submitted (10-NOV-1997) Yasuo Yasui, Kyoto University, Faculty of Agriculture, Plant Germ-Plasm Institute; Mozume, Muko, Kyoto , Japan ( yasyas@mail7.dddd.ne.jp, Tel: , Fax: )", "TITLE" : "Direct Submission", "REFERENCE" : "2 (bases 1 to 2572)", "AUTHORS" : "Yasui,Y." } ], "ACCESSION" : "AB008781", "LOCUS" : "AB bp DNA linear PLN 26-OCT-2007", "SOURCE" : "chloroplast Persicaria hydropiper", "VERSION" : "AB GI: ", "file" : "/mnt/genbank130419/gbpln1.seq.gz", "KEYWORDS" : "rbcl; accd; ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit; acetyl-coa carboxilase beta subunit.", "ORGANISM" : "Persicaria hydropiper\neukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; Caryophyllales; Polygonaceae; Polygonoideae; Persicarieae; Persicaria." } #sequence # db.sequence.find({"accession" : "AB008781"}) /* 0 */ {

5 "_id" : , "VERSION" : "AB GI: ", "ACCESSION" : "AB008781", "file" : "/mnt/genbank130419/gbpln1.seq.gz", "SEQUENCE" : [ [ "atgtcaccac", "aaacagagac", "taaagcaagt", "gttggattca", "aagccggtgt", "taaagaatat" ], [ "aaattgaatt", "attatactcc", "tgactatgaa", "ccccatgcac", "atgatatctt", "ggcagcattt" ], [ "cgagtaactc", "ctcaaccggg", "agttccacca", "gaagaagcag", "gggccgcggt", "agctgccgaa" ], [ "tcttctactg", "gtacatggac", "aactgtgtgg", "accgatggac", "ttaccagcct", "tgatcgttac" ], [ "aaaggacgat", "gctacggcat", "cgagcctgtt", "gctggagaag", "aaaatcaata", "tattgcttat" ], [ "gtagcttacc", "cattagacct", "ttttgaagaa", "ggttctgtta", "ctaacatgtt", "tacttccatt" ], [ "gtaggtaatg", "tatttgggtt", "caaagccctg", "cgtgctctac", "gtttggagga", "tttgcgaatc" ], [ "cctcctgctt", "atacgaaaac", "tttccaaggc", "ccacctcatg", "gtatccaagt", "tgagagagat" ], [ "aaattaaaca", "aatacggacg", "tcccctattg", "ggatgtacta", "ttaaacctaa", "attgggattg" ], [ "tccgctaaga", "actacggtcg", "agcagtttat", "gaatgtcttc", "gtggcgggct", "tgattttacc" ], [ "aaagatgatg", "aaaacgtgaa", "ctcccaacca", "tttatgcgtt", "ggagagaccg", "tttcttattc" ],

6 [ "tgtgccgaag", "ctattttcaa", "atcacagtct", "gaaactggtg", "aaatcaaagg", "acattacttg" ], [ "aatgctactg", "caggtacatg", "cgaagaaatg", "ataaaaagag", "ctgtatttgc", "cagagaattg" ], [ "ggagttccta", "ttgtaatgca", "tgactactta", "acagggggat", "tcactgcaaa", "tacaacttta" ], [ "gctcattatt", "gcagagataa", "tggcctactt", "cttcacatcc", "accgcgcaat", "gcatgcagtt" ], [ "attgatagac", "agaaaaatca", "cggtatgcac", "ttccgtgtac", "tagctaaagc", "cttacgtctg" ], [ "tccggtgggg", "atcatgttca", "tgccggtact", "gtagtaggta", "aacttgaagg", "ggaaagggag" ], [ "ataactttag", "gttttgttga", "tttactgcgt", "gatgactttg", "ttgaaaaaga", "cagaagtcgc" ], [ "ggtatttatt", "tcactcaacc", "ttgggtttcc", "ctgcctggtg", "ttattcctgt", "ggcttccggt" ], [ "ggtattcacg", "tttggcatat", "gcccgctcta", "accgagatct", "ttggggatga", "ttctgtacta" ], [ "cagttcggtg", "gcggaacttt", "aggccacccg", "tggggaaatg", "cgccgggtgc", "tgcagcgaat" ], [ "cgagtagctc", "tagaagcctg", "tgtacaagct", "cgtaatgagg", "ggcgtgatct", "tgctcgcgag" ], [ "ggtaacgaaa", "ttattcgtaa", "agcttgtaaa", "tggagtcctg", "aactagctgc", "cgcttgtgag" ], [ "gtatggaagg", "aaatcaaatt", "tgaattccaa", "gcaatggata", "ctttgtaatc", "cagtaattac" ], [ "tggtcggtcc", "cttaaattga", "attgtaatta", "aactcggccc", "aaccttttac", "ttttagtaaa" ], [ "aggattgggc", "tgaatacgag", "tttgcataga", "tattgaatct", "acaagcaaaa", "tcctaaataa"

