{"id":3601,"date":"2020-02-04T11:50:18","date_gmt":"2020-02-04T16:50:18","guid":{"rendered":"https:\/\/ibol.org\/barcodebulletin\/?p=3601"},"modified":"2020-07-13T15:18:07","modified_gmt":"2020-07-13T19:18:07","slug":"assessing-herbarium-material-with-novel-molecular-techniques-reveals-a-wealth-of-new-data-from-old-treasure-troves","status":"publish","type":"post","link":"https:\/\/ibol.org\/barcodebulletin\/research\/assessing-herbarium-material-with-novel-molecular-techniques-reveals-a-wealth-of-new-data-from-old-treasure-troves\/","title":{"rendered":"Assessing herbarium material with novel molecular techniques reveals a wealth of new data from old treasure troves"},"content":{"rendered":"\n[et_pb_section fb_built=”1″ fullwidth=”on” _builder_version=”3.27.4″ background_blend=”multiply” custom_padding=”0px|0px|3px|0px|false|false”][et_pb_fullwidth_header title=”@ET-DC@eyJkeW5hbWljIjp0cnVlLCJjb250ZW50IjoicG9zdF90aXRsZSIsInNldHRpbmdzIjp7ImJlZm9yZSI6IiIsImFmdGVyIjoiIn19@” subhead=”@ET-DC@eyJkeW5hbWljIjp0cnVlLCJjb250ZW50IjoicG9zdF9leGNlcnB0Iiwic2V0dGluZ3MiOnsiYmVmb3JlIjoiIiwiYWZ0ZXIiOiIiLCJ3b3JkcyI6IiIsInJlYWRfbW9yZV9sYWJlbCI6IiJ9fQ==@” _builder_version=”4.0.6″ _dynamic_attributes=”title,subhead” title_font=”|||||on|||” title_line_height=”1.2em” content_font=”||||||||” content_text_color=”rgba(0,0,0,0.8)” subhead_font=”||on||||||” subhead_text_color=”#ffffff” subhead_font_size=”16px” subhead_line_height=”1.5em” background_color=”rgba(168,211,103,0)” use_background_color_gradient=”on” background_color_gradient_start=”#0a1404″ background_color_gradient_end=”#004552″ background_color_gradient_end_position=”70%” background_image=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2019\/04\/v4.boldsystems.org_7125_animalia.png” custom_margin_tablet=”” custom_margin_phone=”” custom_margin_last_edited=”on|desktop”][\/et_pb_fullwidth_header][et_pb_fullwidth_image src=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2020\/02\/Neville-Main-scaled.jpg” show_in_lightbox=”on” _builder_version=”4.2.2″ max_width=”95%” module_alignment=”center” custom_margin=”-20px||20px” box_shadow_style=”preset1″][\/et_pb_fullwidth_image][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.22.3″ custom_padding=”0|0px|7px|0px|false|false”][et_pb_row module_class=” et_pb_row_fullwidth” _builder_version=”3.25″ width=”89%” width_tablet=”80%” width_phone=”” width_last_edited=”on|desktop” max_width=”89%” max_width_tablet=”80%” max_width_phone=”” max_width_last_edited=”on|desktop” custom_padding=”0|0px|27px|0px|false|false” make_fullwidth=”on”][et_pb_column type=”4_4″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_text _builder_version=”4.2.2″ text_font=”||||||||” text_text_color=”#646564″]Hamersley Range, Pilbara, Western Australia<\/span>\n\nPHOTO CREDIT: Stephen van Leeuwen<\/span>[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ use_custom_gutter=”on” gutter_width=”2″ specialty=”on” _builder_version=”3.27.4″][et_pb_column type=”2_3″ specialty_columns=”2″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_row_inner _builder_version=”3.27.4″][et_pb_column_inner saved_specialty_column_type=”2_3″ _builder_version=”3.27.4″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_text _builder_version=”4.2.2″ text_font=”||||||||” custom_padding=”||0px|||”]

H<\/span>erbaria are valuable sources of extensive curated plant material that are important reference specimens for plant identification. These plant materials are now also accessible to genetic studies because of advances in high-throughput, next-generation sequencing (NGS) methods.<\/p>\n

In our study<\/a>, we conducted a large-scale applied assessment of one such NGS approach \u2013 genome skimming \u2013 and its ability to recover plastid and ribosomal genome sequences from a broad taxonomic sampling of herbarium material for the Western Australian flora. We sequenced 672 samples covering 21 families, 142 genera, and 530 named and proposed named species, and explored the impact of sample age, DNA concentration and quality, read depth and fragment length on plastid assembly error.<\/p>\n

