基因组学与应用生物学

参考文献

ANDERSON J,KANTAR M,BOCK D,et al.,2019.Skim-sequencing reveals the likely origin of the enigmatic endangered sunflower Helianthus schweinitzii.Genes,10(12):1040.

BAKKER F T,2017.Herbarium genomics:skimming and plastomics from archival specimens.Webbia,72(1):35-45.

BAKKER F T,LEI D,YU J Y,et al.,2016.Herbarium geno-mics:plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline.Biol.J.Linn.Soc.,117(1):33-43.

BARRETT C F,BAKER W J,COMER J R,et al.,2016.Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots.New Phytol.,209(2):855-870.

BARRETT C F,DAVIS J I,2012.The plastid genome of the mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation.Am.J.Bot.,99(9):1513-1523.

BELL K L,BURGESS K S,BOTSCH J C,et al.,2019.Quantitative and qualitative assessment of pollen DNA metabarcoding using constructed species mixtures.Mol.Ecol.,28(2):431-455.

BUERKI S,CALLMANDER M W,DEVEY D S,et al.,2012.Straightening out the screw-pines:a first step in understanding phylogenetic relationships within Pandanaceae.TAXON,61(5):1010-1020.

CAFA G,BARONCELLI R,ELLISON C A,et al.,2020.Impatiens glandulifera (Himalayan balsam) chloroplast genome sequence as a promising target for populations studies.PeerJ,8:e8739.

CAI L M,ZHANG H R,DAVIS C C,2022.PhyloHerb:a high-throughput phylogenomic pipeline for processing genome skimming data.Appl.Plant Sci.,10(3):e11475.

CALLENS M,LE BERRE G,VAN DEN BULCKE L,et al.,2025.An accessible metagenomic strategy allows for better characterisation of invertebrate bulk samples.Mol.Ecol.Resour.,25(8):e14126.

CBOL PLANT WORKING GROUP,HOLLINGSWORTH P M,FORREST L L,et al.,2009.A DNA barcode for land plants.Proc.Natl.Acad.Sci.U.S.A.,106(31):12794-12797.

CHASE M W,COWAN R S,HOLLINGSWORTH P M,et al.,2007.A proposal for a standardised protocol to barcode all land plants.TAXON,56(2):295-299.

CHEN X,DONG Z W,LIU G C,et al.,2019.Phylogenetic analysis provides insights into the evolution of Asian fireflies and adult bioluminescence.Mol.Phylogenet.Evol.,140:106600.

DE MEDEIROS B A S,CAI L M,FLYNN P J,et al.,2025.A composite universal DNA signature for the tree of life.Nat.Ecol.Evol.,9(8):1426-1440.

DODSWORTH S A,2015.Genome skimming for phylogenomics,Thesis for PhD.London:Queen Mary University of London.

DODSWORTH S,CHRISTENHUSZ M J M,CONRAN J G,et al.,2020.Extensive plastid-nuclear discordance in a recent radiation of Nicotiana section Suaveolentes (Solanaceae).Bot.J.Linn.Soc.,193(4):546-559.

DONG W P,SUN J H,LIU Y L,et al.,2022.Phylogenomic relationships and species identification of the olive genus Olea (Oleaceae).J.Syst.Evol.,60(6):1263-1280.

ELLIOTT L,BOYER F,LEMANE T,et al.,2025.Wholeskim:utilising genome skims for taxonomically annotating ancient DNA metagenomes.Mol.Ecol.Resour.,25(8):e70001.

EMERSON B C,CICCONARDI F,FANCIULLI P P,et al.,2011.Phylogeny,phylogeography,phylobetadiversity and the molecular analysis of biological communities.Philos.Trans.R.Soc.Lond.B Biol.Sci.,366(1576):2391-2402.

FAN H,IVES A R,SURGET-GROBA Y,et al.,2015.An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data.BMC Genom.,16(1):522.

FAULK C,2023a.De novo sequencing,diploid assembly,and annotation of the black carpenter ant,Camponotus pennsylvanicus,and its symbionts by one person for 1000,using nanopore sequencing.Nucleic Acids Res.,51(1):17-28.

FAULK C,2023b.Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates.Genome Res.,33(6):948-956.

FEITOSA E A,XAVIER H S,RANDAU K P,2012.Chrysoba-lanaceae:traditional uses,phytochemistry and pharmacology.Rev.Bras.Farmacogn.,22(5):1181-1186.

FORD C S,AYRES K L,TOOMEY N,et al.,2009.Selection of candidate coding DNA barcoding regions for use on land plants.Bot.J.Linn.Soc.,159(1):1-11.