7 ], [ "aaaatcgaag", "actaaaaaac", "tcaaaggttt", "ctttggttgt", "gctggatcca", "caattaatcc" ], [ "tatggatctc", "taggattgga", "ttggtgtatt", "cttatatacg", "tatcgcttag", "gaccgaggat" ], [ "agcgagtcag", "gtataagatc", "cccttttacc", "catcctgtat", "attgtccttt", "tttctgtttt" ], [ "ttatattcca", "actaaaagaa", "aaaagcgcta", "tctctcagat", "agcgtgaagt", "gctacccgga" ], [ "ttctgacaaa", "ggagaatctt", "ctatttctca", "cttcttttta", "gtgaattccc", "tttagtaaat" ], [ "gcaaatttca", "aatgactttt", "catcgaatga", "ctattcatct", "attttttttc", "atgcaaatag" ], [ "ggggcaagaa", "agctctatgg", "aaaaatggtg", "gtttaattcg", "atgttgtata", "aggaagagtt" ], [ "agaacatagg", "tgtgagctaa", "gtaaatcaat", "gagcagtctt", "gatcctattg", "acaatacaag" ], [ "tagccgtgaa", "aatacaagta", "taaattttac", "agaaaaaaac", "attcatagtt", "ggagtaatgg" ], [ "ttttagttac", "aggaattatg", "atcttttatt", "cggtatccgg", "gacattcgaa", "atttcatatc" ], [ "tgatgaaact", "tttttagtta", "gggatagtag", "aggggaaact", "tattccattt", "attttgatat" ], [ "tgaaaatcag", "attgttgaga", "ttgaaaacga", "tcactctttt", "tggagtgaac", "tacaaaaaaa" ], [ "attttctaat", "tatttgaatt", "ctagttatgt", "gaatggatct", "aaaagtggcg", "atacccatta" ], [ "tgatctttcc", "atgtacgata", "ctcaatctag", "gttgaataat", "cacattaata", "gttgtattga" ],

8 [ "cagttatctt", "cattctcaaa", "tgcggattga", "gaattctgtt", "ttaagtgcta", "gtgacaatta" ], [ "cagtgatatt", "gacattttgg", "atgaaagtca", "gactcccact", "aacacaaaag", "gtaagaataa" ], [ "gaatcttggg", "gttcctaaaa", "aatataggaa", "tttgtggatt", "caatgtgaaa", "at" ] ] } #feature /* 0 */ { "_id" : , "ACCESSION" : "AB008781", "FEATURES" : [ { "feature_key" : "source.organelle", "feature_values" : [ { "location" : [ { "seq_end" : [ 2572 ], "seq_start" : [ 1 ], "seq_length" : 2572 } ], "value" : "plastid:chloroplast" } ] }, { "feature_key" : "source.db_xref", "feature_values" : [ { "location" : [ { "seq_end" : [

9 2572 ], "seq_start" : [ 1 ], "seq_length" : 2572 } ], "value" : "taxon:46901" } ] }, { "feature_key" : "source.mol_type", "feature_values" : [ { "location" : [ { "seq_end" : [ 2572 ], "seq_start" : [ 1 ], "seq_length" : 2572 } ], "value" : "genomic DNA" } ] }, { "feature_key" : "source.organism", "feature_values" : [ { "location" : [ { "seq_end" : [ 2572 ], "seq_start" : [ 1 ], "seq_length" : 2572

10 } ], "value" : "Persicaria hydropiper" } ] }, { "feature_key" : "gene.gene", "feature_values" : [ { "location" : [ { "seq_end" : [ 1428 ], "seq_start" : [ 1 ], "seq_length" : 1428 } ], "value" : "rbcl" }, { "location" : [ { "seq_end" : [ 2572 ], "seq_start" : [ 1937 ], "seq_length" : 636 } ], "value" : "accd" } ] }, { "feature_key" : "CDS.product", "feature_values" : [ { "location" : [

11 { "seq_end" : [ 1428 ], "seq_start" : [ 1 ], "seq_length" : 1428 } ], "value" : "ribulose-1,5-bisphosphate carboxylase/oxygenaselarge subunit" }, { "location" : [ { "seq_end" : [ 2572 ], "seq_start" : [ 1937 ], "seq_length" : 636 } ], "value" : "acetyl-coa carboxilase beta subunit" } ] }, { "feature_key" : "CDS.codon_start", "feature_values" : [ { "location" : [ { "seq_end" : [ 1428 ], "seq_start" : [ 1 ], "seq_length" : 1428 }, { "seq_end" : [

12 2572 ], "seq_start" : [ 1937 ], "seq_length" : 636 } ], "value" : "1" } ] }, { "feature_key" : "CDS.transl_table", "feature_values" : [ { "location" : [ { "seq_end" : [ 1428 ], "seq_start" : [ 1 ], "seq_length" : 1428 }, { "seq_end" : [ 2572 ], "seq_start" : [ 1937 ], "seq_length" : 636 } ], "value" : "11" } ] }, { "feature_key" : "CDS.db_xref", "feature_values" : [ {

