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The use and domestication of Theobroma cacao during the mid-Holocene in the upper
Amazon
Evidence from starch grains, theobromine residues and ancient DNA demonstrate cacao use in the upper Amazon circa 5,300 years
ago. This is earlier than previous evidence for cacao domestication in Mesoamerica.
Sonia ZarrilloNilesh GaikwadFrancisco Valdez
Research 29 Oct 2018 Nature Ecology & Evolution Volume: 2, P: 1879-1888
The first report of iron-rich population of adapted medicinal spinach (Blitum virgatum L.)
compared with cultivated spinach (Spinacia oleracea L.)
Ali AmmarellouValiollah Mozaffarian
Research Open Access 12 Nov 2021 Scientific Reports Volume: 11, P: 1-8
Rice Domestication Revealed by Reduced Shattering of Archaeological rice from the
Lower Yangtze valley
Yunfei ZhengGary W. CrawfordXugao Chen
Research Open Access 21 Jun 2016 Scientific Reports Volume: 6, P: 1-9
Elucidation of Japanese pepper (Zanthoxylum piperitum De Candolle) domestication using

2. RAD-Seq
Maddumage Dona Ginushika Priyadarshani PremarathneNami FukutomeYukio Nagano
Research Open Access 19 Mar 2021 Scientific Reports Volume: 11, P: 1-16
Chemometric Analysis of Cannabinoids: Chemotaxonomy and Domestication Syndrome
E. M. MudgeS. J. MurchP. N. Brown
Research Open Access 30 Aug 2018 Scientific Reports Volume: 8, P: 1-9
Genetic analyses reveal independent domestication origins of the emerging oil
crop Paeonia ostii, a tree peony with a long-term cultivation history
Li-Ping PengChang-Fu CaiJian-Feng Mao
Research Open Access 13 Jul 2017 Scientific Reports Volume: 7, P: 1-12
Genomic signatures of the evolution of defence against its natural enemies in the poisonous
and medicinal plant Datura stramonium (Solanaceae)
I. M. De-la-CruzA. HallabJ. Núñez-Farfán
Research Open Access 13 Jan 2021 Scientific Reports Volume: 11, P: 1-19
Population sequencing enhances understanding of tea plant evolution
Tea is an important beverage crop with a large and heterozygous genome. Here, the authors assemble the genome of the cultivar
Longjing 43 and conduct a population genetics study to reveal divergent selection for disease resistance and flavor between the two

3. variety groups.
Xinchao WangHu FengYajun Yang
Research Open Access 07 Sept 2020 Nature Communications Volume: 11, P: 1-10
Resequencing of 414 cultivated and wild watermelon accessions identifies selection for
fruit quality traits
An improved watermelon reference genome and whole-genome resequencing of 414 cultivated and wild accessions provide insights
into fruit quality traits and dessert watermelon evolution.
Shaogui GuoShengjie ZhaoYong Xu
Research Open Access 01 Nov 2019 Nature Genetics Volume: 51, P: 1616-1623
The wax gourd genomes offer insights into the genetic diversity and ancestral cucurbit
karyotype
Cucurbits fruits have diverse shapes and sizes, but their genomes evolution and genetic basis of diversity are unclear. Here, the
authors show that the wax gourd genome has the most ancestral karyotype among cucurbits and identify candidate genes
which contribute to large fruit size by comparative and population genomics analyses.
Dasen XieYuanchao XuZhonghua Zhang
Research Open Access 14 Nov 2019 Nature Communications Volume: 10, P: 1-12
The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor
A tomato pan-genome constructed from genome sequences of 725 tomato accessions captures 4,873 genes absent from the reference
genome and identifies a rare allele of TomLoxC regulating fruit flavor.
Lei GaoItay GondaZhangjun Fei
Research 13 May 2019 Nature Genetics Volume: 51, P: 1044-1051
Looking into the flora of Dutch Brazil: botanical identifications of seventeenth century
plant illustrations in the Libri Picturati

