News and Events
合集介绍：基因组是遗传信息的宝库，是生物多样性的基础，是植物领域的重要工具，也是推动生命科学发展的重要力量。
The haplotype-resolved telomere-to-telomere carnation (Dianthus caryophyllus) genome reveals the correlation between genome architecture and gene expression
原文链接：https://doi.org/10.1093/hr/uhad244
文章标题翻译：单体型解析的 T2T 康乃馨（Dianthus caryophyllus）基因组揭示了基因组结构与基因表达之间的相关性
工具链接：
https://github.com/tolkit/telomeric-identifier
https://github.com/marbl/ModDotPlot
https://github.com/lh3/srf
Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes
原文链接：https://doi.org/10.1093/hr/uhad252
文章标题翻译：四倍体栽培草莓的基因组组装揭示了亚基因组之间的遗传和表观遗传差异
工具链接：
https://github.com/tolkit/telomeric-identifier
http://telomerase.asu.edu/sequences_telomere.html
https://github.com/Adamtaranto/TRF2GFF
https://github.com/schneebergerlab/plotsr
http://eggnog-mapper.embl.de/
Populus cathayana genome and population resequencing provide insights into its evolution and adaptation
原文链接：https://doi.org/10.1093/hr/uhad255
微信导读：Hortic Res | 中国林科院林业所胡建军研究员团队在杨树基因组组装及适应性研究取得新进展
https://github.com/Nextomics/NextDenovo
A telomere-to-telomere reference genome of ficus (Ficus hispida) provides new insights into sex determination
原文链接：https://doi.org/10.1093/hr/uhad257
微信导读：Hortic Res | 中国农科院深圳农业基因组研究所发表首个榕属植物T2T基因组
工具链接：
https://github.com/PacificBiosciences/ccs
https://github.com/nathanweeks/exonerate
http://jaspar.genereg.net/
http://planttfdb.gao-lab.org/
Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics
原文链接：https://doi.org/10.1093/hr/uhad260
微信导读：Hortic Res | 西北农林科技大学组装感病葡萄汤普森无核T2T基因组
工具链接：
https://github.com/WenchaoLin/SMRT-Link
https://github.com/Nextomics/NextDenovo
https://github.com/BGI-Qingdao/TGS-GapCloser
https://github.com/wtsi-hpag/scanPAV
https://github.com/steuernb/NLR-Annotator
数据库链接：
Swiss-Prot (http://www.ebi.ac.uk/interpro/),
KEGG (https://www.genome.jp/kegg/),
GO (http://geneontology.org/page/go-database),
Pfam (http://pfam.xfam.org/)
Rfam (https://rfam.org/)
Genome variation and LTR-RT analyses of an ancient peach landrace reveal mechanism of blood-flesh fruit color formation and fruit maturity date advancement
原文链接：https://doi.org/10.1093/hr/uhad265
微信导读：Hortic Res | 中国农科院郑州果树所揭示了桃红肉形成及果实提前成熟的机制
工具链接：
http://www.repeatmasker.org/RepeatModeler/
http://sourceforge.net/projects/cafehahnlab
Phased genomics reveals hidden somatic mutations and provides insight into fruit development in sweet orange
原文链接：https://doi.org/10.1093/hr/uhad268
微信导读：Hortic Res 2月封面文章 | 湖南省农科院园艺所在‘锦和’冰糖橙无性系变异和果实大小发育研究取得重要进展
工具链接：
https://github.com/marbl/meryl
https://github.com/KorfLab/SNAP
https://github.com/kishwarshafin/pepper
https://github.com/Federico77z/aScan/
A chromosome-level genome assembly of Agave hybrid NO.11648 provides insights into the CAM photosynthesis
原文链接：https://doi.org/10.1093/hr/uhad269
微信导读：Hortic Res | 中国热带农业科学院南亚热带作物研究所剑麻研究团队在龙舌兰亚科基因组及CAM进化机制上取得进展
工具链接：
http://github.com/ruanjue/smartdenovo
https://github.com/JinfengChen/Scripts
https://itol.embl.de/
Insights into the Superrosids phylogeny and flavonoid synthesis from the telomere-to-telomere gap-free genome assembly of Penthorum chinense Pursh
原文链接：https://doi.org/10.1093/hr/uhad274
文章标题翻译：T2T为薄荷的的超甾体系统发育和类黄酮合成提供见解
The lemon genome and DNA methylome unveil epigenetic regulation of citric acid biosynthesis during fruit development
原文链接：https://doi.org/10.1093/hr/uhae005
微信导读：Hortic Res | 广西大学农学院团队揭示柠檬果实发育过程中柠檬酸生物合成的表观遗传调控机制
工具链接：
https://github.com/lh3/bwa
https://repeatmasker.org
http://bio-bwa.sourceforge.net/
http://homepage.mac.com/iankorf/
https://pcingola.github.io/SnpEff/se_inputoutput/
数据库链接：
SwissProt（http://www.uniprot.org/）
Nr（http://www.ncbi.nlm.nih.gov/protein）
Pfam（http://pfam.xfam.org/）
KEGG（http://www.genome.jp/kegg/）
InterPro（https://www.ebi.ac.uk/interpro/）
Genome and GWAS analysis identified genes significantly related to phenotypic state of Rhododendron bark
原文链接：https://doi.org/10.1093/hr/uhae008
文章标题翻译：基因组和GWAS分析鉴定了与杜鹃树皮表型状态显著相关的基因
工具链接：
https://github.com/thlee/SNPhylo
https://www.cog-genomics.org/plink2
https://github.com/jiabowang/GAPIT
