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| Open AccessChromosome 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. Bredeson
- , Jessica B. Lyons
- & Daniel S. Rokhsar
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Article
| Open AccessGenomic evidence for homoploid hybrid speciation between ancestors of two different genera
Carpinus fangiana exhibits intermediate morphology between C. viminea and Ostrya rehderiana. Here, the authors report that Carpinus sect. Distegocarpus likely originate through homoploid hybrid speciation (HHS) during the early divergence between Carpinus and Ostrya through genomic analyses.
- Zefu Wang
- , Minghui Kang
- & Jianquan Liu
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Article
| Open AccessReshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax
The role of polyploidization generated genomic diversity in shaping the hierarchical genome architecture remains unclear. Here, the authors show that repatterning of the ancestral eudicot genome has resulted in multi-dimensional genome plasticity and secondary metabolite diversification via comparisons of Panax genomes.
- Zhen-Hui Wang
- , Xin-Feng Wang
- & Lin-Feng Li
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| Open AccessAegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62
Aegilops sharonensis is a wild diploid relative of wheat. Here, the authors assemble the genome of Ae. sharonensis and use the assembly as an aid to clone the Ae. sharonensis-derived stem rust resistance gene Sr62 in the allohexaploid genome of wheat.
- Guotai Yu
- , Oadi Matny
- & Brande B. H. Wulff
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Article
| Open AccessPhylotranscriptomic insights into a Mesoproterozoic–Neoproterozoic origin and early radiation of green seaweeds (Ulvophyceae)
“Ulvophyceae is a remarkably morphologically and ecologically diverse clade of green algae. Here, the authors reconstruct the Ulvophyceae phylogeny, showing that these algae originated earlier than expected and may have influenced biogeochemical cycles at the Mesoproterozoic-Neoproterozoic transition.”
- Zheng Hou
- , Xiaoya Ma
- & Bojian Zhong
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Article
| Open AccessNorway spruce postglacial recolonization of Fennoscandia
Contrasting theories exist regarding how Norway spruce recolonized Fennoscandia after the last glaciation. Here, the authors provide evidences from sedimentary ancient DNA and modern population genomics to support that Norway spruce was present in southern Fennoscandia shortly after deglaciation and the early Holocene migration from the east.
- Kevin Nota
- , Jonatan Klaminder
- & Laura Parducci
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Article
| Open AccessPhylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere
Fagaceae are diverse family including trees of ecological and economic importance. This phylogenomic analysis of nuclear and plastid genomes reconstructs evolutionary history and finds evidence of multiple adaptive introgression events in this important plant family.
- Biao-Feng Zhou
- , Shuai Yuan
- & Baosheng Wang
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Article
| Open AccessGenomic insights into the evolution of Echinochloa species as weed and orphan crop
Echinochloa is an important genus in the grass family as many of them are either problematic weeds or domesticated millets. Here, the authors assemble three polyploidy genomes in this genus using the diploid-assisted scaffolding method DipHic and provide genomic insights into the dual roles of some species as weeds and orphan crops.
- Dongya Wu
- , Enhui Shen
- & Chu-Yu Ye
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Article
| Open AccessBuxus and Tetracentron genomes help resolve eudicot genome history
Gamma triplication arises via two whole-genome duplications early in eudicot history, but the relative timing of these is unclear. Here, the authors report the genomes of Buxales and Trochodendrales and reject the hypothesis of gamma arising via inter-lineage hybridization between ancestral eudicot lineages.
- Andre S. Chanderbali
- , Lingling Jin
- & Pamela S. Soltis
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Article
| Open AccessChloranthus genome provides insights into the early diversification of angiosperms
Chloranthales remain the last lineage of core angiosperms that lacks a nuclear genome assembly. Here, the authors report the genome assembly of Chloranthus spicatus and show its contribution to deepen our understanding on diversification, phylogeny, and genome evolution in angiosperms.