4. Mireia Alcàntara-RodríguezMariana FrançozoTinde Van Andel
Research Open Access 05 Oct 2021 Scientific Reports Volume: 11, P: 1-14
Earliest evidence for human use of tobacco in the Pleistocene Americas
The finding of tobacco seeds in a Pleistocene-age fire hearth suggests people learned of this plant’s intoxicant value shortly after
their arrival in the Americas, initiating a long heritage of use with global societal impact.
Daron DukeEric WohlgemuthD. Craig Young
Research 11 Oct 2021 Nature Human Behaviour Volume: 6, P: 183-192
Transcriptome analysis and codominant markers development in caper, a drought
tolerant orphan crop with medicinal value
Francesco MercatiIgnazio FontanaFrancesco Carimi
Research Open Access 18 Jul 2019 Scientific Reports Volume: 9, P: 1-16
Genome sequences of horticultural plants: past, present, and future
Fei ChenYunfeng SongLiangsheng Zhang
Reviews Open Access 08 Oct 2019 Horticulture Research Volume: 6, P: 1-23
Developing naturally stress-resistant crops for a sustainable agriculture
There are multiple strategies to fortify crop nutrition and support global food security and sustainable agriculture. Here the authors
propose to increase the diversity of crops by devoting more efforts to studying minor crops that are naturally stress resistant.

5. Heng ZhangYuanyuan LiJian-Kang Zhu
Reviews 26 Nov 2018 Nature Plants Volume: 4, P: 989-996
Wild and domesticated Moringa oleifera differ in taste, glucosinolate composition, and
antioxidant potential, but not myrosinase activity or protein content
Gwen M. ChodurMark E. OlsonJed W. Fahey
Research Open Access 22 May 2018 Scientific Reports Volume: 8, P: 1-10
Convergence and divergence of bitterness biosynthesis and regulation in Cucurbitaceae
Different cucurbits produce cucurbitacins with varied structures and activities. A comparative genomic study illustrates the genetic
basis of cucurbitacin differentiation and tissue-specific cucurbitacin synthesis.
Yuan ZhouYongshuo MaSanwen Huang
Research 28 Nov 2016 Nature Plants Volume: 2, P: 1-8
A high-quality carrot genome assembly provides new insights into carotenoid
accumulation and asterid genome evolution
Philipp Simon, Massimo Iorizzo, Allen Van Deynze and colleagues report the high-quality assembly of the carrot genome, providing
an important resource for crop improvement. They find a candidate gene that regulates carotenoid accumulation and gain further
insights into asterid genome evolution, including characterization of two new polyploidization events.
Massimo IorizzoShelby EllisonPhilipp Simon
Research Open Access 09 May 2016 Nature Genetics Volume: 48, P: 657-666
The comparisons of expression pattern reveal molecular regulation of fruit metabolites
in S. nigrum and S. lycopersicum

6. Jung HeoWoo Young BangSoon Ju Park
Research Open Access 23 Mar 2022 Scientific Reports Volume: 12, P: 1-15
Insights into opium poppy (Papaver spp.) genetic diversity from genotyping-by-sequencing
analysis
Uyen Vu Thuy HongMuluneh Tamiru-OliMathew G. Lewsey
Research Open Access 07 Jan 2022 Scientific Reports Volume: 12, P: 1-15
Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea
varieties
Wild teas are considered as valuable resource for studying domestication and breeding. Here, Zhang et al. report genome of wild tea
DASZ and transcriptome of 217 accessions, which clarify pedigree of Chinese tea cultivars and show tea may not have undergone
long-term artificial directional selection on flavor-related metabolites.
Weiyi ZhangYoujun ZhangWeiwei Wen
Research Open Access 24 Jul 2020 Nature Communications Volume: 11, P: 1-12
Effect of plant density on yield and Quality of perilla sprouts
Liuliu WuZhe DengLi Meng
Research Open Access 18 Jun 2020 Scientific Reports Volume: 10, P: 1-8
Research advances in and prospects of ornamental plant genomics