https://meme-suite.org/meme/
http://bioinformatics.psb.ugent.be/webtools/plantcare/html/
A haplotype-resolved gap-free genome assembly provides novel insight into monoterpenoid diversification in Mentha suaveolens ‘Variegata’
原文链接：https://doi.org/10.1093/hr/uhae022
微信导读：Hortic Res | 成都中医药大学在薄荷T2T单倍型基因组研究获得突破
https://github.com/Nextomics/NextDenovo
https://github.com/nanoporetech/medaka
T2T reference genome assembly and genome-wide association study reveal the genetic basis of Chinese bayberry fruit quality
原文链接：https://doi.org/10.1093/hr/uhae033
微信导读：Hortic Res | 浙江省农业科学院在杨梅T2T基因组及果实品质性状的全基因组关联分析上取得进展
https://github.com/dfguan/purge_dups
http://broadinstitute.github.io/picard/
https://pubmed.ncbi.nlm.nih.gov/33126247/
The Cissus quadrangularis genome reveals its adaptive features in an arid habitat
原文链接：https://doi.org/10.1093/hr/uhae038
微信导读：Hortic Res | 中国科学院武汉植物园在方茎白粉藤基因组组装及抗旱机制上取得进展
http://www.bioinfo.ufpr.br/fgap/
https://github.com/BGI-Qingdao/TGS-GapCloser
https://github.com/tolkit/telomeric-identifier
http://www.repeatmasker.org/
http://www.repeatmasker.org/RepeatModeler.html
https://genomethreader.org/
https://services.healthtech.dtu.dk/services/RNAmmer-1.2/
http://plantregmap.gao-lab.org/
https://mummer.sourceforge.net/
http://www.drive5.com/muscle/
http://www.drive5.com/muscle/
https://ggplot2.tidyverse.org/
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
http://bioinfo.cau.edu.cn/agriGO/
https://github.com/CJ-Chen/TBtools
http://bioinformatics.psb.ugent.be/webtools/plantcare/html/
Characterization of O-methyltransferases in the biosynthesis of phenylphenalenone phytoalexins based on the telomere-to-telomere gapless genome of Musella lasiocarpa
原文链接：https://doi.org/10.1093/hr/uhae042
文章标题翻译：基于T2T基因组鉴定O-甲基转移酶在地涌金莲的苯萘酮植保素生物合成中的特性
工具链接：
http://orthomcl.org/orthomcl/
http://sourceforge.net/projects/cafehahnlab/
Haplotype-resolved genome of Prunus zhengheensis provides insight into its evolution and low temperature adaptation in apricot
原文链接：https://doi.org/10.1093/hr/uhae103
微信导读：Hortic Res | 南京农业大学高志红团队通过濒危植物政和杏全基因组测序揭示HSFA1d基因自然变异在杏低温适应性的作用
Chromosome-scale genome, together with transcriptome and metabolome, provides insights into the evolution and anthocyanin biosynthesis of Rubus rosaefolius Sm. (Rosaceae)
原文链接：https://doi.org/10.1093/hr/uhae064
微信导读：Hortic Res | 王云生及其合作者破解了空心泡（Rubus rosaefolius Sm）的基因组
https://github.com/theaidenlab/3d-dna
Haplotype-resolved T2T reference genomes for wild and domesticated accessions shed new insights into the domestication of jujube
原文链接：https://doi.org/10.1093/hr/uhae071
文章标题翻译：酸枣和枣T2T单倍型基因组为酸枣的驯化提供了新的见解
https://github.com/PacificBiosciences/ccs
https://github.com/rrwick/Filtlong
https://github.com/rrwick/Porechop
https://github.com/isovic/racon/tree/liftover
https://github.com/mummer4/mummer
https://github.com/tolkit/telomeric-identifier
https://github.com/ShuaiNIEgithub/Centromics
https://github.com/mummer4/mummer
https://github.com/schneebergerlab/syri
http://itol.embl.de
Chromosome-level genome assemblies of Musa ornata and Musa velutina provide insights into pericarp dehiscence and anthocyanin biosynthesis in banana
原文链接：https://doi.org/10.1093/hr/uhae079
微信导读：Hortic Res | 华南植物园发表紫苞芭蕉和朝天蕉的首个染色体水平基因组
https://jaspar.elixir.no/
https://www.chiplot.online/
数据库链接：
PlantTFDB (http://planttfdb.gao-lab.org/
KEGG PATHWAY Database https://www.kegg.jp/kegg/pathway.html
Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation
原文链接：https://doi.org/10.1093/hr/uhae080
文章标题翻译：马尔贝克葡萄品种的基因组能够实现基于单倍型的转录组差异分析
http://github.com/PacificBiosciences/GenomicConsensus/
http://github.com/PacificBiosciences/SMRT-Analysis
https://github.com/TransDecoder/TransDecoder
https://github.com/andreaminio/AnnotationPipeline-EVM_based-DClab
The high-quality genome of Grona styracifolia uncovers the genomic mechanism of high levels of schaftoside, a promising drug candidate for treatment of COVID-19
原文链接：https://doi.org/10.1093/hr/uhae089
文章标题翻译：广金钱草基因组揭示了高含量夏佛塔苷的基因组机制
https://github.com/Nextomics/NextPolish