FU C N,MO Z Q,YANG J B,et al.,2022.Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron.Mol.Ecol.Resour.,22(1):404-414.

GARCÍA-CÁRDENAS F J,ORTIZ M Á,DEL VALLE J C,et al.,2026.Patterns of interploidy admixture in polyploid complexes:insights from Thymus sect.Mastichina (Lamiaceae).Mol.Ecol.,35(3):e70259.

GONZÁLEZ D,VOVIDES A P,2012.A modification to the SCAR (sequence characterized amplified region) method provides phylogenetic insights within Ceratozomia (Zamia-ceae).Rev.Mex.Biodivers.,83(4):929-938.

GOVINDARAJULU R,PARKS M,TENNESSEN J A,et al.,2015.Comparison of nuclear,plastid,and mitochondrial phylogenies and the origin of wild octoploid strawberry species.Am.J.Bot.,102(4):544-554.

GRANDJEAN F,TAN M H,GAN H M,et al.,2017.Rapid recovery of nuclear and mitochondrial genes by genome skimming from Northern Hemisphere freshwater crayfish.Zool.Scr.,46(6):718-728.

HANDY S M,PAWAR R S,OTTESEN A R,et al.,2021.HPLC-UV,metabarcoding and genome skims of botanical dietary supplements:a case study in echinacea.Planta Med.,87(4):314-324.

HEBERT P D N,CYWINSKA A,BALL S L,et al.,2003.Biological identifications through DNA barcodes.Proc.Biol.Sci.,270(1512):313-321.

HEBERT P D N,STOECKLE M Y,ZEMLAK T S,et al.,2004.Identification of birds through DNA barcodes.PLoS Biol.,2(10):e312.

HIRAI J,2025.Optimal input DNA thresholds for genome skimming in marine crustacean zooplankton.PeerJ,13:e19054.

HUGHES C E,PENNINGTON R T,ANTONELLI A,2013.Neotropical plant evolution:assembling the big picture.Bot.J.Linn.Soc.,171(1):1-18.

HUNTER E S,LITERMAN R,HANDY S M,2021.Utilizing big data to identify tiny toxic components:digitalis.Foods,10(8):1794.

IRISARRI I,URIBE J E,EERNISSE D J,et al.,2020.A mitogenomic phylogeny of chitons (Mollusca:Polyplacophora).BMC Evol.Biol.,20(1):22.

JABAILY R S,SHEPHERD K A,MICHENER P S,et al.,2018.Employing hypothesis testing and data from multiple genomic compartments to resolve recalcitrant backbone nodes in Goodenia s.l.(Goodeniaceae).Mol.Phylogenet.Evol.,127:502-512.

JANTZEN J R,AMARASINGHE P,FOLK R A,et al.,2020.A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae.Appl.Plant Sci.,8(5):e11345.

KANE N C,CRONK Q,2008.Botany without borders:barcoding in focus.Mol.Ecol.,17(24):5175-5176.

KELLER A,DANNER N,GRIMMER G,et al.,2015.Evaluating multiplexed next-generation sequencing as a method in palynology for mixed pollen samples.Plant Biol.,17(2):558-566.

KLEIN A M,VAISSIÈRE B E,CANE J H,et al.,2007.Importance of pollinators in changing landscapes for world crops.Proc.R.Soc.B.,274(1608):303-313.

KRESS W J,ERICKSON D L,2012.DNA barcodes:methods and protocols.New York:Humana Press.

KRESS W J,WURDACK K J,ZIMMER E A,et al.,2005.Use of DNA barcodes to identify flowering plants.Proc.Natl.Acad.Sci.USA,102(23):8369-8374.

LAMB P D,HUNTER E,PINNEGAR J K,et al.,2019.How quantitative is metabarcoding:a meta-analytical approach.Mol.Ecol.,28(2):420-430.

LAMICHHANEY S,CARD D C,GRAYSON P,et al.,2019.Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution.Philos.Trans.R.Soc.Lond.B Biol.Sci.,374(1777):20180248.

LANG D D,TANG M,HU J H,et al.,2019.Genome-skimming provides accurate quantification for pollen mixtures.Mol.Ecol.Resour.,19(6):1433-1446.

LETSCH H,GREVE C,HUNDSDOERFER A K,et al.,2025.Type genomics:a framework for integrating genomic data into biodiversity and taxonomic research.Syst.Biol.,74(6):1029-1044.

LI F,XIE X N,HUANG R,et al.,2021.Chloroplast genome sequencing based on genome skimming for identification of Eriobotryae Folium.BMC Biotechnol.,21(1):69.

