Complete Chloroplast Genome Sequence of Holoparasite Cistanche deserticola (Orobanchaceae) Reveals Gene Loss and Horizontal Gene Transfer from Its Host Haloxylon ammodendron (Chenopodiaceae)
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{"title"=>"Complete Chloroplast Genome Sequence of Holoparasite Cistanche deserticola (Orobanchaceae) Reveals Gene Loss and Horizontal Gene Transfer from Its Host Haloxylon ammodendron (Chenopodiaceae)", "type"=>"journal", "authors"=>[{"first_name"=>"Xi", "last_name"=>"Li", "scopus_author_id"=>"57192494092"}, {"first_name"=>"Ti Cao", "last_name"=>"Zhang", "scopus_author_id"=>"37076087200"}, {"first_name"=>"Qin", "last_name"=>"Qiao", "scopus_author_id"=>"55247058600"}, {"first_name"=>"Zhumei", "last_name"=>"Ren", "scopus_author_id"=>"7402408221"}, {"first_name"=>"Jiayuan", "last_name"=>"Zhao", "scopus_author_id"=>"7410313897"}, {"first_name"=>"Takahiro", "last_name"=>"Yonezawa", "scopus_author_id"=>"16320082300"}, {"first_name"=>"Masami", "last_name"=>"Hasegawa", "scopus_author_id"=>"36056385500"}, {"first_name"=>"M. James C.", "last_name"=>"Crabbe", "scopus_author_id"=>"56913081000"}, {"first_name"=>"Jianqiang", "last_name"=>"Li", "scopus_author_id"=>"55720802100"}, {"first_name"=>"Yang", "last_name"=>"Zhong", "scopus_author_id"=>"55345012500"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23554920", "doi"=>"10.1371/journal.pone.0058747", "sgr"=>"84875011095", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-84875011095", "issn"=>"19326203", "pui"=>"368535339"}, "id"=>"047402ee-cc71-3eb2-bbc6-344e98f53bef", "abstract"=>"BACKGROUND: The central function of chloroplasts is to carry out photosynthesis, and its gene content and structure are highly conserved across land plants. Parasitic plants, which have reduced photosynthetic ability, suffer gene losses from the chloroplast (cp) genome accompanied by the relaxation of selective constraints. Compared with the rapid rise in the number of cp genome sequences of photosynthetic organisms, there are limited data sets from parasitic plants. PRINCIPAL FINDINGS/SIGNIFICANCE: Here we report the complete sequence of the cp genome of Cistanche deserticola, a holoparasitic desert species belonging to the family Orobanchaceae. The cp genome of C. deserticola is greatly reduced both in size (102,657 bp) and in gene content, indicating that all genes required for photosynthesis suffer from gene loss and pseudogenization, except for psbM. The striking difference from other holoparasitic plants is that it retains almost a full set of tRNA genes, and it has lower dN/dS for most genes than another close holoparasitic plant, E. virginiana, suggesting that Cistanche deserticola has undergone fewer losses, either due to a reduced level of holoparasitism, or to a recent switch to this life history. We also found that the rpoC2 gene was present in two copies within C. deserticola. Its own copy has much shortened and turned out to be a pseudogene. Another copy, which was not located in its cp genome, was a homolog of the host plant, Haloxylon ammodendron (Chenopodiaceae), suggesting that it was acquired from its host via a horizontal gene transfer.", "link"=>"http://www.mendeley.com/research/complete-chloroplast-genome-sequence-holoparasite-cistanche-deserticola-orobanchaceae-reveals-gene-l", "reader_count"=>48, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Student > Doctoral Student"=>4, "Researcher"=>6, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>2, "Student > Master"=>6, "Other"=>2, "Student > Bachelor"=>6, "Professor"=>5}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Student > Doctoral Student"=>4, "Researcher"=>6, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>2, "Student > Master"=>6, "Other"=>2, "Student > Bachelor"=>6, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>37, "Medicine and Dentistry"=>2, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>37}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"New Zealand"=>1, "Canada"=>1, "Germany"=>2, "Russia"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/988736"], "description"=>"<p>(A) Alignment of the nucleotide sequences of transferred rpoC2 gene amplified from parasite and host with intact open reading frames of other related species. The inserted cytosine was labeled with colored vertical lines. (B) Inserted cytosine resulted in followed premature termination codon in the transferred rpoC2 in <i>Cistanche deserticola</i>.