- Xing Guo
- , Dongming Fang
- & Huan Liu
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Article
| Open AccessThe identification of grain size genes by RapMap reveals directional selection during rice domestication
Cloning quantitative trait loci (QTL) in crops is often slow and laborious. Here, the authors describe RapMap, a method to rapidly clone multiple QTL based on F2 gradient populations coupled with a co-segregation standard, and show how it can be used to identify genes controlling grain size in rice.
- Juncheng Zhang
- , Dejian Zhang
- & Yibo Li
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Article
| Open AccessAnalysis of 427 genomes reveals moso bamboo population structure and genetic basis of property traits
Moso bamboo is an economically and ecologically important nontimber forestry species. Here, the authors analyze 427 genomes collected from 15 representative geographic areas, and identify genes under balancing selection, putative patterns of historic demography, and candidate genes associated with important traits.
- Hansheng Zhao
- , Shuai Sun
- & Zhimin Gao
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Article
| Open AccessParallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles
Relative contributions of pre-existing versus de novo genomic variation to adaptation remain unclear. Here, the authors address this problem by examining the adaptation of autotetraploid Arabidopsis arenosa to serpentine soils and find that both types of variations contribute to rapid adaptation.
- Veronika Konečná
- , Sian Bray
- & Filip Kolář
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| Open AccessPre-meiotic 21-nucleotide reproductive phasiRNAs emerged in seed plants and diversified in flowering plants
Pre-meiotic anthers of monocots accumulate phased, small interfering RNAs (phasiRNAs) that are absent in many well-studied model eudicots. Here, the authors show that such 21-nt phasiRNAs are in fact present in diverse eudicot species including strawberry, in which production is triggered by miR11308.
- Suresh Pokhrel
- , Kun Huang
- & Blake C. Meyers
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Article
| Open AccessPopulation genomics of apricots unravels domestication history and adaptive events
The evolutionary and domestication history of apricots is poorly understood. Here, the authors provide four apricot high-quality genome assemblies, the genomes of 578 accessions from natural and cultivated populations, and show that Chinese and European apricots constitute two different gene pools, resulting from independent domestication events.
- Alexis Groppi
- , Shuo Liu
- & Véronique Decroocq
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Article
| Open AccessPopulation-scale peach genome analyses unravel selection patterns and biochemical basis underlying fruit flavor
Longhua Shui Mi (LHSM) is a representative of the Chinese Cling peaches that have been central in global peach genetic improvement. Here, the authors assemble the genome of LHSM and show convergent selection for sweetness yet divergent selection for acidity in eastern vs. western cultivars through population genomics analyses.
- Yang Yu
- , Jiantao Guan
- & Hua Xie
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| Open AccessA chromosome-level Camptotheca acuminata genome assembly provides insights into the evolutionary origin of camptothecin biosynthesis
Camptothecin is a monoterpene indole alkaloid with anti-tumor activity. Here, the authors assemble the genome of the camptothecin producing plant Camptotheca acuminata and provide insights into the evolutionary origin of camptothecin biosynthesis by comparing to the vinblastine and vincristine biosynthetic pathway in Catharanthus roseus.
- Minghui Kang
- , Rao Fu
- & Jianquan Liu
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Article
| Open AccessWhole-genome microsynteny-based phylogeny of angiosperms
Molecular phylogenies are traditionally based on sequence variation, but genome rearrangements also contain phylogenetic information. Here, Zhao et al. develop an approach to reconstruct phylogenies based on microsynteny and illustrate it with a reconstruction of the angiosperm phylogeny.
- Tao Zhao
- , Arthur Zwaenepoel
- & Yves Van de Peer
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| Open AccessAnalysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids
Coptis chinensis represents an early-diverging eudicot lineage with diverse medicinal applications. Here, the authors report its chromosome-scale genome assembly, infer a single ancient whole-genome duplication, and characterize the function of CYP719 in diversification of protoberberine-type alkaloids.
- Yifei Liu
- , Bo Wang
- & Jing Nie
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Article
| Open AccessGenomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism
Figs and their wasp pollinators are a classic example of coevolution. By assembling and analysing genomes from across the Ficus clade, authors suggest that fig hybridization driven by pollinator host-switching in this obligate pollination system, is more common than previously thought.