LI X W,YANG Y,HENRY R J,et al.,2015.Plant DNA barcoding:from gene to genome.Biol.Rev.Camb.Philos.Soc.,90(1):157-166.

LIU L X,DU Y X,SHEN C,et al.,2020.The complete chloroplast genome of Papaver setigerum and comparative analyses in Papaveraceae.Genet.Mol.Biol.,43(3):e20190272.

LIU L M,DU X Y,GUO C,et al.,2021a.Resolving robust phylogenetic relationships of core Brassicaceae using genome skimming data.J.Syst.Evol.,59(3):442-453.

LIU L X,ZHANG Y H,LI P,2021b.Development of genomic resources for the genus Celtis (Cannabaceae) based on genome skimming data.Plant Divers.,43(1):43-53.

LU Y Q,DONG Y R,ZHANG M,et al.,2025.Genome and metagenome skimming:future sequencing methods for environmental DNA (eDNA) studies.Mol.Ecol.Resour.,25(6):e14095.

MABRY M E,SIMPSON M G,2018.Evaluating the monophyly and biogeography of Cryptantha (Boraginaceae).Syst.Bot.,43(1):53-76.

MAHIMA K,SUNIL KUMAR K N,RAKHESH K V,et al.,2022.Advancements and future prospective of DNA barcodes in the herbal drug industry.Front.Pharmacol.,13:947512.

MAJURE L C,BAKER M A,CLOUD-HUGHES M,et al.,2019.Phylogenomics in Cactaceae:a case study using the chollas sensu lato (Cylindropuntieae,Opuntioideae) reveals a common pattern out of the Chihuahuan and Sonoran deserts.Am.J.Bot.,106(10):1327-1345.

MALUKIEWICZ J,CARTWRIGHT R A,DERGAM J A,et al.,2021.Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened Primates.Sci.Rep.,11(1):17279.

MANDEL J R,DIKOW R B,FUNK V A,et al.,2014.A target enrichment method for gathering phylogenetic information from hundreds of loci:an example from the Compositae.Appl.Plant Sci.,2(2):1300085.

MEENA R K,NEGI N,UNIYAL N,et al.,2021.Genome skimming-based STMS marker discovery and its validation in temperate hill bamboo Drepanostachyum falcatum.J.Genet.,100(2):28-37.

MEINEKE E K,DAVIS C C,DAVIES T J,2018.The unrea-lized potential of herbaria for global change biology.Ecol.Monogr.,88(4):505-525.

MENSOUS M,VAN DE PAER C,MANZI S,et al.,2017.Diversity and evolution of plastomes in Saharan mimosoids:potential use for phylogenetic and population genetic studies.Tree Genet.Genomes,13(2):48-61.

MO Z Q,FU C N,TWYFORD A D,et al.,2025.Evaluating the utility of deep genome skimming for phylogenomic analyses:a case study in the species-rich genus Rhododendron.Plant Divers.,47(4):593-603.

MORENO-AGUILAR M F,ARNELAS I,SÁNCHEZ-RODRÍGUEZ A,et al.,2020.Museomics unveil the phylogeny and biogeography of the neglected Juan Fernandez Archipelago Megalachne and Podophorus endemic grasses and their connection with relict pampean-ventanian fescues.Front.Plant Sci.,11:819.

MUÑOZ-RODRÍGUEZ P,CARRUTHERS T,WOOD J R I,et al.,2018.Reconciling conflicting phylogenies in the origin of sweet potato and dispersal to Polynesia.Curr.Biol.,28(8):1246-1256.e12.

NAUHEIMER L,CUI L J,CLARKE C,et al.,2019.Genome skimming provides well resolved plastid and nuclear phylogenies,showing patterns of deep reticulate evolution in the tropical carnivorous plant genus Nepenthes (Caryophyllales).Aust.Syst.Bot.,32(3):243-254.

NEVILL P G,ZHONG X,TONTI-FILIPPINI J,et al.,2020.Large scale genome skimming from herbarium material for accurate plant identification and phylogenomics.Plant Methods,16:1-8.

NING W X,MEUDT H M,NICOLAS A N,et al.,2026.Resolving reticulate evolutionary histories of polyploid species of Azorella (Apiaceae) endemic to New Zealand.Mol.Phylogenet.Evol.,214:108469.

NOCK C J,HARDNER C M,MONTENEGRO J D,et al.,2019.Wild origins of Macadamia domestication identified through intraspecific chloroplast genome sequencing.Front.Plant Sci.,10:334-348.