13 "location" : [ { "seq_end" : [ 1428 ], "seq_start" : [ 1 ], "seq_length" : 1428 } ], "value" : "GI: " }, { "location" : [ { "seq_end" : [ 2572 ], "seq_start" : [ 1937 ], "seq_length" : 636 } ], "value" : "GI: " } ] }, { "feature_key" : "CDS.translation", "feature_values" : [ { "location" : [ { "seq_end" : [ 1428 ], "seq_start" : [ 1 ], "seq_length" : 1428 } ],

14 "value" : "MSPQTETKASVGFKAGVKEYKLNYYTPDYEPHAHDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYGIEPVAGEENQ YIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYTKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRG GLDFTKDDENVNSQPFMRWRDRFLFCAEAIFKSQSETGEIKGHYLNATAGTCEEMIKRAVFARELGVPIVMHDYLTGGFTANTTLAHYCRDNGLLLHI HRAMHAVIDRQKNHGMHFRVLAKALRLSGGDHVHAGTVVGKLEGEREITLGFVDLLRDDFVEKDRSRGIYFTQPWVSLPGVIPVASGGIHVWHMPA LTEIFGDDSVLQFGGGTLGHPWGNAPGAAANRVALEACVQARNEGRDLAREGNEIIRKACKWSPELAAACEVWKEIKFEFQAMDTL" }, { "location" : [ { "seq_end" : [ 2572 ], "seq_start" : [ 1937 ], "seq_length" : 636 } ], "value" : "MEKWWFNSMLYKEELEHRCELSKSMSSLDPIDNTSSRENTSINFTEKNIHSWSNGFSYRNYDLLFGIRDIRNFISDETFLVRDSRGETYSIYFDIENQIV EIENDHSFWSELQKKFSNYLNSSYVNGSKSGDTHYDLSMYDTQSRLNNHINSCIDSYLHSQMRIENSVLSASDNYSDIDILDESQTPTNTKGKNKNLG VPKKYRNLWIQCEN" } ] }, { "feature_key" : "CDS.gene", "feature_values" : [ { "location" : [ { "seq_end" : [ 1428 ], "seq_start" : [ 1 ], "seq_length" : 1428 } ], "value" : "rbcl" }, {

15 "location" : [ { "seq_end" : [ 2572 ], "seq_start" : [ 1937 ], "seq_length" : 636 } ], "value" : "accd" } ] }, { "feature_key" : "CDS.protein_id", "feature_values" : [ { "location" : [ { "seq_end" : [ 1428 ], "seq_start" : [ 1 ], "seq_length" : 1428 } ], "value" : "BAA " }, { "location" : [ { "seq_end" : [ 2572 ], "seq_start" : [ 1937 ], "seq_length" : 636 } ],

16 "value" : "BAA " } ] } ] } # statistics #db.statistics.find() /* 0 */ { "_id" : 2, "taxonid" : 1, "count" : 1, "genename" : "MTVR1" } 2. DarwinTree 自测序数据集 : 面向中国陆地植物研究的补充测序数据 ; 自测数据以 fasta 格式存储 本文在样例说明中以原始数据 Abelmoschus_manihot_CPG14101 为例 >Abelmoschus_manihot_CPG14101 GAGTATAAATTGACTTATTATACTCCTCAATATGAAACCAAAGATACTGATAT CTTGGCAGCCTTCCGAGTAACTCCTCAACCTGGAGTTCCGCCTGAGGAAGC AGGGGCCGCGGTAGCTGCTGAATCTTCTACTGGTACATGGACAACCGTGTG GACCGATGGGCTTACCAGCCTTGATCGTTACAAAGGGCGATGCTACCACAT TGATCCCGTTCCTGGAGAAGACGATCAATATATATGTTATGTAGCTTACCCCT TAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCCATTGTGGG TAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTAGAGGATCTGCGA ATCCCTACTGCTTATATTAAAACTTTCCAAGGCCCGCCTCATGGCATCCAGG TTGAAAGAGATAAATTGAACAAGTATGGTCGCCCCCTATTAGGATGTACTAT TAAACCTAAATTGGGGTTATCCGCTAAGAACTACGGTAGAGCAGTTTATGAA