- Gang Wang
- , Xingtan Zhang
- & Jin Chen
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| Open AccessExpansion within the CYP71D subfamily drives the heterocyclization of tanshinones synthesis in Salvia miltiorrhiza
Salvia miltiorrhiza is a medicinal plant that can produce the bioactive tanshinones. Here, the authors report the improved genome assembly and reveal the possible roles of three CYP71Ds in catalyzing the reactions leading to the formation of the characteristic furan D-ring of transhinones.
- Ying Ma
- , Guanghong Cui
- & Luqi Huang
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| Open AccessChromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis
Ophiorrhiza pumila is a medicinal plant that can produce the anti-cancer monoterpene indole alkaloid (MIA) camptothecin. Here, the authors report its genome assembly and propose a working model for MIA evolution and biosynthesis through comparative genomics, synteny, and metabolic gene cluster analyses.
- Amit Rai
- , Hideki Hirakawa
- & Mami Yamazaki
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| Open AccessGenome-enabled discovery of anthraquinone biosynthesis in Senna tora
Anthraquinones are aromatic polyketides and have been used for treating various diseases, but the biosynthetic pathway is unclear. Here, the authors assemble the genome of an anthraquinone-producing medicinal plant Senna tora and show the evidences that CHS-like genes may be involved in anthraquinone biosynthesis.
- Sang-Ho Kang
- , Ramesh Prasad Pandey
- & Jae Kyung Sohng
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Article
| Open AccessMetabolite signatures of diverse Camellia sinensis tea populations
The molecular basis for the unique taste and aroma of tea cultivars is largely unknown, but is critical for breeding new cultivars. Here the authors use transcriptomics and metabolomics to study the relationship among phylogenetic groups and specialized metabolites from 136 tea accessions in China.
- Xiaomin Yu
- , Jiajing Xiao
- & Renyi Liu
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Article
| Open AccessCOMPOSITUM 1 contributes to the architectural simplification of barley inflorescence via meristem identity signals
Grasses have diverse inflorescence morphologies, but the underlying genetic mechanisms are unclear. Here, the authors report a TCP transcription factor COM1 affects cell growth through regulation of cell wall properties and promotes branch formation in non-Triticeae grasses but branch inhibition in barley (Triticeae).
- Naser Poursarebani
- , Corinna Trautewig
- & Thorsten Schnurbusch
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Article
| Open AccessRapid climate change results in long-lasting spatial homogenization of phylogenetic diversity
How past climate change has affected biodiversity over large spatial scales remains underexplored. Here, the authors find marked homogenization in flowering plant phylogenetic diversity across Central and Northern Europe linked to rapid climate change and large distances to glacial refugia.
- Bianca Saladin
- , Loïc Pellissier
- & Niklaus E. Zimmermann
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Article
| Open AccessPyropia yezoensis genome reveals diverse mechanisms of carbon acquisition in the intertidal environment
The nori producing seaweed Pyropia yezoensis has heteromorphic generations that occupy distinct habitats. Here, via genome assembly, transcriptome analysis, and 13 C isotope labeling, the authors show the interplay between inorganic carbon availability and life cycle evolution in the intertidal environment.
- Dongmei Wang
- , Xinzi Yu
- & Yunxiang Mao
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Article
| Open AccessWithin-individual phenotypic plasticity in flowers fosters pollination niche shift
Floral phenotypes impact interactions between plants and pollinators. Here, the authors show that Moricandia arvensis displays discrete seasonal plasticity in floral phenotype, with large, lilac flowers attracting long-tongued bees in spring and small, rounded, white flowers attracting generalist pollinators in summer.
- José M. Gómez
- , Francisco Perfectti
- & Rubén Torices
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| Open AccessNested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae
As one of the most successful angiosperm clades with ~4000 species, the mustard family has been diversifying into many evolutionary lineages. Here, the authors construct plastid-based phylogeny and show nested whole-genome duplications coincide with diversification and high morphological disparity.
