Herbariomics: a new and powerful approach for dendrological studies

YANG Yong, YANG Zhi, DUAN Yifan, FANG Yanming

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2022, Vol. 46 ›› Issue (1) : 1-6.

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JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2022, Vol. 46 ›› Issue (1) : 1-6. DOI: 10.12302/j.issn.1000-2006.202104022

Herbariomics: a new and powerful approach for dendrological studies

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Abstract

Dendrology is a branch of biology, dealing with the characteristics of woody plants; and phylogeny is the basis of dendrology. Common limiting factors in phylogenetic studies include inadequate species sampling and the availability of sufficient sequence data. The application of new approaches may broaden the range of materials to be utilized and thereby improve the resolution of phylogenies, thus advancing dendrological studies to higher levels. Herbaria preserve specimens that are the permanent vouchers for species; they comprise an important resource bank, storing information on morphology, distribution, ecology and phenology, and also plant materials. Herbarium specimens contain deoxyribonucleic acid (DNA) sequences fragmented due to degradation and oxidization during specimen preparation and preservation. As such, Sanger sequencing cannot make full use of herbarium specimens in phylogenetic studies due to these limitations. This study introduces a novel method referred to as herbariomics, in which DNA sequences (i.e., nrITS, plastomes, mitomes and single-copy nuclear genes) can be obtained from herbarium specimens by using next-generation sequencing and bioinformatics methodologie. Herbariomics enable low-cost, time-saving, highly efficient, and accurate dendrological research. Its application is likely to accelerate research associated with reconstructing the Tree of Life, DNA barcoding, species conservation, and the sustainable utilization of trees.

Key words

dendrology and taxonomy / herbariomics / phylogeny

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YANG Yong , YANG Zhi , DUAN Yifan , et al. Herbariomics: a new and powerful approach for dendrological studies[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2022, 46(1): 1-6 https://doi.org/10.12302/j.issn.1000-2006.202104022

