The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development
暂无分享,去创建一个
Jinbo Zhang | Huan Yang | Yi-Zheng Zhang | Honghui Lin | Chunguang Du | F. Lin | Songtao Yang | Lei Zhang | Ji Li | W. Xu | Meifang Peng | Wei Song | Zhongren Zhang | Zhangying Wang | Ming Li | Chang Wei | Kai Wang | Cong Zhang | Z. Pu | W. Tan | S. Qiao | H. Zou | Yan Li | Junyan Feng | A. Liao
[1] G. C. Yencho,et al. Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement , 2018, Nature Communications.
[2] J. Monroe,et al. Review: The Arabidopsis β-amylase (BAM) gene family: Diversity of form and function. , 2018, Plant science : an international journal of experimental plant biology.
[3] David Sankoff,et al. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. , 2018, Nature Genetics.
[4] S. Zhao,et al. Analysis of evolution and genetic diversity of sweetpotato and its related different polyploidy wild species I. trifida using RAD-seq , 2018, BMC Plant Biology.
[5] R. Jarret,et al. Parallel evolution of storage roots in morning glories (Convolvulaceae) , 2018, BMC Plant Biology.
[6] Dong Wang,et al. Starch content differences between two sweet potato accessions are associated with specific changes in gene expression , 2018, Functional & Integrative Genomics.
[7] M. Rausher,et al. Reconciling Conflicting Phylogenies in the Origin of Sweet Potato and Dispersal to Polynesia , 2018, Current Biology.
[8] G. Gheysen,et al. Horizontal Gene Transfer Contributes to Plant Evolution: The Case of Agrobacterium T-DNAs , 2017, Front. Plant Sci..
[9] Martin Vingron,et al. Haplotype-resolved sweet potato genome traces back its hexaploidization history , 2017, Nature Plants.
[10] Kun Lu,et al. Comparative Transcriptome Analysis Reveals Critical Function of Sucrose Metabolism Related-Enzymes in Starch Accumulation in the Storage Root of Sweet Potato , 2017, Front. Plant Sci..
[11] S. Isobe,et al. Challenges to genome sequence dissection in sweetpotato , 2017, Breeding science.
[12] G. Martin,et al. iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases. , 2016, Molecular plant.
[13] H. Zhai,et al. A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition , 2016, BMC Genomics.
[14] Y. Sakakibara,et al. Genome sequence and analysis of the Japanese morning glory Ipomoea nil , 2016, Nature Communications.
[15] Masaru Tanaka. Recent Progress in Molecular Studies on Storage Root Formation in Sweetpotato (Ipomoea batatas) , 2016 .
[16] Sergey Koren,et al. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii , a progenitor of bread wheat , with the mega-reads algorithm , 2016 .
[17] Xingang Li,et al. Construction of a high-density genetic map of Ziziphus jujuba Mill. using genotyping by sequencing technology , 2016, Tree Genetics & Genomes.
[18] J. Weng,et al. Genetic dissection of maize plant architecture with an ultra-high density bin map based on recombinant inbred lines , 2016, BMC Genomics.
[19] Min Zhang,et al. Altered Phenylpropanoid Metabolism in the Maize Lc-Expressed Sweet Potato (Ipomoea batatas) Affects Storage Root Development , 2016, Scientific Reports.
[20] Shucai Wang,et al. Constitutive Expression of OsIAA9 Affects Starch Granules Accumulation and Root Gravitropic Response in Arabidopsis , 2015, Front. Plant Sci..
[21] Evgeny M. Zdobnov,et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..
[22] Xinliang Chen,et al. Temporal patterns of gene expression associated with tuberous root formation and development in sweetpotato (Ipomoea batatas) , 2015, BMC Plant Biology.
[23] A. Xiong,et al. Morphological characteristics, anatomical structure, and gene expression: novel insights into gibberellin biosynthesis and perception during carrot growth and development , 2015, Horticulture Research.
[24] G. C. Yencho,et al. Conventional breeding, marker-assisted selection, genomic selection and inbreeding in clonally propagated crops: a case study for cassava , 2015, Theoretical and Applied Genetics.
[25] R. Jarret,et al. The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop , 2015, Proceedings of the National Academy of Sciences.
