Author Report for: Latreille PNo contact information in database for Latreille P
Wu M, McNulty NP, Rodionov DA, Khoroshkin MS, Griffin NW, Cheng J, Latreille P, Kerstetter RA, Terrapon N and Gordon JI <2 more author(s)> Wu M, McNulty NP, Rodionov DA, Khoroshkin MS, Griffin NW, Cheng J, Latreille P, Kerstetter RA, Terrapon N, Henrissat B, Osterman AL, Gordon JI (- 2) Ref: Science, 350:aac5992, 2015 : PubMed ESTHER: Wu_2015_Science_350_AAC5992 PubMedSearch: Wu 2015 Science 350 AAC5992 PubMedID: 26430127 Gene_locus related to this paper: bactn-BT2379, 9bace-a0a0p0g3y7 Abstract Libraries of tens of thousands of transposon mutants generated from each of four human gut Bacteroides strains, two representing the same species, were introduced simultaneously into gnotobiotic mice together with 11 other wild-type strains to generate a 15-member artificial human gut microbiota. Mice received one of two distinct diets monotonously, or both in different ordered sequences. Quantifying the abundance of mutants in different diet contexts allowed gene-level characterization of fitness determinants, niche, stability, and resilience and yielded a prebiotic (arabinoxylan) that allowed targeted manipulation of the community. The approach described is generalizable and should be useful for defining mechanisms critical for sustaining and/or approaches for deliberately reconfiguring the highly adaptive and durable relationship between the human gut microbiota and host in ways that promote wellness. Title: The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes Chaston JM, Suen G, Tucker SL, Andersen AW, Bhasin A, Bode E, Bode HB, Brachmann AO, Cowles CE and Goodrich-Blair H <46 more author(s)> Chaston JM, Suen G, Tucker SL, Andersen AW, Bhasin A, Bode E, Bode HB, Brachmann AO, Cowles CE, Cowles KN, Darby C, de Leon L, Drace K, Du Z, Givaudan A, Herbert Tran EE, Jewell KA, Knack JJ, Krasomil-Osterfeld KC, Kukor R, Lanois A, Latreille P, Leimgruber NK, Lipke CM, Liu R, Lu X, Martens EC, Marri PR, Medigue C, Menard ML, Miller NM, Morales-Soto N, Norton S, Ogier JC, Orchard SS, Park D, Park Y, Qurollo BA, Sugar DR, Richards GR, Rouy Z, Slominski B, Slominski K, Snyder H, Tjaden BC, van der Hoeven R, Welch RD, Wheeler C, Xiang B, Barbazuk B, Gaudriault S, Goodner B, Slater SC, Forst S, Goldman BS, Goodrich-Blair H (- 46) Ref: PLoS ONE, 6:e27909, 2011 : PubMed ESTHER: Chaston_2011_PLoS.ONE_6_e27909 PubMedSearch: Chaston 2011 PLoS.ONE 6 e27909 PubMedID: 22125637 Gene_locus related to this paper: xenna-d3vdr8, xenne-n1nl20, xenbs-d3v2h2 Abstract Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms. We posited that these differences would be reflected in their respective genomes. To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004. As expected, both Xenorhabdus genomes encode many anti-insecticidal compounds, commensurate with their entomopathogenic lifestyle. Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence. These findings indicate that evolutionary changes shaped by symbiotic interactions can follow different routes to achieve similar end points. Title: Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes Setubal JC, dos Santos P, Goldman BS, Ertesvag H, Espin G, Rubio LM, Valla S, Almeida NF, Balasubramanian D and Wood D <34 more author(s)> Setubal JC, dos Santos P, Goldman BS, Ertesvag H, Espin G, Rubio LM, Valla S, Almeida NF, Balasubramanian D, Cromes L, Curatti L, Du Z, Godsy E, Goodner B, Hellner-Burris K, Hernandez JA, Houmiel K, Imperial J, Kennedy C, Larson TJ, Latreille P, Ligon LS, Lu J, Maerk M, Miller NM, Norton S, O'Carroll IP, Paulsen I, Raulfs EC, Roemer R, Rosser