NURK S,KOREN S,RHIE A,et al.,2022.The complete sequence of a human genome.Science,376(6588):44-53.

OLLERTON J,WINFREE R,TARRANT S,2011.How many flowering plants are pollinated by animals?Oikos,120(3):321-326.

ONDOV B D,TREANGEN T J,MELSTED P,et al.,2016.Mash:fast genome and metagenome distance estimation using MinHash.Genome Biol.,17(1):132-145.

PARKS M,CRONN R,LISTON A,2009.Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes.BMC Biol.,7(1):84-100.

PEEL N,DICKS L V,CLARK M D,et al.,2019.Semi-quantitative characterisation of mixed pollen samples using MinION sequencing and reverse metagenomics (RevMet).Methods Ecol.Evol.,10(10):1691-1701.

PENG F F,ZHAO Z,XU B,et al.,2020.Characteristics of organellar genomes and nuclear internal transcribed spacers in the tertiary relict genus dipelta and their phylogenomic implications.Front.Genet.,11:573226.

POUCHON C,BOYER F,ROQUET C,et al.,2022.ORTHOSKIM:in silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications.Mol.Ecol.Resour.,22(5):2018-2037.

PRATHEEPA M,JALALI S K,AROKIARAJ R S,et al.,2014.Insect barcode information system.Bioinformation,10(2):98-100.

PRUM R O,BERV J S,DORNBURG A,et al.,2015.A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing.Nature,526(7574):569-573.

RACHTMAN E,BAFNA V,MIRARAB S,2021.CONSULT:accurate contamination removal using locality-sensitive hashing.NAR Genom.Bioinform.,3(3):lqab071.

RACLARIU A C,HEINRICH M,ICHIM M C,et al.,2018.Benefits and limitations of DNA barcoding and metabarcoding in herbal product authentication.Phytochem.Anal.,29(2):123-128.

RAIMONDEAU P,MANZI S,BRUCATO N,et al.,2021.Genome skims analysis of betel palms (Areca spp.,Arecaceae) and development of a profiling method to assess their plastome diversity.Gene,800:145845.

RICHARDSON R T,LIN C H,SPONSLER D B,et al.,2015.Application of ITS2 metabarcoding to determine the provenance of pollen collected by honey bees in an agroecosystem.Appl.Plant Sci.,3(1):apps.1400066.

SALUSSOLIA A,LECOQUIERRE N,STOCH F,et al.,2026.Nanopore genome skimming with Illumina polishing yields highly accurate mitogenome sequences:a case study of Niphargus amphipods.Peer Community J.,6:e6.

SANGER F,COULSON A R,1975.A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase.J.Mol.Biol.,94(3):441-448.

SARMASHGHI S,BOHMANN K,P GILBERT M T,et al.,2019.Skmer:assembly-free and alignment-free sample identification using genome skims.Genome Biol.,20(1):34.

SCHAEFER H,HEIBL C,RENNER S S,2009.Gourds afloat:a dated phylogeny reveals an Asian origin of the gourd family (Cucurbitaceae) and numerous oversea dispersal events.Proc.Biol.Sci.,276(1658):843-851.

SCHEUNERT A,DORFNER M,LINGL T,et al.,2020.Can we use it?On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing.PLoS ONE,15(3):e0226234.

SCHMICKL R,LISTON A,ZEISEK V,et al.,2016.Phylogenetic marker development for target enrichment from transcriptome and genome skim data:the pipeline and its application in southern African Oxalis (Oxalidaceae).Mol.Ecol.Resour.,16(5):1124-1135.

SHANG C,LI E Z,YU Z C,et al.,2022.Chloroplast genomic resources and genetic divergence of endangered species Bretschneidera sinensis (Bretschneideraceae).Front.Ecol.Evol.,10:873100.

SIMMONDS S E,SMITH J F,DAVIDSON C,et al.,2021.Phylogenetics and comparative plastome genomics of two of the largest genera of angiosperms,Piper and Peperomia (Piperaceae).Mol.Phylogenet.Evol.,163:107229.

SOLTIS D E,SMITH S A,CELLINESE N,et al.,2011.Angiosperm phylogeny:17 genes,640 taxa.Am.J.Bot.,98(4):704-730.

STRAUB S C K,PARKS M,WEITEMIER K,et al.,2012.Navigating the tip of the genomic iceberg:Next-generation sequencing for plant systematics.Am.J.Bot.,99(2):349-364.

SWENSON U,RICHARDSON J E,BARTISH I V,2008.Multi-gene phylogeny of the pantropical subfamily Chrysophylloideae (Sapotaceae):evidence of generic polyphyly and extensive morphological homoplasy.Cladistics,24(6):1006-1031.

