Author Report for: Bennetzen JLNo contact information in database for Bennetzen JL
Dai X, Liu Y, Zhuang J, Yao S, Liu L, Jiang X, Zhou K, Wang Y, Xie D and Xia T <2 more author(s)> Dai X, Liu Y, Zhuang J, Yao S, Liu L, Jiang X, Zhou K, Wang Y, Xie D, Bennetzen JL, Gao L, Xia T (- 2) Ref: New Phytol, 226:1104, 2020 : PubMed ESTHER: Dai_2020_New.Phytol_226_1104 PubMedSearch: Dai 2020 New.Phytol 226 1104 PubMedID: 32061142 Gene_locus related to this paper: camsi-a0a5b9g8c2, jugre-JrTA, fraan-FaTA, vitvi-VvTA, citcl-CcTA, dioka-DkTA, camsi-CsTA Abstract Plant tannins, including condensed tannins (CTs) and hydrolyzable tannins (HTs), are widely distributed in the plant kingdom. To date, tannase (TA) - is a type of tannin acyl-hydrolase hydrolyzing HTs, CT monomer gallates and depsides - has been reported in microbes only. Whether plants express TA remains unknown. Herein, we report plant TA genes. A native Camellia sinensis TA (CsTA) is identified from leaves. Six TAs are cloned from tea, strawberry (Fragariasxsananassa, Fa) and four other crops. Biochemical analysis shows that the native CsTA and six recombinant TAs hydrolyze tannin compounds, depsides and phenolic glycosides. Transcriptional and metabolic analyses reveal that the expression of CsTA is oppositely associated with the accumulation of galloylated catechins. Moreover, the transient overexpression and RNA interference of FaTA are positively associated with the accumulation of ellagitannins in strawberry fruit. Phylogenetic analysis across different kingdoms shows that 29 plant TA homologs are clustered as a plant-specific TA clade in class I carboxylesterases. Further analysis across the angiosperms reveals that these TA genes are dispersed in tannin-rich plants, which share a single phylogenetic origin c. 120 million yr ago. Plant TA is discovered for the first time in the plant kingdom and is shown to be valuable to improve tannin compositions in plants. Title: A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library Hoffberg SL, Troendle NJ, Glenn TC, Mahmud O, Louha S, Chalopin D, Bennetzen JL, Mauricio R Ref: G3 (Bethesda), 8:1855, 2018 : PubMed ESTHER: Hoffberg_2018_G3.(Bethesda)_8_1855 PubMedSearch: Hoffberg 2018 G3.(Bethesda) 8 1855 PubMedID: 29703783 Gene_locus related to this paper: gamaf-a0a315v5h8, gamaf-a0a315uxq3, gamaf-a0a315vce7, gamaf-a0a315vcq6, gamaf-a0a315vp68, gamaf-a0a315vcr9, gamaf-a0a315v3l0, gamaf-a0a315v4u9 Abstract The western mosquitofish, Gambusia affinis, is a freshwater poecilid fish native to the southeastern United States but with a global distribution due to widespread human introduction. Gambusia affinis has been used as a model species for a broad range of evolutionary and ecological studies. We sequenced the genome of a male G. affinis to facilitate genetic studies in diverse fields including invasion biology and comparative genetics. We generated Illumina short read data from paired-end libraries and in vitro proximity-ligation libraries. We obtained 54.9x coverage, N50 contig length of 17.6 kb, and N50 scaffold length of 6.65 Mb. Compared to two other species in the Poeciliidae family, G. affinis has slightly fewer genes that have shorter total, exon, and intron length on average. Using a set of universal single-copy orthologs in fish genomes, we found 95.5% of these genes were complete in the G. affinis assembly. The number of transposable elements in the G. affinis assembly is similar to those of closely related species. The high-quality genome sequence and