References

[1]
祁承经, 汤庚国. 树木学(南方版)[M]. 北京: 中国林业出版社, 2020.
[2]
JUDD W S, CAMPBELL C S, KELLOGG E A, 等. 植物系统学[M].李德铢,等,译. 北京: 高等教育出版社, 2012.
JUDD W S, CAMPBELL C S, KELLOGG E A, et al. Plant systematics:a phylogenetic approach[M]. LI D Z, et al, trans. Beijing: Higher Education Press, 2012.
[3]
达尔文. 物种起源[M].周建人,等,译. 北京: 商务印书馆, 1995.
DARWIN C. The origin of species[M]. ZHOU J R, et al, trans. Beijing: The Commercial Press, 1995.
[4]
郑万钧, 傅立国. 中国植物志(第7卷): 裸子植物门[M]. 北京: 科学出版社, 1978.
[5]
ARNOLD C A. Classification of gymnosperms from the viewpoint of paleobotany[J]. Bot Gazette, 1948, 110(1):2-12.DOI: 10.1086/335513.
[6]
CHAMBERLAIN C J. Gymnosperms:structure and evolution[J]. Nature, 1935, 136(3434):278-279.DOI: 10.1038/136278a0.
[7]
FU D Z, YANG Y, ZHU G H. A new scheme of classification of living gymnosperms at family level[J]. Kew Bull, 2004, 59(1):111.DOI: 10.2307/4111081.
[8]
KENG H. A new scheme of classification of the conifers[J]. Taxon, 1975, 24(2/3):289-292.DOI: 10.2307/1218337.
[9]
PILGER R. Gymnospermae[M]// ENGLER A. Die Naturlichen Pflanzenfamilien. Leipzig: Verlag von Wilhelm Engelmann, 1926: 1-447.
[10]
PILGER R, MELCHIOR H. XVI: Abteilung: Gymnospermae. Nackstamer. (Archispermae)[M]// MELCHIOR H, WERDERMANN E A. Engler’s Syllabus der Pflanzenfamilien. Band 1. Allgemeiner Teil Bakterien bis Gymnospermen. Allgemeiner Teil Bakterien bis Gymnospermen. Gebruder Borntraeger, Berlin-Nikolassee, 1954: 312-344.
[11]
杨永, 王志恒, 徐晓婷. 世界裸子植物的分类和地理分布[M]. 上海: 上海科学技术出版社, 2017.
YANG Y, WANG Z H, XU X T. Taxonomy and distribution of global gymnosperms[M]. Shanghai: Shanghai Scientific & Technical Publishers, 2017.
[12]
傅德志, 杨亲二. 银杏雌性生殖器官的形态学本质及其系统学意义[J]. 植物分类学报, 1993, 31(3):294-296.
[13]
傅德志, 杨亲二. 银杏雌性生殖器官的形态学本质及其系统学意义(续)[J]. 植物分类学报, 1993, 31(4):309-317.
[14]
DOUGLAS A W, STEVENSON D W, LITTLE D P. Ovule development in Ginkgo biloba L.,with emphasis on the collar and nucellus[J]. Int J Plant Sci, 2007, 168(9):1207-1236.DOI: 10.1086/521693.
[15]
KRAMER K U, GREEN P S. The families and genera of vascular plants I: Pteridophytes and gymnosperms[M]. Berlin: Springer-Verlag, 1990.
[16]
路安民, 汤彦承. 原始被子植物的起源与演化[M]. 北京: 科学出版社, 2020.
[17]
王文采. 当代四被子植物分类系统简介(一)[J]. 植物学通报, 1990, 25(2):1-17.
WANG W C. An introduction to four important current systems of classification of the angiosperms (I)[J]. Chin Bull Bot, 1990, 25(2):1-17.
[18]
王文采. 当代四被子植物分类系统简介(二)[J]. 植物学通报, 1990, 25(3):1-18.
WANG W C. An introduction to four important current systems of classification of the angiosperms(Ⅱ)[J]. Chin Bull Bot, 1990, 25(3):1-18.
[19]
GROUP T A P. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants:APG IV[J]. Bot J Linn Soc, 2016, 181(1):1-20.DOI: 10.1111/boj.12385.
[20]
胡亚亚, 刘兰服, 冀红柳, 等. 简化基因组测序技术研究进展[J]. 江苏师范大学学报(自然科学版), 2018, 36(4):63-68.
HU Y Y, LIU L F, JI H L, et al. Research progress on the reduced-representation genome sequencing technique[J]. J Jiangsu Norm Univ (Nat Sci Ed), 2018, 36(4):63-68.DOI: 10.3969/j.issn.2095-4298.2018.04.012.
[21]
STRAUB S C, PARKS M, WEITEMIER K, et al. Navigating the tip of the genomic iceberg:next-generation sequencing for plant systematics[J]. Am J Bot, 2012, 99(2):349-364.DOI: 10.3732/ajb.1100335.
[22]
BAKKER F T. Herbarium genomics:plant archival DNA explored[M]//Population genomics. Cham: Springer International Publishing, 2018:205-224. DOI: 10.1007/13836_2018_40.
[23]
BESNARD G, CHRISTIN P A, MALÉ P J G, et al. From museums to genomics:old herbarium specimens shed light on a C3 to C4 transition[J]. J Exp Bot, 2014, 65(22):6711-6721.DOI: 10.1093/jxb/eru395.