17 TGTCTACGCGGCGGACTTGATTTTACCAAAGATGATGAGAATGTGAACTCC CAACCATTTATGCGCTGGAGAGACCGTTTCTTATTTTGTGCCGAAGCTCTTT ATAAAGCACAGGCTGAAACAGGTGAAATCAAAGGGCATTACTTGAATGCTA CTGCGGGTACATGTGAAGAAATGATGAAAAGGGCCGCGTGTGCCAGAGAA TTGGGAGTTCCTATCGTAATGCATGACTACTTAACAGGTGGGTTCACTGCAA ATACTACCTTGGCTCATTATTGCCGAGATAACGGTCTACTTCTTCACATCCAT CGCGCAATGCACGCAGTTATTGATAGACAGAAGAATCATGGTATGCACTTTC GTGTACTAGCTAAAGCTTTACGTATGTCTGGTGGAGATCATATTCACGCTGG TACAGTAGTAGGTAAACTTGAAGGAGAAAGGGAAATAACTTTGGGCTTTGT TGATTTATTACGTGATGATTTTATTGAAAAAGATTCAAGCCGTGGTATTTATT TCACTCAAGATTGGGTTTCTCTACCAGGTGTTCTGCCCGTAGCTTCGGGGG GTATTCACGTTTGGCATATGCCTGCTTTGACCGAGATCTTTGGAGATGATTC CGTACTACAATTCGGTGGAGGAACTTTAGGACACCCTTGGGGAAATGCACC GGGTGCCGTAGCGAATCGAGTAGCTTTAGAAGCATGTGTAAAAGCTCGTAA TGAGGGACGTGACCTTGCCGCTCAGGGTAATGAAATTATCCGCGAGGCTAG CAAA 3. DarwinTree 中国维管植物进化数据集 : 已构建的中国维管植物属系统发育树的数据 (Generic tree of Chinese vascular plants) 系统发育树以 newick 格式存储, 本文在样例说明中以中国维管植物系统树为例 (((((((Cycas_taiwaniana: ,Cycas_revoluta: ): [100],(Ginkgo_biloba: ,((Cathaya_argyrophylla: ,(((Cedrus_deodara: ,Cedrus_atlantica: ): [100],(((Keteleeria_davidiana: ,Keteleeria_evelynian a: ): [100],(abies_firma: ,Abies_beshanzuensis: ): [100]): [100],(Pseudolarix_amabilis: ,(Tsuga_longibracteata: ,Tsuga_dumosa: ): [100]): [9

18 1]): [100]): [100],((Pseudotsuga_ menziesii: ,(larix_decidua: ,lari x_gmelinii: ): [100]): [100],((Picea_brachytyla: ,Picea_koraiensis: ): [100],((Pinus_banksiana: ,Pinus_massoniana: ): [44],(Pinus_bungeana: ,Pinus_koraiensis: ): [44]): [100]) : [70]): [43]): [100]): [100],(((Agathis_robusta: ,(Araucaria_cunninghamii: ,Araucaria_bidwillii: ): [100]): [ 100],(Dacrydium_elatum: ,((Podocarpus_macrophyllus: ,Podocarpus_neriifolius: ): [99],(Nageia_fleuryi: ,Nageia_nagi: ): [100]): [99] ): [100]): [100],(Sciadopitys_vert icillata: ,(((cephalotaxus_sinensis: ,Cephalotaxus_fortunei: ): [100],(((Torreya_grandis: ,Torreya_parvifolia: ): [100],(Amentotaxus_formosana: ,Amentotaxus_yunnanensis: ): [100]): [100],(Pseudotaxus_chienii: ,(Taxus_wallichiana: ,Taxus_cuspidata: ): [100]): [100]): [80]): [96],(((Metasequoia_glypt ostroboides: ,(sequoia_sempervirens: ,Sequoiadendron_giganteum: ): [84]): [100],((((Thuja_occidentalis: ,Thuja_plicata: ): [100],Th

19 ujopsis_dolabrata: ): [100],((cha maecyparis_obtusa: ,(fokienia_hodginsii: ,Chamaecyparis_pisifera: ): [20]): [100],(((Juniperus_gaussenii: ,Juniperus_indica: ): [100], (Cupressus_chengiana: ,Cupressus_arizonica: ): [79]): [100],Platycl adus_orientalis: ): [100]): [89]): [100],((Glyptostrobus_pensilis: ,(Taxodium_distichum: ,Taxodium_ mucronatum: ): [100]): [98],Cryptomeria_japonica: ): [100]): [100]): [100 ],(Taiwania_cryptomerioides: ,Cunninghamia_lanceolata: ): [100]): [100]): [100]): [97]): [99]): [97]): [72]): [90],((Brasenia_schreberi: ,((Eur yale_ferox: ,(nymphaea_alba: ,n ymphaea_caerulea: ): [80]): [100],(Nuphar_variegata: ,Nuphar_lut ea: ): [100]): [98]): [100],(((Illicium_parviflorum: ,Illicium_oligandrum: ): [100],((Kadsura_longipedunculata: ,Kadsura_japonica: ): [100],(Schisandra_sphenanthera: ,Schisandra_chinensis: ): [97]): [100]): [1 00],(((((((Symplocarpus_foetidus: ,((((Lemna_minor: ,Lemna_trisulca: ):