</p>", "links"=>[], "tags"=>["inserted", "cytosine", "rpoc2"], "article_id"=>653152, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Xi Li", "Ti-Cao Zhang", "Qin Qiao", "Zhumei Ren", "Jiayuan Zhao", "Takahiro Yonezawa", "Masami Hasegawa", "M. James C Crabbe", "Jianqiang Li", "Yang Zhong"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058747.g004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Position_of_inserted_cytosine_within_the_transferred_rpoC2_gene_/653152", "title"=>"Position of inserted cytosine within the transferred rpoC2 gene.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-16 08:01:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/1012724"], "description"=>"<p>Data in this table came from analyses using sequences on GenBank or plastid chromosomes gene maps in their original report.</p>a<p>Number of genes excluding the pseudogenes. Duplicated genes in the IR regions were counted twice.</p>b<p>Duplicated tRNAs were counted both.</p>", "links"=>[], "tags"=>["plastidome", "compared", "parasitic"], "article_id"=>673132, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Xi Li", "Ti-Cao Zhang", "Qin Qiao", "Zhumei Ren", "Jiayuan Zhao", "Takahiro Yonezawa", "Masami Hasegawa", "M. James C Crabbe", "Jianqiang Li", "Yang Zhong"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058747.t002", "stats"=>{"downloads"=>1, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Global_features_of_Cistanche_deserticola_plastidome_compared_to_Nicotiana_tabacum_and_other_parasitic_plants_/673132", "title"=>"Global features of <i>Cistanche deserticola</i> plastidome compared to <i>Nicotiana tabacum</i> and other parasitic plants.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-15 00:52:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/988730"], "description"=>"<p>Lamiales are coloured in red, and Caryophyllales are coloured in blue. While the ten <i>C. deserticola</i> sequences involved in horizontal gene transfer are coloured in red. Numbers at nodes are posterior probabilities >0.60 and maximum likelihood bootstrap values >60. The Genebank number: <i>Oryza nivara</i>, NC_005973; <i>Antirrhinum indicum</i>, GQ997028; <i>Sesamum indicum</i>, NC_016433; <i>Boea hygrometrica</i>, NC_016468; <i>Jasminum nudiflorum</i>, NC_008407; O<i>lea europaea</i>, NC_013707; <i>Basella alba</i>, HQ843359; <i>Opuntia microdasys</i>, HQ843375; <i>Pereskia aculeata</i>, HQ843376; <i>Portulaca oleracea</i>, HQ843380; Mollugo verticillata, HQ843373; <i>Bougainvillea glabra</i>, HQ843360; <i>Mirabilis jalapa</i>, HQ843372; <i>Phytolacca americana</i>, HQ843378; <i>Celosia cristata</i>, HQ843361; <i>Spinacia oleracea</i>, NC_002202; <i>Silene conica</i>, NC_016729; <i>Stellaria media</i>, HQ843386; <i>Cistanche deserticola</i> (HGT), KC543998.</p>", "links"=>[], "tags"=>["horizontal", "plastid", "rpoc2"], "article_id"=>653146, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Xi Li", "Ti-Cao Zhang", "Qin Qiao", "Zhumei Ren", "Jiayuan Zhao", "Takahiro Yonezawa", "Masami Hasegawa", "M. James C Crabbe", "Jianqiang Li", "Yang Zhong"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058747.g003", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_evidence_for_horizontal_gene_transfer_of_the_plastid_rpoC2_from_Haloxylon_ammodendron_to_Cistanche_deserticola_/653146", "title"=>"Phylogenetic evidence for horizontal gene transfer of the plastid rpoC2 from <i>Haloxylon ammodendron</i> to <i>Cistanche deserticola.