- Nora Walden
- , Dmitry A. German
- & Marcus A. Koch
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Article
| Open AccessRecent accelerated diversification in rosids occurred outside the tropics
There is mixed evidence for how temperature affects diversification rates. Here, authors use a supermatrix of nearly 20,000 rosid species, comprising almost a quarter of flowering plants, to show that tropical groups are older and speciated twice as slowly as their counterparts from cooler climates.
- Miao Sun
- , Ryan A. Folk
- & Robert P. Guralnick
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Article
| Open AccessEvolution of generalist resistance to herbicide mixtures reveals a trade-off in resistance management
Mixtures of antibiotics or pesticides can help reduce the evolution of resistance to individual compounds. Here, Comont et al. show that in blackgrass, an important agricultural weed, herbicide mixtures do reduce specialized resistance but instead can select for a generalized resistance mechanism.
- David Comont
- , Claudia Lowe
- & Paul Neve
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| Open AccessA mycorrhizae-like gene regulates stem cell and gametophore development in mosses
Plant evolution is intimately associated with fungal partners. Here the authors provide evidence that Physcomitrella patens MACRO2, a gene likely derived from early mycorrhizae-like fungi, was transferred to early land plants and plays an important role in regulating stem cell growth and gametophore development in moss.
- Shuanghua Wang
- , Yanlong Guan
- & Jinling Huang
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| Open AccessThe morphology, molecular development and ecological function of pseudonectaries on Nigella damascena (Ranunculaceae) petals
Interspecies interactions, including those between plants and pollinators, can involve deception. The authors characterize the molecular development of Nigella damascena pseudonectaries, and their adaptive function in attracting specific pollinators to concealed nectaries with visual cues.
- Hong Liao
- , Xuehao Fu
- & Hongzhi Kong
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Article
| Open AccessChromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics
Despite tremendous genomic resources in the Arabidopsis community, only a few whole genome de novo assemblies are available. Here, the authors report chromosome-level reference-quality assemblies of seven A. thaliana accessions and reveal hotspots of rearrangements with altered evolutionary dynamics.
- Wen-Biao Jiao
- & Korbinian Schneeberger
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Article
| Open AccessNeo-functionalization of a Teosinte branched 1 homologue mediates adaptations of upland rice
A transposon insertion in the regulatory region of maize Tb1 gene leads to increased apical dominance and a reduction of tillering. Here, the authors showed that a duplicated rice Tb1 orthologue, OsTb2, has gained a regulatory effect on tillering opposite that of OsTb1 during artificial selection only in upland japonica rice.
- Jun Lyu
- , Liyu Huang
- & Fengyi Hu
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Article
| Open AccessExtreme genetic signatures of local adaptation during Lotus japonicus colonization of Japan
Local adaptation contributes to plant colonization across extreme environmental gradients. Here, the authors reconstruct the colonization history of Lotus japonicus in Japan and identify extreme genetic signatures of local adaptation to a cold climate using genome resequencing and common garden experiments.
- Niraj Shah
- , Tomomi Wakabayashi
- & Stig Uggerhøj Andersen
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Article
| Open AccessRelaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation
Why transposable elements (TEs) accumulate in polyploids and the evolutionary implications remain unclear. Here, the authors show that following whole genome duplication, relaxed purifying selection is the main driver of TE over-accumulation, which provides variants for rapid local adaptation.
- Pierre Baduel
- , Leandro Quadrana
- & Vincent Colot
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Article
| Open AccessGenome-wide analysis of Cushion willow provides insights into alpine plant divergence in a biodiversity hotspot
Exceptional alpine plant diversity exists in the Hengduan Mountains. Here, through genome assembly and population genomics studies, the authors find notable intraspecific divergence among Cushion willow populations isolated by the sky island-like habitats and consider it contributes to speciation and biodiversity.
- Jia-hui Chen
- , Yuan Huang
- & Hang Sun
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Article
| Open AccessInterspecific introgression mediates adaptation to whole genome duplication
Whole genome duplication (WGD) presents new challenges to the establishment of optimal allelic combinations and to the meiotic machinery. Here, the authors show that adaptive gene flow from Arabidopsis arenosa could rescue the nascent A. lyrata from extinction following WGD.