annotations we report will be valuable resources for scientists to map the genetic architecture of traits of interest in this species. Title: Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality Wei C, Yang H, Wang S, Zhao J, Liu C, Gao L, Xia E, Lu Y, Tai Y and Wan X <33 more author(s)> Wei C, Yang H, Wang S, Zhao J, Liu C, Gao L, Xia E, Lu Y, Tai Y, She G, Sun J, Cao H, Tong W, Gao Q, Li Y, Deng W, Jiang X, Wang W, Chen Q, Zhang S, Li H, Wu J, Wang P, Li P, Shi C, Zheng F, Jian J, Huang B, Shan D, Shi M, Fang C, Yue Y, Li F, Li D, Wei S, Han B, Jiang C, Yin Y, Xia T, Zhang Z, Bennetzen JL, Zhao S, Wan X (- 33) Ref: Proc Natl Acad Sci U S A, 115:E4151, 2018 : PubMed ESTHER: Wei_2018_Proc.Natl.Acad.Sci.U.S.A_115_E4151 PubMedSearch: Wei 2018 Proc.Natl.Acad.Sci.U.S.A 115 E4151 PubMedID: 29678829 Gene_locus related to this paper: camsi-a0a4s4dr18, camsi-a0a4s4etg9, camsi-a0a4s4e3j5, camsi-a0a4s4d2s5, camsi-a0a4s4duc4, camsi-a0a4v3wr80 Abstract Tea, one of the world's most important beverage crops, provides numerous secondary metabolites that account for its rich taste and health benefits. Here we present a high-quality sequence of the genome of tea, Camellia sinensis var. sinensis (CSS), using both Illumina and PacBio sequencing technologies. At least 64% of the 3.1-Gb genome assembly consists of repetitive sequences, and the rest yields 33,932 high-confidence predictions of encoded proteins. Divergence between two major lineages, CSS and Camellia sinensis var. assamica (CSA), is calculated to approximately 0.38 to 1.54 million years ago (Mya). Analysis of genic collinearity reveals that the tea genome is the product of two rounds of whole-genome duplications (WGDs) that occurred approximately 30 to 40 and approximately 90 to 100 Mya. We provide evidence that these WGD events, and subsequent paralogous duplications, had major impacts on the copy numbers of secondary metabolite genes, particularly genes critical to producing three key quality compounds: catechins, theanine, and caffeine. Analyses of transcriptome and phytochemistry data show that amplification and transcriptional divergence of genes encoding a large acyltransferase family and leucoanthocyanidin reductases are associated with the characteristic young leaf accumulation of monomeric galloylated catechins in tea, while functional divergence of a single member of the glutamine synthetase gene family yielded theanine synthetase. This genome sequence will facilitate understanding of tea genome evolution and tea metabolite pathways, and will promote germplasm utilization for breeding improved tea varieties. Title: New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication Kim S, Park J, Yeom SI, Kim YM, Seo E, Kim KT, Kim MS, Lee JM, Cheong K and Choi D <27 more author(s)> Kim S, Park J, Yeom SI, Kim YM, Seo E, Kim KT, Kim MS, Lee JM, Cheong K, Shin HS, Kim SB, Han K, Lee J, Park M, Lee HA, Lee HY, Lee Y, Oh S, Lee JH, Choi E, Lee SE, Jeon J, Kim H, Choi G, Song H, Lee SC, Kwon JK, Koo N, Hong Y, Kim RW, Kang WH, Huh JH, Kang BC, Yang TJ, Lee YH, Bennetzen JL, Choi D (- 27) Ref: Genome Biol, 18:210, 2017 : PubMed ESTHER: Kim_2017_Genome.Biol_18_210 PubMedSearch: Kim 2017 Genome.Biol 18 210 PubMedID: 29089032 Gene_locus related to this paper: capch-q75qh4, capan-a0a1u8fuf5, capan-a0a1u8gmz3, capch-a0a2g3bqp0, capba-a0a2g2vcw4, capan-a0a1u8flz5, capch-a0a2g3bau3, capch-a0a2g3b6c0, capan-a0a2g2y016, capch-a0a2g3cje8, capba-a0a2g2xr67, capan-a0a1u8fpc9, capan-a0a1u8fqs3, capan-a0a1u8ft99, capan-a0a2g2xtt0, capan-a0a1u8eu02, capan-a0a1u8hd13 