J, Segura D, Slater S, Stricklin SL, Studholme DJ, Sun J, Viana CJ, Wallin E, Wang B, Wheeler C, Zhu H, Dean DR, Dixon R, Wood D (- 34) Ref: Journal of Bacteriology, 191:4534, 2009 : PubMed ESTHER: Setubal_2009_J.Bacteriol_191_4534 PubMedSearch: Setubal 2009 J.Bacteriol 191 4534 PubMedID: 19429624 Gene_locus related to this paper: azovd-c1dex6, azovd-c1df21, azovd-c1dfb5, azovd-c1dg75, azovd-c1dgm6, azovd-c1dh91, azovd-c1di03, azovd-c1dib3, azovd-c1dif2, azovd-c1dIq5, azovd-c1dir1, azovd-c1dis2, azovd-c1djq5, azovd-c1djw3, azovd-c1dk37, azovd-c1dkb2, azovd-c1dkj0, azovd-c1dli6, azovd-c1dng8, azovd-c1dni5, azovd-c1dpr0, azovd-c1dqu3, azovd-c1dri5, azovd-c1drx0, azovd-c1dsl7, azovd-c1dsq7, azovd-c1dss1, azovd-metx, azovi-PHBC, azovd-c1dem4 Abstract Azotobacter vinelandii is a soil bacterium related to the Pseudomonas genus that fixes nitrogen under aerobic conditions while simultaneously protecting nitrogenase from oxygen damage. In response to carbon availability, this organism undergoes a simple differentiation process to form cysts that are resistant to drought and other physical and chemical agents. Here we report the complete genome sequence of A. vinelandii DJ, which has a single circular genome of 5,365,318 bp. In order to reconcile an obligate aerobic lifestyle with exquisitely oxygen-sensitive processes, A. vinelandii is specialized in terms of its complement of respiratory proteins. It is able to produce alginate, a polymer that further protects the organism from excess exogenous oxygen, and it has multiple duplications of alginate modification genes, which may alter alginate composition in response to oxygen availability. The genome analysis identified the chromosomal locations of the genes coding for the three known oxygen-sensitive nitrogenases, as well as genes coding for other oxygen-sensitive enzymes, such as carbon monoxide dehydrogenase and formate dehydrogenase. These findings offer new prospects for the wider application of A. vinelandii as a host for the production and characterization of oxygen-sensitive proteins. Title: Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut Samuel BS, Hansen EE, Manchester JK, Coutinho PM, Henrissat B, Fulton R, Latreille P, Kim K, Wilson RK, Gordon JI Ref: Proc Natl Acad Sci U S A, 104:10643, 2007 : PubMed ESTHER: Samuel_2007_Proc.Natl.Acad.Sci.U.S.A_104_10643 PubMedSearch: Samuel 2007 Proc.Natl.Acad.Sci.U.S.A 104 10643 PubMedID: 17563350 Gene_locus related to this paper: mets3-a5ujk2, metsm-d2zrn4 Abstract The human gut is home to trillions of microbes, thousands of bacterial phylotypes, as well as hydrogen-consuming methanogenic archaea. Studies in gnotobiotic mice indicate that Methanobrevibacter smithii, the dominant archaeon in the human gut ecosystem, affects the specificity and efficiency of bacterial digestion of dietary polysaccharides, thereby influencing host calorie harvest and adiposity. Metagenomic studies of the gut microbial communities of genetically obese mice and their lean littermates have shown that the former contain an enhanced representation of genes involved in polysaccharide degradation, possess more archaea, and exhibit a greater capacity to promote adiposity when transplanted into germ-free recipients. These findings have led to the hypothesis that M. smithii may be a therapeutic target for reducing energy harvest in obese humans. To explore this possibility, we have sequenced its 1,853,160-bp genome and compared it to other human gut-associated M. smithii strains and other Archaea. We have also examined M. smithii's transcriptome and metabolome in gnotobiotic mice that do or do not harbor