20 67671[100],(Wolffia_neglecta: ,Landoltia_punctata: ): [37]): [100],Spirodela_polyrrhiza: ): [100],((( Epipremnum_pinnatum: ,((Epipremnum_sp: ,Amydrium_humile: ): [75],(Scindapsus_hederaceus: ,Rhaphidophora_crassifolia: ): [73]): [100]): [100],(Pothos_scandens: ,Pothoidium_lobbianum: ): [100 ]): [99],(Lasia_spinosa: ,(((Homal omena_occulta: ,homalomena_speariae: ): [100],(Aglaonema_crispum: ,Aglaonema_modestum: ): [ 95]): [95],(((Cryptocoryne_zaidiana: ,Cryptocoryne_bullosa: ): [10 0],(Schismatoglottis_brevicuspis: ,Schismatoglottis_erecta: ): [100]): [100],(((Hapaline_benthamiana: ,(Amorphophallus_alb us: ,amorphophallus_coaetaneus: ): [100]): [88],(Pistia_stratiotes: ,(((Colocasia_antiquorum: ,((Ste udnera_kerrii: ,steudnera_colocasiifolia: ): [90],Remusatia_hookeriana: ): [68]): [95],(Alocasia_cucu llata: ,alocasia_macrorrhizos: ): [100]): [25],((((sauromatum_gaol igongense: ,(typhonium_blumei: ,typhonium_flagelliforme: ): [87 ]): [40],(Sauromatum_giganteum: ,Arum_jacquemontii: ): [76]):0.

21 [65],((Arisaema_tortuosum: ,Arisa ema_flavum: ): [76],((arisaema_ heterophyllum: ,((arisaema_speciosum: ,Arisaema_costatum: ): [6 7],Arisaema_franchetianum: ): [7 2]): [25],((Arisaema_amurense: , Arisaema_serratum: ): [95],Arisa ema_triphyllum: ): [95]): [38]): [99]): [3 0],(Pinellia_pedatisecta: ,Pinellia_cordata: ): [100]): [56]): [61]): [100]): [ 100],Calla_palustris: ): [67]): [73]): [99]): [85]): [68]): [100]): [98],((((((Alisma_gramineum: ,Alisma_orient ale: ): [35],alisma_plantago: ): [100],((Butomopsis_latifolia: ,Limnocharis_flava: ): [94],(Ranalisma_humile: ,((Sagittaria_guayanen sis: ,sagittaria_lichuanensis: ): [100],(Caldesia_parnassifolia: ,Cald esia_grandis: ): [100]): [50]): [37]): [54]) : [100],(Butomus_umbellatus: ,((( ((Halophila_ovalis: ,Halophila_decipiens: ): [84],Halophila_beccarii: ): [100],(Thalassia_hemprichii: ,Enhalus_acoroides: ): [59]): [100],((Najas_flexilis: ,Najas_gracil

22 lima: ): [100],(hydrilla_verticillat a: ,(nechamandra_alternifolia: ,( Vallisneria_asiatica: ,Vallisneria_natans: ): [98]): [99]): [100]): [81]): [95], ((Egeria_densa: ,((Ottelia_emersa: ,(Ottelia_acuminata: ,Ottelia_sinensis: ): [100]): [100],(Blyxa_jap onica: ,blyxa_echinosperma: ): [100]): [100]): [100],Hydrocharis_dubia: ): [74]): [100]): [79]): [100],((Aponogeton_lakhonensis: ,Aponogeto n_vanbruggenii: ): [100],(((triglo chin_maritima: ,triglochin_palustris: ): [100],((Posidonia_australis: ,(Ruppia_maritima: ,(Cymodocea_rotundata: ,(Syringodium_isoetifolium: ,Halodule_pinif olia: ): [100]): [82]): [87]): [100],((Zanni chellia_palustris: ,((potamogeton_distinctus: ,((Potamogeton_berchtoldii: ,Potamogeton_oxy phyllus: ): [70],potamogeton_cris tatus: ): [100]): [100],(Stuckenia_filiformis: ,Stuckenia_pectinata: ): [100]): [62]): [100],((Zostera_asiatica: ,Zostera_caespitosa: ): [100],(Phy llospadix_iwatensis: ,phyllospadix_torreyi: ): [100]): [100]):0.0306