https://github.com/adeylab/fragScaff
http://www.repeatmasker.org/RepeatModeler.html
http://www.repeatmasker.org
http://evidencemodeler.sourceforge.net/
数据库链接：
InterPro (http://www.ebi.ac.uk/interpro/),
Pfam (http://pfam.xfam.org/)
HMMER (http://www.hmmer.org/),
GO (http://www.geneontology.org/page/go-database),
KEGG (http://www.kegg.jp/kegg/kegg1.html)
Genomic, transcriptomic, and metabolomic analyses provide insights into the evolution and development of a medicinal plant Saposhnikovia divaricata (Apiaceae)
原文链接：https://doi.org/10.1093/hr/uhae105
微信导读：Hortic Res | 吉林农业大学联合南京农业大学伞形科基因组研究团队揭示首个高质量的防风基因组
https://github.com/pacificbiosciences/unanimity
https://github.com/lh3/gfatools
https://github.com/davidemms/OrthoFinder
https://github.com/StoreyLab/qvalue
http://deweylab.github.io/RSEM
A phased genome of the highly heterozygous ‘Texas’ almond uncovers patterns of allele-specific expression linked to heterozygous structural variants
原文链接：https://doi.org/10.1093/hr/uhae106
文章标题翻译：杏仁的阶段性基因组揭示了与杂合结构变异相关的等位基因特异性表达模式
https://github.com/rrwick/Filtlong#full-usage
https://github.com/lh3/seqtk
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
http://arthropods.eugenes.org/EvidentialGene/
https://www.repeatmasker.org/
Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis
原文链接：https://doi.org/10.1093/hr/uhae107
微信导读：Hortic Res | 基因组所李伟团队通过人参T2T基因组揭示活性皂苷多样化的形成机制
https://github.com/aidenlab/Juicebox
https://github.com/chenlianfu/geta
https://github.com/sc-zhang/T2Tools
Chromosome-level genome assembly and population genomics reveals crucial selection for subgynoecy development in chieh-qua
原文链接：https://doi.org/10.1093/hr/uhae113
微信导读：Hortic Res | 广东省农业科学院蔬菜研究所通过染色体水平基因组组装和群体基因组学揭示节瓜强雌性型发育和驯化机制
数据库链接：
PGSB Repeat Element Database (http://pgsb.helmholtz-muenchen.de/plant/recat/)
Repbase (http://www.girinst.org/repbase)
De novo assembling a high-quality genome sequence of Amur grape (Vitis amurensis Rupr.) gives insight into Vitis divergence and sex determination
原文链接：https://doi.org/10.1093/hr/uhae117
微信导读：Hortic Res | 山东省葡萄研究院在中国山葡萄基因组组装与性别决定研究取得新进展
https://github.com/BGI-flexlab/SOAPnuke
https://github.com/marbl/canu/releases
https://github.com/ruanjue/smartdenovo
https://github.com/isovic/racon
https://github.com/nanoporetech/medaka
https://github.com/broadinstitute/pilon/
http://www.drive5.com/piler/
http://tandem.bu.edu/trf/trf.html
http://lowelab.ucsc.edu/tRNAscan-SE/
http://infernal.janelia.org/
Haplotype-resolved chromosomal-level genome assembly reveals regulatory variations in mulberry fruit anthocyanin content
原文链接：https://doi.org/10.1093/hr/uhae120
微信导读：Hortic Res | 西南大学赵爱春教授课题组在桑果色泽调控研究中取得新发现
https://github.com/josephryan/estimate_genome_size.pl
http://qb.cshl.edu/genomescope/genomescope2.0/
https://github.com/chhylp123/hifiasm
http://samtools.github.io/bcftools
https://github.com/tangerzhang/calc_switchErr
https://github.com/TransDecoder
http://TimeTree.org
https://gitlab.com/rhee-lab/E2P2
https://PlantCyc.org/
https://github.com/yushuen/MFSelector_STAR-Protocol
https://broadinstitute.github.io/picard/
A telomere-to-telomere gap-free reference genome assembly of avocado provides useful resources for identifying genes related to fatty acid biosynthesis and disease resistance
原文链接：https://doi.org/10.1093/hr/uhae119
微信导读：Hortic Res | 中国科学院西双版纳热带植物园发表首个牛油果T2T无间隙参考基因组
https://github.com/marbl/meryl
https://github.com/lastz/lastz
https://github.com/phasegenomics
http://www.repeatmasker.org
https://repeatexplorer-elixir.cerit-sc.cz/galaxy
http://www.repeatmasker.org
http://eggnog-mapper.embl.de/
数据库链接：
RectChr v1.36 ( https://github.com/hewm2008/RectChr )
SMART ( http://smart.emblheidelberg.de/ )
Haplotype-resolved genome assembly for tetraploid Chinese cherry (Prunus pseudocerasus) offers insights into fruit firmness
原文链接：https://doi.org/10.1093/hr/uhae142
微信导读：Hortic Res | 上海交大张才喜教授团队联合云南农大董扬教授团队首次破译中国樱桃单倍型基因组，解明果实硬度低的内在机理
https://sourceforge.net/projects/mummer/files/
https://github.com/bbuchfink/diamond
https://github.com/tanghaibao/jcvi