7. Tangchun ZhengPing LiQixiang Zhang
Reviews Open Access 01 Apr 2021 Horticulture Research Volume: 8, P: 1-19
Natural diversity in phenolic components and antioxidant properties of oregano
(Origanum vulgare L.) accessions, grown under the same conditions
Ghazaleh Jafari KhorsandMohammad Reza MorshedlooAbdolvahab Khademi
Research Open Access 06 Apr 2022 Scientific Reports Volume: 12, P: 1-9
Reshaping the future of ethnobiology research after the COVID-19 pandemic
A geographically diverse group of 29 ethnobiologists addresses three common themes in response to the COVID-19 global health
crisis: impact on local communities, future interactions between researchers and communities, and new (or renewed) conceptual
and/or applied research priorities for ethnobiology.
Ina VandebroekAndrea PieroniFarid Dahdouh-Guebas
Reviews 22 Jun 2020 Nature Plants Volume: 6, P: 723-730
Chromosome-level genome assembly of Zizania latifolia provides insights into its seed
shattering and phytocassane biosynthesis
Yan, Yang, Yu, Shang et al. provide a chromosome-level reference genome for Chinese wild rice (Zizania latifolia) along with
phylogenetic and transcriptomic analyses. Their results identify candidate genes related to seed shattering and synteny with the rice
phytocassane biosynthetic gene cluster.
Ning YanTing YangZhong-Feng Zhang
Research Open Access 11 Jan 2022 Communications Biology Volume: 5, P: 1-11
Advances in research on the carrot, an important root vegetable in the Apiaceae family

8. Feng QueXi-Lin HouAi-Sheng Xiong
Reviews Open Access 01 Jun 2019 Horticulture Research Volume: 6, P: 1-15
The surprising place where pot farming first blossomed
Humans first began cultivating cannabis, a source of both fibres and drugs, some 12,000 years ago.
Research Highlights 21 Jul 2021 Nature Volume: 595, P: 628
Ancient DNA analysis
This Primer outlines the best ways to find, handle and analyse ancient DNA from various sources. The authors summarize ethical
considerations and the importance of working closely with all stakeholders, including archaeologists, curators and descendant
communities.
Ludovic OrlandoRobin AllabyChristina Warinner
Reviews 11 Feb 2021 Nature Reviews Methods Primers Volume: 1, P: 1-26
Selection of a subspecies-specific diterpene gene cluster implicated in rice disease
resistance
A rice diterpenoid gene cluster is reported that controls the biosynthesis of 5,10-diketo-casbene, a phytoalexin that confers resistance
to rice bacterial blight and blast fungus. It recently evolved in the japonica subspecies under artificial selection.
Chuansong ZhanLong LeiJie Luo
Research 07 Dec 2020 Nature Plants Volume: 6, P: 1447-1454
Regulatory change at Physalis Organ Size 1 correlates to natural variation in tomatillo
reproductive organ size
The genetic basis of plant reproductive organ size is poorly understood. Here, the authors suggest that variation in the gene, Physalis

9. Organ Size 1, regulates reproductive organ size in tomatillo and provides insight into the evolution of the genetic regulation of plant
morphology.
Li WangLingli HeChaoying He
Research 01 Jul 2014 Nature Communications Volume: 5, P: 1-12
Chromosome evolution and the genetic basis of agronomically important traits in greater
yam
While greater yam provides food and income security for millions of people around the world, there are limited genomic resources
available. Here, the authors report a chromosome-scale assembly of the greater yam genome as well as quantitative trait loci
associated with anthracnose resistance and tuber traits.
Jessen V. BredesonJessica B. LyonsDaniel S. Rokhsar
Research Open Access 14 Apr 2022 Nature Communications Volume: 13, P: 1-16
Comparative analysis of tuberous root metabolites between cultivated and wild varieties
of Rehmannia glutinosa by widely targeted metabolomics
Yanqing ZhouLuying ShaoHongying Duan
Research Open Access 01 Jun 2021 Scientific Reports Volume: 11, P: 1-12
Mangifera sylvatica (Wild Mango): A new cocoa butter alternative
Sayma AkhterMorag A. McDonaldRay Marriott
Research Open Access 24 Aug 2016 Scientific Reports Volume: 6, P: 1-9
Plant microbiome-dependent immune enhancing action of Echinacea purpurea is
enhanced by soil organic matter content