We demonstrate that herbaria are a valuable source of plant material for building a comprehensive DNA sequence database which serves various applications from modernizing plant surveys to improving the resolution of plant phylogenies.<\/p>[\/et_pb_text][\/et_pb_column_inner][\/et_pb_row_inner][et_pb_row_inner column_structure=”1_2,1_2″ _builder_version=”4.2.2″][et_pb_column_inner type=”1_2″ saved_specialty_column_type=”2_3″ _builder_version=”4.2.2″][et_pb_image src=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2020\/06\/Neville-Figure2.png” show_in_lightbox=”on” _builder_version=”4.4.7″ hover_enabled=”0″ title_text=”Neville-Figure2″][\/et_pb_image][et_pb_text _builder_version=”4.2.2″ text_font=”||||||||” text_text_color=”#646564″ text_font_size=”16px” custom_padding=”||3px|||”]Gastrolobium grandiflorum<\/em>, Pilbara, Western Australia <\/span>\n\nPHOTO CREDIT: Stephen van Leeuwen<\/span>[\/et_pb_text][et_pb_text _builder_version=”4.2.2″]

Genome skimming1<\/sup> was effective at producing genomic information at large scale. Substantial sequence information on the chloroplast genome was obtained from 96.1% of samples, and complete or near-complete sequences of the nuclear ribosomal RNA gene repeat were obtained from 93.3% of samples.<\/p>[\/et_pb_text][\/et_pb_column_inner][et_pb_column_inner type=”1_2″ saved_specialty_column_type=”2_3″ _builder_version=”4.2.2″][et_pb_image src=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2020\/06\/Neville-Figure1-1.png” _builder_version=”4.2.2″ hover_enabled=”0″ title_text=”Neville-Figure1″][\/et_pb_image][et_pb_text _builder_version=”4.2.2″ text_font=”||||||||” text_text_color=”#646564″ text_font_size=”16px” custom_padding=”||3px|||”]Eucalyptus kingsmillii<\/em>, Pilbara, Western Australia <\/span>\n\nPHOTO CREDIT: Stephen van Leeuwen<\/span>[\/et_pb_text][et_pb_image src=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2020\/06\/Neville-Figure3.png” _builder_version=”4.4.7″ hover_enabled=”0″ title_text=”Neville-Figure3″][\/et_pb_image][et_pb_text _builder_version=”4.2.2″ text_font=”||||||||” text_text_color=”#646564″ text_font_size=”16px” custom_padding=”||3px|||”]Grevillea wickhamii<\/em>, Pilbara, Western Australia <\/span>\n\nPHOTO CREDIT: Stephen van Leeuwen<\/span>[\/et_pb_text][\/et_pb_column_inner][\/et_pb_row_inner][et_pb_row_inner _builder_version=”3.29.3″][et_pb_column_inner saved_specialty_column_type=”2_3″ _builder_version=”3.29.3″][et_pb_text _builder_version=”4.2.2″]

We extracted sequences for plastid markers rbcL<\/em> and matK<\/em>\u00a0\u2013 the core DNA barcode regions\u00a0\u2013 from 96.4% and 93.3% of samples, respectively. Read quality and DNA fragment length had significant effects on sequencing outcomes and error correction of reads proved essential. Assembly problems were specific to certain taxa with low GC and high repeat content (e.g. Goodenia, Scaevola, Cyperus, Bulbostylis, Fimbristylis<\/em>), suggesting the influence of biological rather than technical factors. The structure of related genomes was needed to guide the assembly of repeats that exceeded the read length. DNA-based matching proved highly effective and showed that the efficacy for species identification declined in the following order: total chloroplast DNA\u00a0<\/span>>> ribosomal DNA > matK<\/em> >> rbcL<\/em>.<\/p>[\/et_pb_text][\/et_pb_column_inner][\/et_pb_row_inner][et_pb_row_inner _builder_version=”3.29.3″ custom_padding=”||65px|||”][et_pb_column_inner saved_specialty_column_type=”2_3″ _builder_version=”3.29.3″][et_pb_image src=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2020\/02\/Neville-Figure4.jpg” show_in_lightbox=”on” _builder_version=”4.2.2″][\/et_pb_image][et_pb_text _builder_version=”4.2.2″ text_font=”||||||||” text_text_color=”#646564″ text_font_size=”16px” custom_padding=”||3px|||”]Ptilotus rotundifolius<\/em>, Pilbara, Western Australia \n\nPHOTO CREDIT: Stephen van Leeuwen<\/span>[\/et_pb_text][et_pb_text _builder_version=”4.2.2″ custom_padding=”||31px|||”]