https://github.com/wolski/imsbInfer
Genome assembly and resequencing shed light on evolution, population selection, and sex identification in Vernicia montana
原文链接：https://doi.org/10.1093/hr/uhae141
微信导读：Hortic Res | 中南林业科技大学张琳教授团队在千年桐基因组学及性别鉴定方面研究取得新进展
https://github.com/josephryan/estimate_genome_size.pl
https://github.com/CAFS-bioinformatics/LR_Gapcloser
https://github.com/broadinstitute/pilon
https://github.com/TransDecoder/TransDecoder
https://github.com/tseemann/barrnap
https://github.com/EddyRivasLab/infernal/
https://github.com/sffjunkie/astra
https://github.com/cran/pracma
(https://treesoft.sourceforge.net
(https://github.com/chrchang/plink-ng
数据库链接:
RFAMSEQ10 database ( http://ftp.ebi.ac.uk/pub/databases/Rfam/ )
Genome resequencing reveals the genetic basis of population evolution, local adaptation, and rewiring of the rhizome metabolome in Atractylodes lancea
原文链接：https://doi.org/10.1093/hr/uhae167
微信导读：Hortic Res | 中国中医科学院中药资源中心利用mGWAS揭示苍术道地药材根茎代谢物的遗传变异及环境适应性特征
The gapless genome assembly and multi-omics analyses unveil a pivotal regulatory mechanism of oil biosynthesis in the olive tree
原文链接：https://doi.org/10.1093/hr/uhae168
微信导读：Hortic Res | 兰州大学万东石教授团队，甘肃省林业科学研究院姜成英研究员团队，联合发表油橄榄首个T2T无间隙参考基因组
https://www.omicshare.com/tools
The gap-free genome and multi-omics analysis of Citrus reticulata ‘Chachi’ reveal the dynamics of fruit flavonoid biosynthesis
原文链接：https://doi.org/10.1093/hr/uhae177
微信导读：Hortic Res | 广东省农业科学院果树研究所联合浙江农林大学在茶枝柑基因组组装及类黄酮类物质生物合成研究上取得重要进展
工具链接：
https://github.com/tanghaibao/jcvi
Haplotype-resolved genome and mapping of freezing tolerance in the wild potato Solanum commersonii
原文链接：https://doi.org/10.1093/hr/uhae181
微信导读：Hortic Res | 华中农业大学马铃薯课题组发布了抗寒野生种单倍型解析基因组和抗寒性遗传图谱
https://github.com/ShuaiNIEgithub/Centromics
https://github.com/Dfam-consortium/RepeatModeler
http://www.repeatmasker.org
https://github.com/Gaius-Augustus/BRAKER
https://github.com/davidemms/OrthoFinder
https://github.com/hahnlab/CAFE
https://github.com/GSLBiotech/mafft
https://github.com/stamatak/standard-RAxML
https://github.com/sabifo4/Tutorial_MCMCtree
(https://github.com/vigsterkr/circos
https://github.com/s-andrews/FastQC
https://github.com/OpenGene/fastp
https://github.com/broadinstitute/gatk
https://github.com/WGLab/doc-ANNOVAR
The gap-free genome of Forsythia suspensa illuminates the intricate landscape of centromeres
原文链接：https://doi.org/10.1093/hr/uhae185
微信导读：Hortic Res | 中国科学院遗传与发育生物学研究所发表首个连翘无间隙参考基因组
工具链接：https://repeatexplorer-elixir.cerit-sc.cz/galaxy/
Genomic data provides insights into the evolutionary history and adaptive differentiation of two tetraploid strawberries
原文链接：https://doi.org/10.1093/hr/uhae194
微信导读：Hortic Res | 中国特有四倍体伞房草莓和西南草莓进化历史
Chromosome-scale reference genome of an ancient landrace: unveiling the genetic basis of seed weight in the food legume crop pigeonpea (Cajanus cajan)
原文链接：https://doi.org/10.1093/hr/uhae201
文章标题翻译：基因组揭示木豆种子重量的遗传基础
https://github.com/theaidenlab/juicer
https://github.com/aidenlab/3d-dna
https://github.com/EVidenceModeler/EVidenceModeler
http://prgdb.org/prgdb/drago2
http://prgdb.org/prgdb/drago2
https://github.com/xiaolei-lab/rMVP
https://github.com/BGI-shenzhen/LDBlockShow
https://github.com/ZhangRenL/geneHapR
A genome assembly of decaploid Houttuynia cordata provides insights into the evolution of Houttuynia and the biosynthesis of alkaloids
原文链接：https://doi.org/10.1093/hr/uhae203
微信导读：Hortic Res | 湖南农业大学及岳麓山实验室曾建国教授团队成功构建十倍体药用植物鱼腥草染色体水平基因组
https://github.com/lh3/gfatools
https://github.com/aidenlab/juicer
https://github.com/tpoorten/dotPlotly
github.com/tanghaibao/jcvi/wiki/MCscan
Exploring genetic diversity, population structure, and subgenome differences in the allopolyploid Camelina sativa: implications for future breeding and research studies
原文链接：https://doi.org/10.1093/hr/uhae247
文章标题翻译：异源多倍体亚麻荠的遗传多样性、群体结构和亚基因组差异对未来育种和研究的启示
工具链接：
http://cpc2.gao-lab.org/index.php
http://www.ebi.ac.uk/Tools/pfa/pfamscan
https://github.com/sjteresi/Camelina_TE_Annotation.