23 [100]): [99]): [100],Scheuchzeria_palustris: ): [ 77]): [75]): [100],(Tofieldia_diver gens: ,tofieldia_coccinea: ): [100]): [74]): [98],(((((((((((Costus_nitidus: ,Costus_scaber: ): [99],((Siliquamomum_tonkinense: ,((Elettariopsis_kerbyi: ,(Amomum_comp actum: ,(amomum_maximum: , Amomum_glabrum: ): [56]): [27]): [94],(Alpinia_galanga: ,((Etlingera_baramensis: ,((((Amomum_ microcarpum: ,amomum_villosum: ): [85],Etlingera_littoralis: ): [92],(Plagiostachys_austrosinensis: ,Hornstedtia_hainanensis: ): [97 ]): [41],Hornstedtia_reticulata: ): [32]): [88],((Alpinia_oxyphylla: ,Alpinia_officinarum: ): [99],(Alpinia_oblongifolia: ,(Alpinia_zeru mbet: ,alpinia_platychilus: ): [75]): [75]): [100]): [81]): [86]): [86]): [100],(Rhynchanthus_beesianus: ,((Caulokaempferia_saxicola: ,(((Hedyc hium_flavum: ,((hedychium_flavescens: ,(Hedychium_spicatum: ,Hedychium_coronarium: ): [86]): [99],Pyrgophyllum_yunnanense: ): [12]): [1],(Pommereschea_lackneri:

24 36371,(Caulokaempferia_coenobialis: ,((Roscoea_auriculat a: ,(roscoea_cautleyoides: ,rosc oea_humeana: ): [100]): [39],((Cautleya_spicata: ,(Cautleya_gracil is: ,cautleya_cathcartii: ): [99]): [66],((Kaempferia_elegans: ,Kaempferia_galanga: ): [80],(((Zingiber_recurvatum: ,Zingiber_mioga: ): [98],((Zingiber_officinale: ,Zingiber_spectabile: ): [74],Zingiber_gramineum: ): [26]): [37],(Boesenbergia_lambirensis: ,Boesenbergia_albomaculata: ): [57]): [2]): [4]): [0]): [0]): [0 ]): [0]): [1],(Stahlianthus_involuc ratus: ,(curcuma_phaeocaulis: ,c urcuma_sichuanensis: ): [100]): [81]): [14]): [5],(Globba_curtisii: ,Globba_laeta: ): [99]): [20]): [44]): [100]): [72],( Canna_indica: ,((Maranta_arundinacea: ,Stachyphrynium_sumatranum: ): [86],((Phrynium_giganteum: ,Phrynium_maximum : ): [93],Donax_canniformis: ): [98]): [1 00]): [100]): [75],((Musa_balbisi ana: ,musa_acuminata: ): [96],(Musella_lasiocarpa: ,Ensete_glauc

25 um: ): [89]): [99]): [59],(Orchidantha_chinensis: ,Orchidantha_inouei: ): [ 100]): [99],(((((Monochoria_korsakowii: ,Monochoria_vaginalis: ): [100],Eichhornia_crassipes: ): [8 3],Eichhornia_paradoxa: ): [100], ((((Pollia_thyrsiflora CPG15046: ,Rhopalephora_scaberrim a: ): [94],((commelina_communi s: ,dictyospermum_scaberrimum CPG24011: ): [5],(Commelina_paludosa: ,Commelina_benghalensis: ): [47]): [86]): [99],(Floscopa_ scandens: ,(murdannia_clarkeana: ,(Murdannia_keisak CPG22233: ,Murdannia_satheeshiana : ): [100]): [58]): [56]): [99],((Streptoliri on_volubile: ,spatholirion_longifolium: ): [100],((Callisia_repens: ,(Tradescantia_zebrina: ,Tradescantia_spathacea: ): [100]): [100], ((Amischotolype_monosperma: ,Porandra_sp: ): [96],(Belosynapsis_ciliata: ,(Cyanotis_speciosa: ,Cyanotis_cristata: ): [97]): [100]): [100]): [100]): [100]): [100]): [73],Phily drum_lanuginosum: ): [91]): [91],(((Typha_latifolia: ,Typha_angus tifolia: ): [94],(sparganium_stolo

26 niferum: ,(sparganium_emersum: ,Sparganium_eurycarpum: ): [12 ]): [100]): [94],(((((Luzula_multif lora: ,luzula_pilosa: ): [100],(((Juncus_gerardii: ,Juncus_filiformis : ): [100],((Juncus_tenuis: ,Juncus_bufonius: ): [100],(Juncus_inflexus: ,Juncus_effusus: ): [100]): [58]): [100],(Juncus_acutus: ,Juncus_articul atus: ): [62]): [99]): [100],((Lepironia_articulata: ,(Mapania_meditensis: ,(Hypolytrum_bullatum: ,Hypolytrum_nemorum: ): [100]): [47]): [1 00],(Cladium_mariscus: ,(((Tricostularia_pauciflora: ,(((Gahnia_javanica: ,Gahnia_baniensis : ): [100],(Schoenus_nigricans: ,Schoenus_brevifolius: ): [99]): [47],(Lepidosperma_tortuosum: ,(Machaerina_mariscoides: ,Machaer ina_scirpoidea: ): [93]): [100]): [53]): [8 7],(((((Isolepis_wakefieldiana: ,(Bolboschoenus_maritimus: ,Bolboschoenus_planiculmis: ): [99]): [53],((Fuirena_umbellata: ,Fuirena_ciliaris: ): [100],(((Cyperus_eragrostis: ,(Courtoisina_assi milis: ,cyperus_luzulae: ): [17]): [91],((Cyperus_capitatus:

27 ,((Lipocarpha_nana: ,Lipocarpha_microc ephala: ): [87],((kyllinga_brevifo lia: ,(((cyperus_esculentus: ,pycr eus_polystachyos: ): [16],kylling a_flava: ): [7],((cyperus_digitatu s: ,pycreus_sanguinolentus: ): [8],Cyperus_papyrus: ): [8]): [15]): [16],Re mirea_maritima: ): [28]): [69]): [100],(Cyperus_involucratus: ,Cyperus_alternifolius: ): [100]): [95]): [100], (Actinoscirpus_grossus: ,(Schoenoplectus_tabernaemontani : ,Schoenoplectus_lacustris: ): [100]): [98]): [54]): [61]): [91],(((Bulbostyli s_densa: ,bulbostylis_barbata: ): [98],((actinoschoenus_repens: ,a ctinoschoenus_thouarsii: ): [84],( Fimbristylis_verrucifera: ,(Fimbristylis_littoralis: ,(Fimbristylis_complanata: ,(Fimbristylis_f erruginea: ,((fimbristylis_aestivalis: ,Fimbristylis_dichotoma: ): [9 1],Fimbristylis_sieboldii: ): [25]): [68]): [55]): [22]): [97]): [84]): [86],((Eleocharis_quinqueflora: ,(Eleochar is_uniglumis: ,(eleocharis_geniculata: ,(Eleocharis_erythropoda: ,Eleocharis_palustris: ): [100]): [9

28 0]): [100]): [70],Eleocharis_plant agineiformis: ): [99]): [85]): [94],(((Trichophorum_dioicum: ,Trichophorum_alpinum: ): [85],(((Scirpus_atrovirens: ,Scirpus_sylvatic us: ): [80],eriophorum_gracile: ): [89],((Kobresia_nepalensis: ,((Carex_peregrina: ,(((Carex_chordo rrhiza: ,(carex_interior: ,((carex_ cristatella: ,(carex_canescens: ,( Carex_lachenalii: ,((Carex_dioica: ,Carex_gynocrates: ): [91],Care x_glareosa: ): [54]): [49]): [62]): [49],Ca rex_maritima: ): [12]): [11]): [4],((Carex_otrubae: ,(Carex_divulsa: ,(Carex_muricata: ,Carex_lamprocarpa: ): [69]): [57]): [81],((Carex_dian dra: ,carex_paniculata: ): [48],(Carex_remota: ,Carex_ovalis: ): [16]): [51] ): [28]): [91],Kobresia_humilis: ): [80]): [37],((Kobresia_simpliciuscula: ,(Kobresia_sibirica: ,Kobresia_myosuroides: ): [73]): [84],(Carex_rupestris: ,((Carex_pauciflora: ,Carex_cordillerana: ): [89],Carex_nardina: ): [68]): [85]):

29 [66]): [58]): [57],( Carex_fuliginosa: ,((((Carex_atrofusca: ,(Carex_livida: ,(Carex_aurea: ,((Carex_ormostachya: ,Carex_blanda: ): [58],(Carex_aggregata: ,Carex_laxiflora: ): [5]): [72]): [95]): [ 41]): [24],Carex_hostiana: ): [6],(((((((Carex_magellanica: ,(Carex _lasiocarpa: ,carex_limosa: ): [79]): [27],(Carex_elata: ,((Carex_dimorpholepis: ,Carex_heterolepis: ): [39],Carex_aquatilis: ): [35]): [7]): [0],Carex_bigelowii: ): [41],Carex_capillaris: ): [0],((Carex_rotundata: ,Carex_rhynchophysa: ): [66],((((Carex_pseudocyperus: ,(Carex_hystericina: ,Carex_retrorsa: ): [67]): [71],(Carex_riparia: ,Carex_rostrata: ) : [5]): [2],Carex_hirta: ): [7],Carex_saxatilis: ): [5]): [25]): [0],((Carex_pilulifera: ,Carex_pensylvanica: ): [23],(Carex_depauperata: ,(Carex_montana: ,((Carex_oligocarpa: ,Carex_amphibola: ): [100],Carex_pedunculata: ): [39]): [0]): [0]):

30 [0]): [17],Carex_caryophyllea: ): [2]): [1],((Carex_ extensa: ,carex_punctata: ): [92],(Carex_media: ,(Carex_debilis: ,((Carex_humilis: ,Carex_scirpoid ea: ): [48],(carex_pallescens: ,Carex_acutiformis: ): [21]): [30]): [23]): [17]): [3]): [34]): [89]): [100]): [59]): [74],Blysmus_compressus: ): [100]): [96],(Rhyn chospora_alba: ,rhynchospora_schiedeana: ): [100]): [99]): [100],((Diplacrum_caricinum: ,Diplacr um_africanum: ): [100],(scleria_l atifolia: ,scleria_lithosperma: ): [100]): [100]): [78]): [100]): [100]): [100],(((Flagellaria_indica: ,(Leptaspis_ cochleata: ,(((((((digitaria_sanguinalis: ,Digitaria_gayana: ): [100], (((Panicum_bisulcatum: ,(Sacciolepis_indica: ,Sacciolepis_vilvoides: ): [100]): [98],(((Alloteropsis_semialata: ,Alloteropsis_cimicina: ): [99],(Echinochloa_esculenta: ,Echinochloa_colona: ): [100]): [ 81],((((Oplismenus_hirtellus: ,Oplismenus_compositus: ): [100],(Cyrtococcum_patens:0.007