[26] S. Tabata,et al. Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don , 2015, DNA research : an international journal for rapid publication of reports on genes and genomes.
[27] J. W. Allwood,et al. Acclimation of metabolism to light in A rabidopsis thaliana: the glucose 6‐phosphate/phosphate translocator GPT2 directs metabolic acclimation , 2015, Plant, cell & environment.
[28] Jayarama,et al. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis , 2014, Science.
[29] Paul Theodor Pyl,et al. HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.
[30] Steven Maere,et al. Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.
[31] H. Zhai,et al. Identification of QTLs for storage root yield in sweetpotato , 2014 .
[32] Tetsuya Hayashi,et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads , 2014, Genome research.
[33] A. M. Kayastha,et al. Β-Amylase from Starchless Seeds of Trigonella Foenum-Graecum and Its Localization in Germinating Seeds , 2014, PloS one.
[34] L. An. The Construction of Genomic Fosmid Library and Library PCR Screening System on Ipomoea trifida( Kunth) G. Don , 2014 .
[35] 李飞,et al. 三个耐冻性不同的马铃薯野生种中 FAD2 基因的克隆及表达分析 , 2013 .
[36] Genoveva Rossel,et al. Disentangling the Origins of Cultivated Sweet Potato (Ipomoea batatas (L.) Lam.) , 2013, PloS one.
[37] D. McKey,et al. Historical collections reveal patterns of diffusion of sweet potato in Oceania obscured by modern plant movements and recombination , 2013, Proceedings of the National Academy of Sciences.
[38] Cole Trapnell,et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.
[39] Katsutoshi Watanabe,et al. A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae) , 2013, BMC Genomics.
[40] R. Gibbs,et al. Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology , 2012, PloS one.
[41] R. Senthilkumar,et al. Multiple biological functions of sporamin related to stress tolerance in sweet potato (Ipomoea batatas Lam). , 2012, Biotechnology advances.
[42] Qiang Wang,et al. The oyster genome reveals stress adaptation and complexity of shell formation , 2012, Nature.
[43] R. Henry,et al. SNP in starch biosynthesis genes associated with nutritional and functional properties of rice , 2012, Scientific Reports.
[44] Guangrui Huang,et al. HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies , 2012, Genome research.
[45] Mingfang Zhang,et al. Starch accumulation and starch related genes expression in novel inter-specific inbred squash line and their parents during fruit development , 2012 .
[46] Jeremy D. DeBarry,et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity , 2012, Nucleic acids research.
[47] J. V. Ooijen,et al. Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. , 2011 .
[48] David M. A. Martin,et al. Genome sequence and analysis of the tuber crop potato , 2011, Nature.
[49] Youzhi Ma,et al. Functions and application of the AP2/ERF transcription factor family in crop improvement. , 2011, Journal of integrative plant biology.
[50] N. Friedman,et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.
[51] J. V. van Ooijen. Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. , 2011, Genetics research.
[52] Zhao-Bang Zeng,et al. Windows QTL Cartographer 2·5 , 2011 .
[53] W. Huber,et al. which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .
[54] J. Shin,et al. SRD1 is involved in the auxin-mediated initial thickening growth of storage root by enhancing proliferation of metaxylem and cambium cells in sweetpotato (Ipomoea batatas) , 2010, Journal of experimental botany.
[55] Huanming Yang,et al. De novo assembly of human genomes with massively parallel short read sequencing. , 2010, Genome research.
[56] R. Sederoff,et al. Towards a systems approach for lignin biosynthesis in Populus trichocarpa: transcript abundance and specificity of the monolignol biosynthetic genes. , 2010, Plant & cell physiology.
[57] V. Njiti,et al. Wx intron variations support an allohexaploid origin of the sweetpotato [Ipomoea batatas (L.) Lam] , 2010, Euphytica.
[58] M. Estelle,et al. Mechanism of auxin-regulated gene expression in plants. , 2009, Annual review of genetics.
[59] A. Meyer,et al. The evolutionary significance of ancient genome duplications , 2009, Nature Reviews Genetics.
[60] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[61] Nansheng Chen,et al. Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences , 2009, Current protocols in bioinformatics.