https://www.repeatmasker.org/RepeatModeler
High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry
原文链接：https://doi.org/10.1093/hr/uhad002
微信导读：Hortic Res | 沈阳农业大学草莓科研团队组装出八倍体栽培草莓高质量单倍型基因组
Diploid chromosome-level reference genome and population genomic analyses provide insights into Gypenoside biosynthesis and demographic evolution of Gynostemma pentaphyllum (Cucurbitaceae)
原文链接：https://doi.org/10.1093/hr/uhac231
微信导读：Hortic Res | 西北大学赵桂仿教授和李忠虎教授团队破译绞股蓝高质量基因组并揭示其群体进化历史
Telomere-to-telomere genome assembly of bitter melon (Momordica charantia L. var. abbreviata Ser.) reveals fruit development, composition and ripening genetic characteristics
原文链接：https://doi.org/10.1093/hr/uhac228
文章标题翻译：T2T基因组揭示了金陵紫果实发育、组成和成熟遗传特性
https://github.com/JinfengChen/Scripts
Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color
原文链接：https://doi.org/10.1093/hr/uhac241
微信导读：Hortic Res | 杜鹃花gapless基因组揭示种间花色转变遗传基础
工具链接：
https://github.com/Nextomics/NextDenovo
http://github.com/broadinstitute/pilon
https://github.com/aidenlab/juicer
https://github.com/CAFS-bioinformatics/LR_Gapcloser
https://github.com/lh3/bwa
https://github.com/infphilo/hisat2
http://bioinf.uni-greifswald.de/augustus/
https://github.com/tseemann/barrnap
http://eggnogdb.embl.de
https://gitlab.com/rhee-lab/E2P2
https://meme-suite.org/meme
http://www.ebi.ac.uk/interpro
数据库链接：
RepeatModeler v1 (http://www.repeatmasker.org)
RepeatMasker v4.0.5 (http://www.repeatmasker.org)
A chromosome-level phased genome enabling allele-level studies in sweet orange: a case study on citrus Huanglongbing tolerance
原文链接：https://doi.org/10.1093/hr/uhac247
文章标题翻译：利用染色体水平的定相基因组研究甜橙橙子的耐黄龙病性
https://github.com/TheLuoFengLab/DVS-assembly-and-allele-aware-RNAseq-pipeline.git
https://github.com/lh3/wgsim
Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis
原文链接：https://doi.org/10.1093/hr/uhac264
微信导读：Hortic Res | 猕猴桃T2T参考基因组
工具链接：
https://www.pacb.com/products-and-services/analytical-software/smrt-analysis/
https://github.com/PacificBiosciences/ccs
https://github.com/aaranyue/CTGA
https://github.com/Nextomics/NextDenovo
数据库链接：
Pfam database (https://pfam.xfam.org/)
Genome assembly of wild loquat (Eriobotrya japonica) and resequencing provide new insights into the genomic evolution and fruit domestication in loquat
原文链接：https://doi.org/10.1093/hr/uhac265
微信导读：Hortic Res | 西南大学梁国鲁教授团队在野生枇杷高质量基因组和种质资源重测序方面取得新进展
https://github.com/ruanjue/smartdenovo
http://broadinstitute.github.io/picard/
www.cog-genomics.org/plink2
The high-quality Pinellia pedatisecta genome reveals a key role of tandem duplication in the expansion of its agglutinin genes
原文链接：https://doi.org/10.1093/hr/uhac289
文章标题翻译：掌叶半夏基因组揭示了串联复制在其凝集素基因扩张中的关键作用
Gap-free genome assembly and comparative analysis reveal the evolution and anthocyanin accumulation mechanism of Rhodomyrtus tomentosa
原文链接：https://doi.org/10.1093/hr/uhad005
微信导读：Hortic Res | Gap-free基因组与比较分析揭示桃金娘进化与花青素积累机制
https://github.com/Nextomics/NextDenovo
https://cran.r-project.org/web/packages/Hmisc/
Pan-genome and transcriptome analyses provide insights into genomic variation and differential gene expression profiles related to disease resistance and fatty acid biosynthesis in eastern black walnut (Juglans nigra)
原文链接：https://doi.org/10.1093/hr/uhad015
微信导读：Hortic Res | 西北大学联合西北农林科技大学在黑胡桃基因组学和抗病及油脂代谢基因方面取得新进展
工具链接：
https://mafft.cbrc.jp/alignment/software
http://www.interactivenn.net/
A gap-free and haplotype-resolved lemon genome provides insights into flavor synthesis and huanglongbing (HLB) tolerance
原文链接：https://doi.org/10.1093/hr/uhad020
文章标题翻译：柠檬基因组味风味合成和黄龙病耐受性提供了见解
The telomere-to-telomere genome of Fragaria vesca reveals the genomic evolution of Fragaria and the origin of cultivated octoploid strawberry
原文链接：https://doi.org/10.1093/hr/uhad027
微信导读：Hortic Res | 首个草莓完整基因组发布
工具链接：