TAN M H,GAN H M,BRACKEN-GRISSOM H,et al.,2021.More from less:genome skimming for nuclear markers for animal phylogenomics,a case study using decapod crusta-ceans.J.Crustac.Biol.,41(2):ruab009.

TIMM L,BRACKEN-GRISSOM H D,2015.The forest for the trees:evaluating molecular phylogenies with an emphasis on higher-level Decapoda.J.Crustac.Biol.,35(5):577-592.

TREVISAN B,ALCANTARA D M C,MACHADO D J,et al.,2019.Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies.PeerJ,7:e7543.

URIBE J E,WILLIAMS S T,TEMPLADO J,et al.,2017.Denser mitogenomic sampling improves resolution of the phylogeny of the superfamily Trochoidea (Gastropoda:Vetigastropoda).J.Molluscan Stud.,83(1):111-118.

VARGAS O M,ORTIZ E M,SIMPSON B B,2017.Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae:Astereae:Diplostephium).New Phytol.,214(4):1736-1750.

VARMA A,PADH H,SHRIVASTAVA N,2007.Plant genomic DNA isolation:an art or a science.Biotechnol.J.,2(3):386-392.

WAGNER N D,VOLF M,HÖRANDL E,2021.Highly diverse shrub willows (Salix L.) share highly similar plastomes.Front.Plant Sci.,12:662715.

WANG J,FU C N,MO Z Q,et al.,2022.Testing the complete plastome for species discrimination,cryptic species discovery and phylogenetic resolution in Cephalotaxus (Cephalotaxa-ceae).Front.Plant Sci.,13:768810.

WANG S Y,ZHOU N,SHI N X,et al.,2023.Testing and using complete plastomes for authentication of medicinal Polygonatum species (Asparagaceae).Ind.Crops Prod.,197:116557.

WANG W C,CHEN S Y,ZHANG X Z,2016.Chloroplast genome evolution in Actinidiaceae:clpP loss,heterogenous divergence and phylogenomic practice.PLoS ONE,11(9):e0162324.

WANG W C,CHEN S Y,ZHANG X Z,2017.The complete chloroplast genome of the endangered Chinese paperbark maple,Acer griseum (Sapindaceae).Conserv.Genet.Resour.,9(4):527-529.

WANG W C,CHEN S Y,ZHANG X Z,2018.Whole-genome comparison reveals divergent IR borders and mutation hotspots in chloroplast genomes of herbaceous bamboos (Bambusoideae:Olyreae).Molecules,23(7):1537.

WATSON J D,CRICK F H C,1953.The structure of DNA.Cold Spring Harb.Symp.Quant.Biol.,18:123-131.

WEITEMIER K,STRAUB S C K,CRONN R C,et al.,2014.Hyb-Seq:combining target enrichment and genome skimming for plant phylogenomics.Appl.Plant Sci.,2(9):apps.1400042.

WHITFIELD J B,LOCKHART P J,2007.Deciphering ancient rapid radiations.Trends Ecol.Evol.,22(5):258-265.

WU L,WU M L,CUI N,et al.,2021.Plant super-barcode:a case study on genome-based identification for closely related species of Fritillaria.Chin.Med.,16(1):52-62.

YANG Y,LI Q,KONG L F,et al.,2019.Mitogenomic phylogeny of Nassariu (Gastropoda:Neogastropoda).Zool.Scr.,48(3):302-312.

YE L J,FU C N,WANG Y H,et al.,2018.Characterization of the complete plastid genome of a Chinese endemic species Carya kweichowensis.Mitochondrial DNA Part B,3(2):492-493.

ZARDOYA R,MEYER A,1996.Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates.Mol.Biol.Evol.,13(7):933-942.

ZEDANE L,HONG-WA C,MURIENNE J,et al.,2016.Museomics illuminate the history of an extinct,paleoendemic plant lineage (Hesperelaea,Oleaceae) known from an 1875 collection from Guadalupe Island,Mexico.Biol.J.Linn.Soc.,117(1):44-57.

ZENG C X,HOLLINGSWORTH P M,YANG J,et al.,2018.Genome skimming herbarium specimens for DNA barcoding and phylogenomics.Plant Methods,14(1):43-56.

ZHANG X Z,CHEN S Y,2016.Genome skimming reveals the complete chloroplast genome of Ampelocalamus naibunensis (Poaceae:Bambusoideae:Arundinarieae) with phylogenomic implication.Mitochondrial DNA B Resour.,1(1):635-637.