31 ,(Pseudechinolaena_polystachya: ,Cyrt ococcum_multinode: ): [61]): [82]): [98],Acroceras_tonkinense: ): [90],(Ottochloa_gracillima: ,Ottochloa_nodosa: ): [100]): [81]): [96]): [84],((Andropogon_chinensis: ,(Pani cum_virgatum: ,pseudoraphis_spinescens: ): [100]): [19],(((((Setar ia_palmifolia: ,spinifex_sericeus: ): [37],(Cenchrus_echinatus: ,Ce nchrus_ciliaris: ): [100]): [17],(Paspalidium_jubiflorum: ,Paspalidi um_flavidum: ): [98]): [45],(Pseudoraphis_paradoxa: ,(Stenotaphr um_dimidiatum: ,stenotaphrum_secundatum: ): [100]): [43]): [100],((Thuarea_involuta: ,Brachiaria_ umbellata: ): [100],((melinis_min utiflora: ,melinis_repens: ): [100],((Urochloa_villosa: ,Urochloa_p anicoides: ): [74],(eriochloa_vill osa: ,brachiaria_deflexa: ): [72]): [99]): [ 97]): [100]): [53]): [64]): [72]): [90],(((I chnanthus_pallens: ,((axonopus_fissifolius: ,Axonopus_ramosus: ): [100],(Paspalum_dilatatum: ,Paspalum_distichum: ): [100]): [96])

32 : [96],(Hymenachne_grumosa: ,H ymenachne_amplexicaulis: ): [94 ]): [100],((Arundinella_hirta: ,Ar undinella_deppeana: ): [100],(ga rnotia_fergusonii: ,((arthraxon_lanceolatus: ,Chionachne_koenigii: ): [55],(Zea_mays: ,(((Pseudopogonatherum_contortum: ,((Apluda_mutica: ,((((Hyparrhenia _rufa: ,(spodiopogon_cotulifer: ,( Coix_aquatica: ,(Saccharum_spontaneum: ,(((Themeda_avenacea: ,(Themeda_triandra: ,Spodiopogon_sibiricus: ): [59]): [37],((Schizachyrium_brevifolium: ,Schizachyrium_scoparium: ): [33],(Andropogon_gerardii: ,Hyparrhe nia_hirta: ): [12]): [15]): [5],((((Arthraxon_hispidus: ,(Bothriochloa_ischaemum: ,Bothriochloa_sacc haroides: ): [89]): [54],Capillipedium_parviflorum: ): [57],Cymbopogon_citratus: ): [8],Heteropogon_contortus: ): [5]): [1]): [12]): [14]): [3]): [6],(( (Sorghum_bicolor: ,((Miscanthus_sacchariflorus: ,Miscanthus_sinensis: ): [57],Saccharum_officinarum: ): [58]): [2],((Pogonatherum_paniceum: ,Pogonatherum_crinitum: ): [96],(Imperata_cylindrica: ,Germainia_truncatiglumis

33 : ): [59]): [60]): [0],(Ischaemum_timorense: ,Ischaemum_koleostachys: ): [80]): [0]): [0],(Imperata_cheese manii: ,eulalia_aurea: ): [1]): [0],Eulalia_villosa: ): [0]): [1],(Coix_lacrym a: ,(chrysopogon_latifolius: ,(mi crostegium_japonicum: ,microstegium_vimineum: ): [94]): [31]): [5]): [0]): [2],((((Rottboellia_cochinchinensis: ,Sehima_nervosum: ): [48],((Dimeria_lawsonii: ,Dichanthium_aristatum: ): [11],(Ophiuros_exaltatus: ,(Mnesithea_afrau rita: ,(hemarthria_altissima: ,he marthria_uncinata: ): [88]): [81]): [88]): [6]): [12],(((Apocopis_wrightii: , Capillipedium_assimile: ): [1],(P hacelurus_latifolius: ,eremochloa_ophiuroides: ): [23]): [1],Cymb opogon_distans: ): [0]): [0],Hackelochloa_sp: ): [0]): [16],Phacelurus_digitatus: ): [57]): [57]): [88]): [39]): [93]): [91]): [96],((Thysanolaena_latifo lia: ,centotheca_lappacea: ): [100],Lophatherum_gracile: ):0.0014