https://github.com/Nextomics/NextDenovo
https://github.com/aidenlab/juicer/wiki
https://github.com/marbl/merqury
https://github.com/lh3/bwa
https://github.com/lh3/minimap2
https://github.com/ShuaiNIEgithub/Centromics
https://github.com/nathanweeks/exonerate
http://daehwankimlab.github.io/hisat2/
https://ccb.jhu.edu/software/stringtie
https://github.com/TransDecoder/TransDecoder
https://orthovenn2.bioinfotoolkits.net/
https://github.com/steuernb/NLR-Annotator
Haplotype resolved chromosome level genome assembly of Citrus australis reveals disease resistance and other citrus specific genes
原文链接：https://doi.org/10.1093/hr/uhad058
文章标题翻译：单倍型染色体水平基因组组装揭示了柑橘的抗病性和其他特异基因
Chromosome-scale genome assembly of Prunus pusilliflora provides novel insights into genome evolution, disease resistance, and dormancy release in Cerasus L
原文链接：https://doi.org/10.1093/hr/uhad062
微信导读：Hortic Res | 上海交大张才喜教授团队联合云南农大董扬教授团队发布滇西边境细花樱桃高质量基因组揭秘高抗病遗传机制
https://github.com/xiaochuanle/NECAT
(https://github.com/dfguan/purge_dups
https://github.com/aidenlab/Juicebox
http://mummer.sourceforge.net
https://github.com/tanghaibao/jcvi/wiki/MCscan-Python-version
http://www.timetree.org
http://www.microbesonline.org/fasttree/
https://bitbucket.org/yaanlpc/rgaugury
https://bedtools.readthedocs.io/en/latest/index.html
https://github.com/tidyverse/ggplot2
Chromosome-level genome assembly of Salvia miltiorrhiza with orange roots uncovers the role of Sm2OGD3 in catalyzing 15,16-dehydrogenation of tanshinones
原文链接：https://doi.org/10.1093/hr/uhad069
文章标题翻译：橙根丹参基因组揭示Sm2OGD3在催化丹参酮15,16-脱氢中的作用
工具链接：
https://github.com/PacificBiosciences/FALCON/
http://shendurelab.github.io/LACHESIS/
http://www.repeatmasker.org/
Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae
原文链接：https://doi.org/10.1093/hr/uhad073
微信导读：Hortic Res | 华北理工大学王金朋团队在菊科植物多倍化及祖先基因组重建和进化方面取得新进展
http://smart.embl.de/smart/batch.pl
https://toolkit.tuebingen.mpg.de/tools/marcoil
https://meme-suite.org/meme/tools/meme
Genome of tetraploid sour cherry (Prunus cerasus L.) ‘Montmorency’ identifies three distinct ancestral Prunus genomes
原文链接：https://doi.org/10.1093/hr/uhad097
工具链接：
https://github.com/goeckeritz/Montmorency_genome
Telomere-to-telomere carrot (Daucus carota) genome assembly reveals carotenoid characteristics
原文链接：https://doi.org/10.1093/hr/uhad103
微信导读：Hortic Res | 南京农业大学联合贵州农科院和淮阴工学院发表首个胡萝卜完整参考基因组并揭示类胡萝卜素积累特性
工具链接：
https://github.com/rrwick/Filtlong
http://www.bioinformatics.babraham.ac.uk/projects/hicup/
https://github.com/isovic/racon/
数据库链接：
Telomere database (http://telomerase.asu.edu/sequences_telomere.html)
The gap-free genome of mulberry elucidates the architecture and evolution of polycentric chromosomes
原文链接：https://doi.org/10.1093/hr/uhad111
微信导读：Hortic Res | 西南大学何宁佳团队发表首个桑树完整参考基因组
工具链接：
https://github.com/PacificBiosciences/ccs
https://github.com/Nextomics/NextDenovo
https://www.bioinformatics.babraham.ac.uk/projects/hicup/
https://github.com/wdecoster/nanofilt
https://github.com/epi2me-labs/pychopper
https://github.com/TransDecoder/TransDecoder
https://github.com/TransDecoder/TransDecoder
https://github.com/nanoporetech/tombo
The genome of okra (Abelmoschus esculentus) provides insights into its genome evolution and high nutrient content
原文链接：https://doi.org/10.1093/hr/uhad120
微信导读：Hortic Res | 河北大学杜会龙团队在锦葵科基因组进化方面取得重要进展
工具链接：
https://github.com/OpenGene/fastp
Genome assembly of Polygala tenuifolia provides insights into its karyotype evolution and triterpenoid saponin biosynthesis
原文链接：https://doi.org/10.1093/hr/uhad139
微信导读：Hortic Res | 成都中医药大学成功解析远志基因组并详细描述其多倍化历史中的核型进化过程
http://tandem.bu.edu/trf/trf.html
http://www.repeatmasker.org/RepeatModeler.html
Genome assembly and resequencing analyses provide new insights into the evolution, domestication and ornamental traits of crape myrtle
原文链接：https://doi.org/10.1093/hr/uhad146