Abstract BACKGROUND: Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants. RESULTS: We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific. CONCLUSIONS: Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants. Title: Reference genome sequence of the model plant Setaria Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN and Devos KM <24 more author(s)> Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, Jenkins J, Barry K, Lindquist E, Hellsten U, Deshpande S, Wang X, Wu X, Mitros T, Triplett J, Yang X, Ye CY, Mauro-Herrera M, Wang L, Li P, Sharma M, Sharma R, Ronald PC, Panaud O, Kellogg EA, Brutnell TP, Doust AN, Tuskan GA, Rokhsar D, Devos KM (- 24) Ref: Nat Biotechnol, 30:555, 2012 : PubMed ESTHER: Bennetzen_2012_Nat.Biotechnol_30_555 PubMedSearch: Bennetzen 2012 Nat.Biotechnol 30 555 PubMedID: 22580951 Gene_locus related to this paper: setit-k3xwe0, setit-k3xfs7, setit-k3yh36, setit-k3zes3, setit-k3zlj8, setvi-a0a4u6wd58, setit-a0a368qif6, setit-a0a368sru6, setit-a0a368q9x4, setit-k3zri0, setit-k3ysv0, setit-k3xj49 Abstract We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The approximately 400-Mb assembly covers approximately 80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum). Title: The Selaginella genome identifies genetic changes associated with the evolution of vascular plants Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T and Grigoriev IV <93 more author(s)> Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga S, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riano-Pachon DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Sorensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theissen G, Ulvskov P, Wakazuki S, Weng JK, Willats WW, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loque D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D, Grigoriev IV (- 93) Ref: Science, 332:960, 2011 : PubMed ESTHER: Banks_2011_Science_332_960 PubMedSearch: Banks 2011 Science 332 960 PubMedID: 21551031 Gene_locus related to this paper: selml-d8qua5, selml-d8qva1, selml-d8qyh7, selml-d8qza0, selml-d8r5d4, selml-d8r6d4, selml-d8r504, selml-d8r506, selml-d8rbi1, selml-d8rbs1, selml-d8rck8, selml-d8rf38, selml-d8rkl6, selml-d8rpr1, selml-d8rpy0, selml-d8ru47, selml-d8ry54, selml-d8rzp6, selml-d8rzy7, selml-d8s0c9, selml-d8s0u3, selml-d8s2t1, selml-d8s3z8, selml-d8s401, selml-d8sba6, selml-d8sch9, selml-d8spq2, selml-d8sq37, selml-d8ssx7, selml-d8swp2, selml-d8t7a3, selml-d8t8v4, selml-d8taz4, selml-d8tdq6, selml-d8rai8, selml-d8qt54, selml-d8r2d8, selml-d8rmd3, selml-d8rra9, selml-d8slg4, selml-d8swp0, selml-d8s7i0, selml-d8qz37, selml-d8sz00, selml-d8s776, selml-d8qw15, selml-d8ska7, selml-d8t0c4, selml-d8r194, selml-d8s5m8, selml-d8s7r2, selml-d8ta80 Abstract Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes. Title: Foxtail millet: a sequence-driven grass model system Doust AN, Kellogg EA, Devos KM, Bennetzen JL Ref: Plant Physiol, 149:137, 2009 : PubMed ESTHER: Doust_2009_Plant.Physiol_149_137 PubMedSearch: Doust 2009 Plant.Physiol 149 137 PubMedID: 19126705 Gene_locus related to this paper: setit-k3xif5, setit-k3zcw9, setit-k3xkv4, setit-k3xkx1, setit-k3xl04, setit-k3xl15, setit-k3xl35, setit-k3yv13, setit-k3z8r4, setit-k4aj70, setit-k3z699, setit-k3xhw7, setit-k4aa77, setit-k3xi18, setit-k3xsy6, setit-k3xi59, setit-k3xi65, setit-k3xia2, setit-k3ztq6, setit-k3y7s9, setit-k3xrx3, setit-k3zuh1, setit-k4ac16 Title: The B73 maize genome: complexity, diversity, and