[62] Haibao Tang,et al. Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. , 2008, Genome research.
[63] M. Nakatani,et al. Expression of class I knotted1-like homeobox genes in the storage roots of sweetpotato (Ipomoea batatas). , 2008, Journal of plant physiology.
[64] K. Yeh,et al. IbMADS1 (Ipomoea batatas MADS-box 1 gene) is Involved in Tuberous Root Initiation in Sweet Potato (Ipomoea batatas) , 2008, Annals of botany.
[65] Robert D Schnabel,et al. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries , 2008, Nature Methods.
[66] Jonathan E. Allen,et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments , 2007, Genome Biology.
[67] Ziheng Yang. PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.
[68] Zhao Xu,et al. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons , 2007, Nucleic Acids Res..
[69] Keith Bradnam,et al. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes , 2007, Bioinform..
[70] B. Sosinski,et al. The effect of replicate number and image analysis method on sweetpotato [Ipomoea batatas (L.) Lam.] cDNA microarray results , 2005, Plant Molecular Biology Reporter.
[71] Enrique Blanco,et al. Using geneid to Identify Genes , 2002, Current protocols in bioinformatics.
[72] Alexandros Stamatakis,et al. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..
[73] Nello Cristianini,et al. CAFE: a computational tool for the study of gene family evolution , 2006, Bioinform..
[74] Burkhard Morgenstern,et al. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources , 2006, BMC Bioinformatics.
[75] Richard G. F. Visser,et al. RECORD: a novel method for ordering loci on a genetic linkage map , 2005, Theoretical and Applied Genetics.
[76] J. Jurka,et al. Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.
[77] Eugene W. Myers,et al. PILER : identification and classification of genomic repeats , 2005 .
[78] Pavel A. Pevzner,et al. De novo identification of repeat families in large genomes , 2005, ISMB.
[79] Steven Salzberg,et al. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders , 2004, Bioinform..
[80] Ian Korf,et al. Gene finding in novel genomes , 2004, BMC Bioinformatics.
[81] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[82] A. Kriegner,et al. A genetic linkage map of sweetpotato [Ipomoea batatas (L.) Lam.] based on AFLP markers , 2003, Molecular Breeding.
[83] K. Yeh,et al. Functional activity of sporamin from sweet potato (Ipomoea batatas Lam.): a tuber storage protein with trypsin inhibitory activity , 1997, Plant Molecular Biology.
[84] I. Nishiyama,et al. Evolutionary autoploidy in the sweet potato (Ipomoea batatas (L.) Lam.) and its progenitors , 1975, Euphytica.
[85] C. Stoeckert,et al. OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.
[86] P. Shewry. Tuber storage proteins. , 2003, Annals of botany.
[87] W. Yi.,et al. β-Amylase Is Predominantly Localized to Plastids in the Developing Tuberous Root of Sweet Potato , 2003 .
[88] L. Jouanin,et al. AtBXL1, a novel higher plant (Arabidopsis thaliana) putative beta-xylosidase gene, is involved in secondary cell wall metabolism and plant development. , 2003, The Plant journal : for cell and molecular biology.
[89] Peer Bork,et al. Systematic identification of novel protein domain families associated with nuclear functions. , 2002, Genome research.
[90] V. Solovyev,et al. Ab initio gene finding in Drosophila genomic DNA. , 2000, Genome research.
[91] K. Katayama,et al. Root Thickness of Diploid lpomoea trifida (H. B. K.) G. Don and Performance of Progeny Derived from the Cross with Sweetpotato , 1999 .
[92] Ziheng Yang,et al. PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..
[93] M. Kitamura,et al. Construction of adenovirus vectors through Cre-lox recombination , 1997, Journal of virology.
[94] J. Woolfe. Sweet Potato: An Untapped Food Resource , 1992 .
[95] I. Shiotani,et al. Genomic Structure of the Sweet Potato and Hexaploids in Ipomoea trifida (H.B.K.) DON. , 1989 .
[96] D. Austin. The Ipomoea batatas complex - I. Taxonomy. , 1978 .
[97] I. Nishiyama. Evolution and Domestication of the Sweet Potato , 1971 .