- Sarah Marburger
- , Patrick Monnahan
- & Levi Yant
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Article
| Open AccessThe chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis
Black pepper (Piper nigrum) belongs to the long-isolated lineage of basal angiosperm and its fruit has been used for food spice and phytomedicines for thousands of years. Here, the authors assemble the reference genome of this species and analyze gene families associated with piperine biosynthesis.
- Lisong Hu
- , Zhongping Xu
- & Shuangxia Jin
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Article
| Open AccessResequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil
Ginkgo is one of the living fossils from the plant kingdom. Here, authors conduct population genomics analyses to reveal its refugia and demographic history, and provide evidence of multiple anthropogenic introductions of ginkgo from eastern China into different continents.
- Yun-Peng Zhao
- , Guangyi Fan
- & Song Ge
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Article
| Open AccessEvolution of fast root gravitropism in seed plants
Root gravitropism anchors land plants to the ground and enables water uptake. Here, Zhang et al. define polar targeting of PIN2-like proteins as a major evolutionary innovation promoting shootward auxin transport and faster gravitropic responses of seed plants compared to basal vascular relatives.
- Yuzhou Zhang
- , Guanghui Xiao
- & Jiří Friml
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Article
| Open AccessTransposition favors the generation of large effect mutations that may facilitate rapid adaption
The contribution of transposable elements (TEs) to the creation of heritable mutations is unknown. Here the authors show in Arabidopsis that TEs accumulate exponentially once mobilized and that COPIA retrotransposons preferentially integrate in environmental response genes in a H2A.Z-dependent manner.
- Leandro Quadrana
- , Mathilde Etcheverry
- & Vincent Colot
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Article
| Open AccessRepeated evolution of cytochrome P450-mediated spiroketal steroid biosynthesis in plants
Diosgenin is a spiroketal natural product that is used as a precursor in the industrial synthesis of steroids. Here, the authors identified key cytochrome P450 enzymes responsible for the conversion of cholesterol to diosgenin from two phylogenetical distinct diosgenin-producing plant species.
- Bastien Christ
- , Chengchao Xu
- & Jing-Ke Weng
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Article
| Open AccessTranscriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus
Despite the economic importance of the allotetraploid crop Brassica napus, our knowledge of its phylogenomic relationships, genetic structure, and diversification is limited. Here, the authors show its complex origin and diversification by analyzing transcriptome and organellar sequencing data.
- Hong An
- , Xinshuai Qi
- & J. Chris Pires
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Article
| Open AccessAn asymmetric allelic interaction drives allele transmission bias in interspecific rice hybrids
Our limited understanding of the hybrid sterility (HS) mechanism in Asian–African rice hybrids hampers utilization of the interspecific heterosis for rice production. Here, the authors identify S1-mediated HS-related tripartite gamete killer-protector system, and explore their evolutionary relationship.
- Yongyao Xie
- , Jintao Tang
- & Letian Chen
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Article
| Open AccessRdDM-independent de novo and heterochromatin DNA methylation by plant CMT and DNMT3 orthologs
Whether plants have true DNMT3 orthologs and their role in establishing DNA methylation are still unclear. Here, the authors show that DNMT3s are persistent through plant evolution and mediates both de novo and heterochromatin DNA methylation in the early divergent land plant Physcomitrella patens.
- Rafael Yaari
- , Aviva Katz
- & Nir Ohad
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Article
| Open AccessResolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes
Mosses are a highly diverse lineage of land plants. Here, the authors provide a detailed phylogeny of 29 orders of moss, using nuclear and organelle data to provide robust hypotheses for most of the ordinal moss relationships.
- Yang Liu
- , Matthew G. Johnson
- & Bernard Goffinet
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Article
| Open AccessWhole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses
Despite the importance of grapevine cultivation in human history and the economic values of cultivar improvement, large-scale genomic variation data are lacking. Here the authors resequence 472 Vitis accessions and use the identified genetic variations for domestication history, demography, and GWAS analyses.
- Zhenchang Liang
- , Shengchang Duan
- & Yang Dong