10. Mona H. HaronHeather L. TylerDavid S. Pasco
Research Open Access 15 Jan 2019 Scientific Reports Volume: 9, P: 1-11
Integration of transcriptome and targeted metabolome profiling reveals hormone related
genes involved in the growth of Bletilla striata
Hengwei ZouHanxiao JiangRongshao Huang
Research Open Access 09 Nov 2021 Scientific Reports Volume: 11, P: 1-11
Comparative analysis of the Dicer-like gene family reveals loss of miR162 target site
in SmDCL1 from Salvia miltiorrhiza
Fenjuan ShaoDeyou QiuShanfa Lu
Research Open Access 13 May 2015 Scientific Reports Volume: 5, P: 1-12
Genetic Diversity Analysis Reveals Genetic Differentiation and Strong Population
Structure in Calotropis Plants
Nkatha G. MuriiraAlice MuchugiAizhong Liu
Research Open Access 18 May 2018 Scientific Reports Volume: 8, P: 1-10
Evolutionary analysis of the Moringa oleifera genome reveals a recent burst of plastid to
nucleus gene duplications

11. José Ojeda-LópezJuan Pablo Marczuk-RojasLorenzo Carretero-Paulet
Research Open Access 19 Oct 2020 Scientific Reports Volume: 10, P: 1-15
Diversity and selection of the continuous-flowering gene, RoKSN, in rose
Vanessa Soufflet-FreslonEmilie AraouFabrice Foucher
Research Open Access 01 Apr 2021 Horticulture Research Volume: 8, P: 1-11
Assessment of Genetic Diversity and Population Structure in Iranian Cannabis
Germplasm
Aboozar SoorniReza FatahiAureliano Bombarely
Research Open Access 15 Nov 2017 Scientific Reports Volume: 7, P: 1-10
Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale
DNA variation
Alberto AcquadroLorenzo BarchiSergio Lanteri
Research Open Access 17 Jul 2017 Scientific Reports Volume: 7, P: 1-15
Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol
biosynthetic pathway

12. Hong-Lei LiLin WuYiqing Liu
Research Open Access 05 Aug 2021 Horticulture Research Volume: 8, P: 1-13
The genome of Eucalyptus grandis
The Eucalyptus grandis genome has been sequenced, revealing the greatest number of tandem duplications of any plant genome
sequenced so far, and the highest diversity of genes for specialized metabolites that act as chemical defence and provide unique
pharmaceutical oils; genome sequencing of the sister species E. globulus and a set of inbred E. grandis tree genomes reveals
dynamic genome evolution and hotspots of inbreeding depression.
Alexander A. MyburgDario GrattapagliaJeremy Schmutz
Research Open Access 11 Jun 2014 Nature Volume: 510, P: 356-362
Direct dating reveals the early history of opium poppy in western Europe
Aurélie SalavertAntoine ZazzoIvana Vostrovská
Research Open Access 20 Nov 2020 Scientific Reports Volume: 10, P: 1-10
Arabica-like flavour in a heat-tolerant wild coffee species
Coffea stenophylla is a recently rediscovered, narrow-leaved wild coffee from Upper West Africa. Rigorous sensory evaluation
(tasting) rates its flavour profile as analogous to high-quality Arabica coffee, but it can grow at much higher temperatures.
Aaron P. DavisDelphine MieuletJeremy Haggar
Research 19 Apr 2021 Nature Plants Volume: 7, P: 413-418
The pineapple genome and the evolution of CAM photosynthesis
Ray Ming, Robert Paull, Qingyi Yu and colleagues report the genome sequences of two cultivated pineapple varieties and one wild

13. pineapple relative. Their analysis supports the use of the pineapple as a reference genome for monocot comparative genomics and
provides insight into the evolution of crassulacean acid metabolism photosynthesis.
Ray MingRobert VanBurenQingyi Yu
Research Open Access 02 Nov 2015 Nature Genetics Volume: 47, P: 1435-1442
Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the
neglected potential for crop improvement
Qiang LiManoj SapkotaEsther van der Knaap
Reviews Open Access 15 Mar 2020 Horticulture Research Volume: 7, P: 1-11
The importance of genomic variation for biodiversity, ecosystems and people
The effects of genetic variation on the adaptive potential of species depend on the frequencies of alleles at other loci in the individual
or in the population, and the patterns of spatio-temporal co-occurrence between alleles in interacting species. This Review explores
these population and community genomic contexts and their direct and indirect effects on biodiversity, ecosystems and people.
Madlen StangeRowan D. H. BarrettAndrew P. Hendry
Reviews 16 Oct 2020 Nature Reviews Genetics Volume: 22, P: 89-105
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