Bacteroides thetaiotaomicron, a prominent saccharolytic bacterial member of our gut microbiota. Our results indicate that M. smithii is well equipped to persist in the distal intestine through (i) production of surface glycans resembling those found in the gut mucosa, (ii) regulated expression of adhesin-like proteins, (iii) consumption of a variety of fermentation products produced by saccharolytic bacteria, and (iv) effective competition for nitrogenous nutrient pools. These findings provide a framework for designing strategies to change the representation and/or properties of M. smithii in the human gut microbiota. Title: Evolution of symbiotic bacteria in the distal human intestine Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM, Minx P and Gordon JI <9 more author(s)> Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM, Minx P, Latreille P, Cordum H, Van Brunt A, Kim K, Fulton RS, Fulton LA, Clifton SW, Wilson RK, Knight RD, Gordon JI (- 9) Ref: PLoS Biol, 5:e156, 2007 : PubMed ESTHER: Xu_2007_PLoS.Biol_5_e156 PubMedSearch: Xu 2007 PLoS.Biol 5 e156 PubMedID: 17579514 Gene_locus related to this paper: 9bace-b6w170, 9bace-c6z6f2, 9bace-e1z049, 9porp-c7xbp3, 9porp-c7xci2, 9porp-c7xdx2, bacv8-a6kwf6, bacv8-a6kzc1, bacv8-a6kze8, bacv8-a6l0d9, bacv8-a6l1d0, bacv8-a6l1u9, bacv8-a6l7p9, bacv8-a6l7w1, bacv8-a6l018, bacv8-a6l378, bacv8-a6l415, bacv8-a6l715, pard8-a6lc23, pard8-a6lca7, pard8-a6ld87, pard8-a6le10, pard8-a6le63, pard8-a6lfj2, pard8-a6lgh2, pard8-a6lgi6, pard8-a6lgn7, pard8-a6lhe1, pard8-a6li91, bacv8-a6l3w9 Abstract The adult human intestine contains trillions of bacteria, representing hundreds of species and thousands of subspecies. Little is known about the selective pressures that have shaped and are shaping this community's component species, which are dominated by members of the Bacteroidetes and Firmicutes divisions. To examine how the intestinal environment affects microbial genome evolution, we have sequenced the genomes of two members of the normal distal human gut microbiota, Bacteroides vulgatus and Bacteroides distasonis, and by comparison with the few other sequenced gut and non-gut Bacteroidetes, analyzed their niche and habitat adaptations. The results show that lateral gene transfer, mobile elements, and gene amplification have played important roles in affecting the ability of gut-dwelling Bacteroidetes to vary their cell surface, sense their environment, and harvest nutrient resources present in the distal intestine. Our findings show that these processes have been a driving force in the adaptation of Bacteroidetes to the distal gut environment, and emphasize the importance of considering the evolution of humans from an additional perspective, namely the evolution of our microbiomes. Title: Generation and annotation of the DNA sequences of human chromosomes 2 and 4 Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K and Wilson RK <111 more author(s)> Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Kremitzki C, Oddy L, Du H, Sun H, Bradshaw-Cordum H, Ali J, Carter J, Cordes M, Harris A, Isak A, Van Brunt A, Nguyen C, Du F, Courtney L, Kalicki J, Ozersky P, Abbott S, Armstrong J, Belter EA, Caruso L, Cedroni M, Cotton M, Davidson T, Desai A, Elliott G, Erb T, Fronick C, Gaige T, Haakenson W, Haglund K, Holmes A, Harkins R, Kim K, Kruchowski SS, Strong CM, Grewal N, Goyea E, Hou S, Levy A, Martinka S, Mead K, McLellan MD, Meyer R, Randall-Maher J, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Shah N, Swearengen-Shahid S, Snider J, Strong JT, Thompson J, Yoakum M, Leonard S, Pearman C, Trani L, Radionenko M, Waligorski JE, Wang