微信导读：Hortic Res | 北京林业大学张启翔团队在紫薇基因组组装和群体重测序研究方面取得新进展
http://www.girinst.org/repbase
http://repeatmasker.org/RepeatModeler/
http://treesoft.sourceforge.net/treebest.shtml
https://www.cog-genomics.org/plink/
http://dalexander.github.io/admixture/index.html
https://github.com/bmansfeld/QTLseqr
Telomere-to-telomere haplotype-resolved reference genome reveals subgenome divergence and disease resistance in triploid Cavendish banana
原文链接：https://doi.org/10.1093/hr/uhad153
微信导读：Hortic Res | 首个三倍体栽培香蕉T2T参考基因组发布
工具链接：
https://github.com/PacificBiosciences/ccs
https://github.com/Nextomics/NextDenovo
https://github.com/tolkit/telomeric-identifier
https://github.com/YangJianshun/LINKVIEW
http://repeatmasker.org/
https://github.com/nextgenusfs/funannotate
Chromosome-scale genome sequence of Suaeda glauca sheds light on salt stress tolerance in halophytes
原文链接：https://doi.org/10.1093/hr/uhad161
微信导读：Hortic Res | 福建农林大学碱蓬基因组解析工作揭示“DNA/染色质稳定性维持”耐盐新机制
https://github.com/lardo/khaper
https://github.com/aidenlab/Juicebox
https://www.evolgenius.info/evolview/
Genome assembly of the snow lotus species Saussurea involucrata provides insights into acacetin and rutin biosynthesis and tolerance to an alpine environment
原文链接：https://doi.org/10.1093/hr/uhad180
文章标题翻译：基因组组装提供了对雪莲杨梅素和芦丁生物合成及对高山环境耐受性的深入了解
The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon
原文链接：https://doi.org/10.1093/hr/uhad182
微信导读：Hortic Res | 中国农科院郑州果树研究所联合中国农业大学组装首个野生型甜瓜T2T基因组
工具链接：
http://grass.cgs.hku.hk/gec/register.php
https://cran.r-project.org/web/packages/qqman/
A gap-free reference genome reveals structural variations associated with flowering time in rapeseed (Brassica napus
原文链接：https://doi.org/10.1093/hr/uhad171
文章标题翻译：Gap-free基因组揭示油菜与开花时间相关的结构变化
https://github.com/pacificbiosciences/unanimity
https://github.com/fanagislab/GCE
https://github.com/rrwick/Filtlong
https://github.com/rrwick/Porechop
https://github.com/PacificBiosciences/ccs
https://github.com/OpenGene/fastp
http://www.bioinformatics.babraham.ac.uk/projects/hicup/
https://github.com/Nextomics/NextDenovo
https://github.com/chhylp123/hifiasm
https://github.com/tangerzhang/ALLHiC
https://github.com/isovic/racon/tree/liftover
https://github.com/nanoporetech/medaka
https://github.com/oushujun/LTR_retriever
https://github.com/mummer4/mummer
https://github.com/schneebergerlab/syri
https://github.com/wdecoster/nanofilt
https://github.com/Dfam-consortium/RepeatModeler
https://github.com/rmhubley/RepeatMasker
The high-quality sequencing of the Brassica rapa ‘XiangQingCai’ genome and exploration of genome evolution and genes related to volatile aroma
原文链接：https://doi.org/10.1093/hr/uhad187
微信导读：Hortic Res | 苏州市农业科学院联合华北理工大学解析特色白菜品种‘香青菜’基因组及香味关键基因挖掘
Telomere-to-telomere genome assembly of melon (Cucumis melo L. var. inodorus) provides a high-quality reference for meta-QTL analysis of important traits
原文链接：https://doi.org/10.1093/hr/uhad189
微信导读：Hortic Res | 华中农业大学联合新疆农业科学院发布首个哈密瓜T2T基因组
工具链接：
https://github.com/VGP/vgpassembly/
https://github.com/tseemann/barrnap
A telomere-to-telomere reference genome provides genetic insight into the pentacyclic triterpenoid biosynthesis in Chaenomeles speciosa
原文链接：https://doi.org/10.1093/hr/uhad183
文章标题翻译：T2T基因组为皱皮木瓜的五环三萜生物合成提供遗传学见解
https://github.com/PacificBiosciences/ccs
https://github.com/gmarcais/Jellyfish
https://github.com/fanagislab/GCE
www.bioinformatics.babraham.ac.uk/projects/fastqc/
https://github.com/aidenlab/3d-dna
https://github.com/aiden
www.repeatmasker.org
www.girinst.org/repbase
www.repeatmasker.org/RepeatModeler/
https://github.com/UCSC-LoweLab/tRNAscan-SE
https://ngdc.cncb.ac.cn/tools/paraat
https://ngdc.cncb.ac.cn/tools/kaks
A chromosome-level genome assembly provides insights into Cornus wilsoniana evolution, oil biosynthesis, and floral bud development