</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-16 08:00:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1012755"], "description"=>"<p>Nt, <i>Nicotiana tabacum</i>; Cr, <i>Cuscuta reflexa</i>; Co, <i>Cuscuta obtusiflora</i>; Cg, <i>Cuscuta gronovii</i>; Ce, <i>Cuscuta exaltata</i>; Cd, <i>Cistanche deserticola</i>; Ev, <i>Epifagus virginiana</i>; Rg, <i>Rhizanthella gardneri</i>; Nn, <i>Neottia nidus-avis</i>; Ψ, pseudogene; •, present; ○, missing.</p>", "links"=>[], "tags"=>["contents", "plastidome", "compared", "parasitic", "plants", "reports"], "article_id"=>673155, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Xi Li", "Ti-Cao Zhang", "Qin Qiao", "Zhumei Ren", "Jiayuan Zhao", "Takahiro Yonezawa", "Masami Hasegawa", "M. James C Crabbe", "Jianqiang Li", "Yang Zhong"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058747.t001", "stats"=>{"downloads"=>6, "page_views"=>29, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_contents_of_plastidome_of_Cistanche_deserticola_compared_to_Nicotiana_tabacum_and_other_parasitic_plants_based_on_this_research_and_previous_reports_6_9_67_/673155", "title"=>"Gene contents of plastidome of <i>Cistanche deserticola</i> compared to <i>Nicotiana tabacum</i> and other parasitic plants (based on this research and previous reports [6], [9], [67]).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-15 00:52:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/988729"], "description"=>"<p>*indicates gene lost, <sup>#</sup>indicates the absence of non synonymous substitutions, <sup>$</sup>indicates the absence of synonymous substitutions.</p>", "links"=>[], "tags"=>["protein-coding"], "article_id"=>653145, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Xi Li", "Ti-Cao Zhang", "Qin Qiao", "Zhumei Ren", "Jiayuan Zhao", "Takahiro Yonezawa", "Masami Hasegawa", "M. James C Crabbe", "Jianqiang Li", "Yang Zhong"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058747.g002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_dN_dS_value_of_C_deserticola_Cd_E_virginiana_Ev_and_N_tabacum_Nt_vs_O_europaea_Oe_for_all_shared_protein_coding_genes_/653145", "title"=>"Pairwise dN/dS value of <i>C. deserticola</i> (Cd), <i>E. virginiana</i> (Ev) and <i>N. tabacum</i> (Nt) vs. <i>O. europaea</i> (Oe) for all shared protein-coding genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-16 08:00:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/988728"], "description"=>"<p>Genes shown inside the circle are transcribed clockwise, those outside the circle are transcribed counterclockwise. The large single copy region (LSC) and the small single copy region (SSC) are separated by two inverted repeats (IRa and IRb). Asterisks indicate intron containing genes. Pseudogenes are marked by Ψ.</p>", "links"=>[], "tags"=>["maps", "plastid", "chromosomes"], "article_id"=>653144, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Xi Li", "Ti-Cao Zhang", "Qin Qiao", "Zhumei Ren", "Jiayuan Zhao", "Takahiro Yonezawa", "Masami Hasegawa", "M. James C Crabbe", "Jianqiang Li", "Yang Zhong"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058747.g001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_Maps_of_the_plastid_chromosomes_of_C_deserticola_/653144", "title"=>"Gene Maps of the plastid chromosomes of <i>C. deserticola</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-16 07:59:56"}

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Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Biotechnology", "average_usage"=>[259, 472, 622, 759, 885, 1009, 1123, 1232, 1335, 1437, 1533, 1627, 1698]}, {"subject_area"=>"/Biology and life sciences/Computational biology", "average_usage"=>[295, 511, 651, 775, 882, 992, 1100, 1201, 1304, 1400, 1486, 1570, 1650]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[284, 491, 620, 738, 843, 945, 1043, 1137, 1225, 1315, 1400, 1479, 1555]}, {"subject_area"=>"/Biology and life sciences/Parasitology", "average_usage"=>[354, 586, 723, 820, 941, 1045, 1176, 1283, 1391, 1469, 1526, 1639, 1730]}, {"subject_area"=>"/Biology and life sciences/Plant science", "average_usage"=>[269, 451, 577, 699, 812, 922, 1019, 1126, 1225, 1309, 1404, 1493, 1563]}]}
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