dynamics Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L and Wilson RK <147 more author(s)> Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (- 147) Ref: Science, 326:1112, 2009 : PubMed ESTHER: Schnable_2009_Science_326_1112 PubMedSearch: Schnable 2009 Science 326 1112 PubMedID: 19965430 Gene_locus related to this paper: maize-b4ffc7, maize-b6u7e1, maize-c0pcy5, maize-c0pgf7, maize-c0pgw1, maize-c0pfl3, maize-b4fpr7, maize-k7vy73, maize-a0a096swr3, maize-k7v3i9, maize-b6u9v9, maize-a0a3l6e780, maize-b4fv80, maize-a0a1d6nse2, maize-c4j9a1 Abstract We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize. Title: Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set Ammiraju JS, Lu F, Sanyal A, Yu Y, Song X, Jiang N, Pontaroli AC, Rambo T, Currie J and Wing RA <9 more author(s)> Ammiraju JS, Lu F, Sanyal A, Yu Y, Song X, Jiang N, Pontaroli AC, Rambo T, Currie J, Collura K, Talag J, Fan C, Goicoechea JL, Zuccolo A, Chen J, Bennetzen JL, Chen M, Jackson S, Wing RA (- 9) Ref: Plant Cell, 20:3191, 2008 : PubMed ESTHER: Ammiraju_2008_Plant.Cell_20_3191 PubMedSearch: Ammiraju 2008 Plant.Cell 20 3191 PubMedID: 19098269 Abstract Oryza (23 species; 10 genome types) contains the world's most important food crop - rice. Although the rice genome serves as an essential tool for biological research, little is known about the evolution of the other Oryza genome types. They contain a historical record of genomic changes that led to diversification of this genus around the world as well as an untapped reservoir of agriculturally important traits. To investigate the evolution of the collective Oryza genome, we sequenced and compared nine orthologous genomic regions encompassing the Adh1-Adh2 genes (from six diploid genome types) with the rice reference sequence. Our analysis revealed the architectural complexities and dynamic evolution of this region that have occurred over the past approximately 15 million years. Of the 46 intact genes and four pseudogenes in the japonica genome, 38 (76%) fell into eight multigene families. Analysis of the evolutionary history of each family revealed independent and lineage-specific gain and loss of gene family members as frequent causes of synteny disruption. Transposable elements were shown to mediate massive replacement of intergenic space (>95%), gene disruption, and gene/gene fragment movement. Three cases of long-range structural variation (inversions/deletions) spanning several hundred kilobases were identified that contributed significantly to genome diversification. Title: Pathogen corruption and site-directed recombination at a plant disease resistance gene cluster Nagy ED, Bennetzen JL Ref: Genome Res, 18:1918, 2008 : PubMed ESTHER: Nagy_2008_Genome.Res_18_1918 PubMedSearch: Nagy 2008 Genome.Res 18 1918 PubMedID: 18719093 Gene_locus related to this paper: sorbi-b3vtb2 Abstract The Pc locus of sorghum (Sorghum bicolor) determines dominant sensitivity to a host-selective toxin produced by the fungal pathogen Periconia circinata. The Pc region was cloned by a map-based approach and found to contain three tandemly repeated genes with the structures of nucleotide binding site-leucine-rich repeat (NBS-LRR) disease resistance genes. Thirteen independent Pc-to-pc mutations were analyzed, and each was found to remove all or part of the central gene of the threesome. Hence, this central gene is Pc. Most Pc-to-pc mutations were associated with unequal recombination. Eight recombination events were localized to different sites in a 560-bp region within the