原文链接：https://doi.org/10.1093/hr/uhad196
微信导读：Hortic Res | 南京大学何祯祥教授团队合作发表光皮梾木染色体水平参考基因组
工具链接：
http://tandem.bu.edu/trf/trf.html
http://www.repeatmasker.org
https://github.com/xzhub/LTR_Finder
http://www.repeatmasker.org/
http://www.repeatmasker.org/RepeatModeler.html
Telomere-to-telomere assembly of cassava genome reveals the evolution of cassava and divergence of allelic expression
原文链接：https://doi.org/10.1093/hr/uhad200
微信导读：Hortic Res | 广西大学陈玲玲教授团队与广西农科院严华兵团队联合发表首个木薯T2T基因组
工具链接：
https://github.com/schatzlab/pseudohaploid
https://github.com/lh3/gfatools
https://github.com/lh3/gfatools
https://itol.embl.de/
https://github.com/SunPengChuan/wgdi-example
https://github.com/dpryan79/MethylDackel
Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts
原文链接：https://doi.org/10.1093/hr/uhad202
文章标题翻译：蓝莓和蔓越莓泛基因组作为未来遗传研究和育种工作的资源
工具链接：https://github.com/sjteresi/Vaccinium_Pangenome_TE_Analysis
Telomere-to-telomere pear (Pyrus pyrifolia) reference genome reveals segmental and whole genome duplication driving genome evolution
原文链接：https://doi.org/10.1093/hr/uhad201
微信导读：Hortic Res | 南京农业大学完成梨首个T2T基因组组装和解析
https://github.com/Nextomics/NextDenovo
https://github.com/tolkit/telomeric-identifier
http://www.repeatmasker.org/RepeatModeler/
http://repeatmasker.org/
http://web.expasy.org/docs/swiss-prot/guideline.html
https://github.com/FelixKrueger/TrimGalore
The telomere-to-telomere gap-free reference genome of wild blueberry (Vaccinium duclouxii) provides its high soluble sugar and anthocyanin accumulation
原文链接：https://doi.org/10.1093/hr/uhad209
微信导读：Hortic Res | 首个野生蓝莓T2T参考基因组发布
工具链接：
https://github.com/Nextomics/NextDenovo
https://github.com/isovic/racon/tree/liftover
https://github.com/VGP/vgp-assembly
https://github.com/ShuaiNIEgithub/Centromics
http://plantpan.itps.ncku.edu.tw/index.html
https://www.ncbi.nlm.nih.gov/cdd/
https://www.chiplot.online/
Genome sequencing revealed the red-flower trait candidate gene of a peach landrace
原文链接：https://doi.org/10.1093/hr/uhad210
微信导读：Hortic Res | 基因组测序发现桃红花性状决定候选基因
工具链接：
http://github.com/chenlianfu/geta
Pangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization
原文链接：https://doi.org/10.1093/hr/uhad203
微信导读：Hortic Res | 中国科学院武汉植物园邱英雄团队在孤儿作物-菱属的泛基因组和结构变异研究中取得新进展
工具链接：
https://github.com/PacificBiosciences/IsoSeq
https://github.com/vgteam/giraffe-sv-paper/blob/master/scripts/sv
https://github.com/vgteam/giraffe-svpaper/blob/master/scripts/read_simulation/
The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes
原文链接：https://doi.org/10.1093/hr/uhad205
文章标题翻译：T2T基因组揭示了葡萄花青素生物合成的遗传基础
工具链接：
https://github.com/unavailable-2374/Genome-Wide-Annotation-Pipeline
Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea (Hydrangea macrophylla) and insights into Asterid evolution
原文链接：https://doi.org/10.1093/hr/uhad217
文章标题翻译：两个高质量单倍型参考基因组揭示了大叶绣球花重要花性状
https://github.com/OpenGene/fastp
http://www.bioinformatics.babraham.ac.uk/projects/fastqc
The haplotype-resolved autotetraploid genome assembly provides insights into the genomic evolution and fruit divergence in wax apple (Syzygium samarangense (Blume) Merr. and Perry)
原文链接：https://doi.org/10.1093/hr/uhad214
微信导读：Hortic Res | 福建省农业科学院果树研究所联合中国农业科学院深圳农业基因组所发表莲雾高质量基因组
工具链接：
https://github.com/BGI-shenzhen/VCF2Dis
http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Gap-free genome assembly and CYP450 gene family analysis reveal the biosynthesis of anthocyanins in Scutellaria baicalensis
原文链接：https://doi.org/10.1093/hr/uhad235
微信导读：Hortic Res | 上海辰山植物园发表黄芩T2T基因组
数据库链接：
Rfam database (https://rfam.org/)
High-quality assembly and methylome of a Tibetan wild tree peony genome (Paeonia ludlowii) reveal the evolution of giant genome architecture
原文链接：https://doi.org/10.1093/hr/uhad241
文章标题翻译：西藏野生牡丹基因组的高质量组装和甲基化揭示了巨大基因组结构的进化
工具链接：
http://www.gpmaw.com/html/swiss-prot.html