[24]
ZEDANE L, HONG-WA C, MURIENNE J, et al. Museomics illuminate the history of an extinct,paleoendemic plant lineage (Hesperelaea,Oleaceae) known from an 1875 collection from Guadalupe Island,Mexico[J]. Biol J Linn Soc, 2016, 117(1):44-57.DOI: 10.1111/bij.12509.
[25]
DODSWORTH S, GUIGNARD M S, CHRISTENHUSZ M J M, et al. Potential of herbariomics for studying repetitive DNA in angiosperms[J]. Front Ecol Evol, 2018, 6:174.DOI: 10.3389/fevo.2018.00174.
[26]
JIN J J, YU W B, YANG J B, et al. GetOrganelle:a fast and versatile toolkit for accurate de novo assembly of organelle genomes[J]. Genome Biol, 2020, 21(1):241.DOI: 10.1186/s13059-020-02154-5.
[27]
DIERCKXSENS N, MARDULYN P, SMITS G. NOVOPlasty:de novo assembly of organelle genomes from whole genome data[J]. Nucleic Acids Res, 2017, 45(4):e18.DOI: 10.1093/nar/gkw955.
[28]
JOHNSON M G, GARDNER E M, LIU Y, et al. HybPiper:Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment[J]. Appl Plant Sci, 2016, 4(7):1600016.DOI: 10.3732/apps.1600016.
[29]
ALSOS I G, LAVERGNE S, MERKEL M K F, et al. The treasure vault can be opened:large-scale genome skimming works well using herbarium and silica gel dried material[J]. Plants, 2020, 9(4):432.DOI: 10.3390/plants9040432.
[30]
NEVILL P G, ZHONG X, TONTI-FILIPPINI J, et al. Large scale genome skimming from herbarium material for accurate plant identification and phylogenomics[J]. Plant Methods, 2020, 16:1.DOI: 10.1186/s13007-019-0534-5.
[31]
ZENG C X, HOLLINGSWORTH P M, YANG J, et al. Genome skimming herbarium specimens for DNA barcoding and phylogenomics[J]. Plant Methods, 2018, 14:43.DOI: 10.1186/s13007-018-0300-0.
[32]
BAKKER F T, LEI D, YU J Y, et al. Herbarium genomics:plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline[J]. Biol J Linn Soc, 2016, 117(1):33-43.DOI: 10.1111/bij.12642.
[33]
LIU B B, MA Z Y, REN C, et al. Capturing single-copy nuclear genes,organellar genomes,and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics:a case study in Vitaceae[J]. J Syst Evol, 2021, 59(5):1124-1138.DOI: 10.1111/jse.12806.
[34]
DODSWORTH S. Genome skimming for next-generation biodiversity analysis[J]. Trends Plant Sci, 2015, 20(9):525-527.DOI: 10.1016/j.tplants.2015.06.012.
[35]
LEMMON A R, EMME S A, LEMMON E M. Anchored hybrid enrichment for massively high-throughput phylogenomics[J]. Syst Biol, 2012, 61(5):727-744.DOI: 10.1093/sysbio/sys049.
[36]
YU X, YANG D, GUO C, et al. Plant phylogenomics based on genome-partitioning strategies: progress and prospects[J]. Plant Divers, 2018, 40(4):158-164.DOI: 10.1016/j.pld.2018.06.005.
[37]
DODSWORTH S, POKORNY L, JOHNSON M G, et al. Hyb-seq for flowering plant systematics[J]. Trends Plant Sci, 2019, 24(10):887-891.DOI: 10.1016/j.tplants.2019.07.011.
[38]
STAATS M, ERKENS R H, VAN DE VOSSENBERG B, et al. Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens[J]. PLoS One, 2013, 8(7):e69189.DOI: 10.1371/journal.pone.0069189.
[39]
SHEE Z Q, FRODIN D G, CÁMARA-LERET R, et al. Reconstructing the complex evolutionary history of the papuasian Schefflera radiation through herbariomics[J]. Front Plant Sci, 2020, 11:258.DOI: 10.3389/fpls.2020.00258.
[40]
SCHNEIDER J V, PAULE J, JUNGCURT T, et al. Resolving recalcitrant clades in the pantropical Ochnaceae: insights from comparative phylogenomics of plastome and nuclear genomic data derived from targeted sequencing[J]. Front Plant Sci, 2021, 12:638650.DOI: 10.3389/fpls.2021.638650.
[41]