approximately 3.7-kb NBS-LRR genes. Because any unequal recombination located within the flanking NBS-LRR genes would have removed Pc, the clustering of cross-over events within a 560-bp segment indicates that a site-directed recombination process exists that specifically targets unequal events to generate LRR diversity in NBS-LRR loci. Title: The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA and Boore JL <60 more author(s)> Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin IT, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL (- 60) Ref: Science, 319:64, 2008 : PubMed ESTHER: Rensing_2008_Science_319_64 PubMedSearch: Rensing 2008 Science 319 64 PubMedID: 18079367 Gene_locus related to this paper: phypa-a9rbi6, phypa-a9rfh1, phypa-a9rg19, phypa-a9rgt9, phypa-a9rhz9, phypa-a9rkj1, phypa-a9rns2, phypa-a9rp52, phypa-a9rq03, phypa-a9ry17, phypa-a9ry72, phypa-a9s5n8, phypa-a9s6w1, phypa-a9s8c7, phypa-a9s299, phypa-a9san7, phypa-a9sc75, phypa-a9se75, phypa-a9sg07, phypa-a9skf7, phypa-a9skr1, phypa-a9skw1, phypa-a9sl58, phypa-a9slp7, phypa-a9smq5, phypa-a9sp13, phypa-a9ssb0, phypa-a9sse1, phypa-a9ssf6, phypa-a9st85, phypa-a9sx74, phypa-a9sy58, phypa-a9syy4, phypa-a9t0n4, phypa-a9t0p4, phypa-a9t1j2, phypa-a9t5h1, phypa-a9t7g6, phypa-a9t8u8, phypa-a9t9c9, phypa-a9t9d9, phypa-a0a7i4d2t7, phypa-a9t498, phypa-a9tbu4, phypa-a9tc36, phypa-a9tds0, phypa-a9te64, phypa-a9tfw2, phypa-a9tin6, phypa-a9tja4, phypa-a9tmp3, phypa-a9tmr4, phypa-a9tql4, phypa-a9tr83, phypa-a9tsl1, phypa-a9tsv6, phypa-a9tu05, phypa-a9tw81, phypa-a9tyr8, phypa-a9u0c9, phypa-a9u0k3, phypa-a9u0p4, phypa-a9u2u7, phypa-a9u3s0, phypa-a9tfm7, phypa-a9tfp6, phypa-a9syg9, phypa-a9tzk2, phypa-a9tvg4, phypa-a9t1y4, phypa-a9tqt6, phypa-a9st18, phypa-a9tix9, phypa-a0a2k1kfe3, phypa-a9sqk3, phypa-a0a2k1ie71, phypa-a0a2k1kg29, phypa-a0a2k1iji3 Abstract We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics. Title: Fine mapping of the Pc locus of Sorghum bicolor, a gene controlling the reaction to a fungal pathogen and its host-selective toxin Nagy ED, Lee TC, Ramakrishna W, Xu Z, Klein PE, SanMiguel P, Cheng CP, Li J, Devos KM and Bennetzen JL <2 more author(s)> Nagy ED, Lee TC, Ramakrishna W, Xu Z, Klein PE, SanMiguel P, Cheng CP, Li J, Devos KM, Schertz K, Dunkle L, Bennetzen JL (- 2) Ref: Theor Appl Genet, 114:961, 2007 : PubMed ESTHER: Nagy_2007_Theor.Appl.Genet_114_961 PubMedSearch: Nagy 2007 Theor.Appl.Genet 114 961 PubMedID: 17356869 Gene_locus related to this paper: sorbi-b3vtb2 Abstract Milo disease in sorghum is caused by isolates of the soil-borne fungus Periconia circinata that produce PC-toxin. Susceptibility to milo disease is conditioned by a single, semi-dominant gene, termed Pc. The susceptible allele (Pc) converts to a resistant form (pc) spontaneously at a gametic frequency of 10(-3) to 10(-4). A high-density genetic map was constructed around the Pc locus using DNA markers, allowing the Pc gene to be delimited to a 0.9 cM region on the short arm of sorghum chromosome 9. Physically, the Pc-region was covered by a single BAC clone. Sequence analysis of this BAC revealed twelve gene candidates. Several of the predicted genes in the region are homologous to disease resistance loci, including one NBS-LRR resistance gene analogue that is present in multiple tandem copies. Analysis of pc isolines derived from Pc/Pc sorghum suggests that one or more members of this NBS-LRR gene family are the Pc genes that condition susceptibility. | |||||||
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