Our success is important as it demonstrates that herbaria can be used as a source of plant material for building a comprehensive DNA sequence database. These data form the basis of development of a molecular identification system for the Western Australian flora. This will enable identification of specimens throughout the year (e.g., non-flowering times) and for hard-to-identify species (e.g., those with constrained or reduced morphological characters) or for specimens where only fragments of non-diagnostic material are available. The availability of this technology will modernize plant surveys by reducing constraints on survey effort through moderating sampling timing restrictions and seasonal effects, as well as enabling rapid verifiable identification. It will also have practical applications in a wide range of ecological contexts using eDNA metabarcoding, such as gut and scat analysis of animals to determine dietary preferences of threatened species and livestock, and checking the integrity of seed collections for seed banking and use in land restoration\/revegetation programs. Other potential uses of extensive plastid sequence data, beyond species identification, include improving the resolution of plant phylogenies and studies on the evolution of plastid genome function, including understanding adaptive changes.<\/p>[\/et_pb_text][et_pb_text disabled_on=”off|off|off” _builder_version=”4.2.2″ text_font=”||||||||” text_font_size=”15px” custom_padding=”43px|||||”]

References:<\/h4>\n1. Straub S, Parks M, Weitemier K, Fishbein M, Cronn R, Liston A (2012) Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics. American Journal of Botany<\/em> 99(2), 349-364. https:\/\/dx.doi.org\/10.3732\/ajb.1100335[\/et_pb_text][\/et_pb_column_inner][\/et_pb_row_inner][et_pb_row_inner _builder_version=”4.2.2″ background_color=”#f2f2f2″][et_pb_column_inner saved_specialty_column_type=”2_3″ _builder_version=”4.2.2″][et_pb_text _builder_version=”4.2.2″ text_text_color=”#646564″ text_font_size=”17px”]

For full details, please refer to the\u00a0publication<\/a> in BMC Plant Methods<\/em>.<\/p>[\/et_pb_text][\/et_pb_column_inner][\/et_pb_row_inner][\/et_pb_column][et_pb_column type=”1_3″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_text _builder_version=”3.27.4″ text_font=”||on||||||” text_text_color=”#646564″ text_orientation=”center”]

Written by<\/p>[\/et_pb_text][et_pb_team_member name=”Paul Nevill” position=”Curtin University, School of Molecular and Life Sciences, ARC Centre for Mine Site Restoration” image_url=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2020\/02\/Paul_Nevil.png” _builder_version=”4.2.2″ header_font=”||||||||” header_text_align=”center” header_font_size=”17px” body_font=”||||||||” body_text_color=”rgba(100,101,100,0.66)” body_font_size=”15px” text_orientation=”center” width=”85%” module_alignment=”center” link_option_url_new_window=”on”]

& Trace and Environmental DNA (TrEnD) Lab, Perth, Western Australia<\/p>[\/et_pb_team_member][et_pb_divider divider_position=”center” _builder_version=”3.23.3″ custom_margin=”||1px”][\/et_pb_divider][et_pb_text _builder_version=”3.27.4″ _dynamic_attributes=”content” text_font=”||||||||” text_text_color=”#003254″ text_orientation=”center”]@ET-DC@eyJkeW5hbWljIjp0cnVlLCJjb250ZW50IjoicG9zdF9kYXRlIiwic2V0dGluZ3MiOnsiYmVmb3JlIjoiIiwiYWZ0ZXIiOiIiLCJkYXRlX2Zvcm1hdCI6ImRlZmF1bHQiLCJjdXN0b21fZGF0ZV9mb3JtYXQiOiIifX0=@[\/et_pb_text][et_pb_button button_url=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2020\/02\/2020-Nevill.pdf” url_new_window=”on” button_text=”Download PDF” button_alignment=”center” disabled_on=”off|off|off” _builder_version=”4.2.2″ custom_button=”on” button_text_size=”12px” button_text_color=”#ffffff” button_bg_color=”#003254″ button_icon=”%%26%%” button_icon_color=”#ffffff” box_shadow_style=”preset3″ box_shadow_horizontal=”3px” box_shadow_vertical=”11px”][\/et_pb_button][et_pb_text _builder_version=”4.2.2″ text_font=”||||||||” text_text_color=”#646564″ text_font_size=”12px” text_orientation=”center”]

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Using large-scale genome skimming to build a resilient resource for the future <\/p>\n","protected":false},"author":42,"featured_media":3604,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","_et_gb_content_width":"2880","_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"footnotes":""},"categories":[2],"tags":[6,284,64,45],"coauthors":[283],"class_list":["post-3601","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-research","tag-australia","tag-genome-skimming","tag-herbarium","tag-reference-library"],"_links":{"self":[{"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/posts\/3601","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/users\/42"}],"replies":[{"embeddable":true,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/comments?post=3601"}],"version-history":[{"count":17,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/posts\/3601\/revisions"}],"predecessor-version":[{"id":4550,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/posts\/3601\/revisions\/4550"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/media\/3604"}],"wp:attachment":[{"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/media?parent=3601"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/categories?post=3601"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/tags?post=3601"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/coauthors?post=3601"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}