VAN DE PAER C, HONG-WA C, JEZIORSKI C, et al. Mitogenomics of Hesperelaea,an extinct genus of Oleaceae[J]. Gene, 2016, 594(2):197-202.DOI: 10.1016/j.gene.2016.09.007.
[42]
ANDERMANN T, TORRES JIMÉNEZ M F, MATOS-MARAVÍ P, et al. A guide to carrying out a phylogenomic target sequence capture project[J]. Front Genet, 2019, 10:1407.DOI: 10.3389/fgene.2019.01407.
[43]
BREWER G E, CLARKSON J J, MAURIN O, et al. Factors affecting targeted sequencing of 353 nuclear genes from herbarium specimens spanning the diversity of angiosperms[J]. Front Plant Sci, 2019, 10:1102.DOI: 10.3389/fpls.2019.01102.
[44]
SCHNEIDER J V, JUNGCURT T, CARDOSO D, et al. Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa[J]. TAXON, 2021, 70(1):48-71.DOI: 10.1002/tax.12421.
[45]
GARDNER E M, JOHNSON M G, PEREIRA J T, et al. Paralogs and off-target sequences improve phylogenetic resolution in a densely sampled study of the breadfruit genus (Artocarpus,Moraceae)[J]. Syst Biol, 2021, 70(3):558-575.DOI: 10.1093/sysbio/syaa073.
[46]
VILLAVERDE T, POKORNY L, OLSSON S, et al. Bridging the micro-and macroevolutionary levels in phylogenomics:Hyb-Seq solves relationships from populations to species and above[J]. New Phytol, 2018, 220(2):636-650.DOI: 10.1111/nph.15312.
[47]
HART M L, FORREST L L, NICHOLLS J A, et al. Retrieval of hundreds of nuclear loci from herbarium specimens[J]. TAXON, 2016, 65(5):1081-1092.DOI: 10.12705/655.9.
[48]
GERNANDT D S, AGUIRRE DUGUA X, VÁZQUEZ-LOBO A, et al. Multi-locus phylogenetics,lineage sorting,and reticulation in Pinus subsection Australes[J]. Am J Bot, 2018, 105(4):711-725.DOI: 10.1002/ajb2.1052.
[49]
王文采. 植物标本馆在植物分类学研究中的重要性[J]. 生命世界, 2011(9):1.
[50]
BAKKER F T, BIEKER V C, MARTIN M D. Editorial:herbarium collection-based plant evolutionary genetics and genomics[J]. Front Ecol Evol, 2020, 8:603948.DOI: 10.3389/fevo.2020.603948.
[51]
ALBANIROCCHETTI G, ARMSTRONG C G, ABELI T, et al. Reversing extinction trends: new uses of (old) herbarium specimens to accelerate conservation action on threatened species[J]. New Phytol, 2021, 230(2):433-450.DOI: 10.1111/nph.17133.
[52]
BAKKER F T, ANTONELLI A, CLARKE J A, et al. The global museum: natural history collections and the future of evolutionary science and public education[J]. PeerJ, 2020, 8:e8225.DOI: 10.7717/peerj.8225.
[53]
马金双. 中国植物分类学的现状与挑战[J]. 科学通报, 2014, 59(6):510-521.
MA J S. Current status and challenges of Chinese plant taxonomy[J]. Chin Sci Bull, 2014, 59(6):510-521.
[54]
贺鹏, 陈军, 乔格侠. 中国科学院生物标本馆(博物馆)的现状与未来[J]. 中国科学院院刊, 2019, 34(12):1359-1370.
HE P, CHEN J, QIAO G X. Current situation and future of biological collections of Chinese academy of sciences[J]. Bull Chin Acad Sci, 2019, 34(12):1359-1370.DOI: 10.16418/j.issn.1000-3045.2019.12.005.
[55]
胡启明, VIDA J E. 中南半岛紫金牛科植物志预报[J]. 热带亚热带植物学报, 1996(4):1-15.
HU Q M, VIDA J E. Towards a revision of the Myrsinaceae of Indochina[J]. J Trop Subtrop Bot, 1996(4):1-15.
[56]
ZHU X Y, ZHANG R P, HE Y L. An inventory of legume species diversity of Myanmar[M]. Beijing: China Minzu University Press, 2021.
[57]
贺鹏, 陈军, 孔宏智, 等. 生物样本: 生物多样性研究与保护的重要支撑[J]. 中国科学院院刊, 2021, 36(4):425-435.
HE P, CHEN J, KONG H Z, et al. Important supporting role of biological specimen in biodiversity conservation and research[J]. Bull Chin Acad Sci, 2021, 36(4):425-435.DOI: 10.16418/j.issn.1000-3045.20210323001.
[58]
WANDELER P, HOECK P E, KELLER L F. Back to the future: museum specimens in population genetics[J]. Trends Ecol Evol, 2007, 22(12):634-642.DOI: 10.1016/j.tree.2007.08.017.

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