C, Rock SM, Tin-Wollam AM, Maupin R, Latreille P, Wendl MC, Yang SP, Pohl C, Wallis JW, Spieth J, Bieri TA, Berkowicz N, Nelson JO, Osborne J, Ding L, Sabo A, Shotland Y, Sinha P, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Jones TA, She X, Ciccarelli FD, Izaurralde E, Taylor J, Schmutz J, Myers RM, Cox DR, Huang X, McPherson JD, Mardis ER, Clifton SW, Warren WC, Chinwalla AT, Eddy SR, Marra MA, Ovcharenko I, Furey TS, Miller W, Eichler EE, Bork P, Suyama M, Torrents D, Waterston RH, Wilson RK (- 111) Ref: Nature, 434:724, 2005 : PubMed ESTHER: Hillier_2005_Nature_434_724 PubMedSearch: Hillier 2005 Nature 434 724 PubMedID: 15815621 Gene_locus related to this paper: human-ABHD1, human-LDAH, human-ABHD18, human-KANSL3, human-PGAP1, human-PREPL Abstract Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions. Title: Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid McClelland M, Sanderson KE, Clifton SW, Latreille P, Porwollik S, Sabo A, Meyer R, Bieri T, Ozersky P and Wilson RK <25 more author(s)> McClelland M, Sanderson KE, Clifton SW, Latreille P, Porwollik S, Sabo A, Meyer R, Bieri T, Ozersky P, McLellan M, Harkins CR, Wang C, Nguyen C, Berghoff A, Elliott G, Kohlberg S, Strong C, Du F, Carter J, Kremizki C, Layman D, Leonard S, Sun H, Fulton L, Nash W, Miner T, Minx P, Delehaunty K, Fronick C, Magrini V, Nhan M, Warren W, Florea L, Spieth J, Wilson RK (- 25) Ref: Nat Genet, 36:1268, 2004 : PubMed ESTHER: McClelland_2004_Nat.Genet_36_1268 PubMedSearch: McClelland 2004 Nat.Genet 36 1268 PubMedID: 15531882 Gene_locus related to this paper: salen-OPDB, salty-AES, salty-BIOH, salty-DLHH, salty-ENTF, salty-FES, salty-IROD, salty-IROE, salty-P74847, salty-PLDB, salty-STM2547, salty-STM4506, salty-STY1441, salty-STY2428, salty-STY3846, salty-yafa, salty-YBFF, salty-ycfp, salty-YFBB, salty-YHET, salty-YQIA Abstract Salmonella enterica serovars often have a broad host range, and some cause both gastrointestinal and systemic disease. But the serovars Paratyphi A and Typhi are restricted to humans and cause only systemic disease. It has been estimated that Typhi arose in the last few thousand years. The sequence and microarray analysis of the Paratyphi A genome indicates that it is similar to the Typhi genome but suggests that it has a more recent evolutionary origin. Both genomes have independently accumulated many pseudogenes among their approximately 4,400 protein coding sequences: 173 in Paratyphi A and approximately 210 in Typhi. The recent convergence of these two similar genomes on a similar phenotype is subtly reflected in their genotypes: only 30 genes are degraded in both serovars. Nevertheless, these 30 genes include three known to be important in gastroenteritis, which does not occur in these serovars, and four for Salmonella-translocated effectors, which are normally secreted into host cells to subvert host functions. Loss of function also occurs by mutation in different genes in the same pathway (e.g., in chemotaxis and in the production of fimbriae). Title: The DNA sequence of human chromosome 7 Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S and Wilson RK <97 more author(s)> Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK (- 97) Ref: Nature, 424:157, 2003 : PubMed ESTHER: Hillier_2003_Nature_424_157 PubMedSearch: Hillier 2003 Nature 424 157 PubMedID: 12853948 Gene_locus related to this paper: human-ABHD11, human-ACHE, human-CPVL, human-DPP6, human-MEST Abstract Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated with various forms of cancer. Here we present more than 153 million base pairs representing 99.4% of the euchromatic sequence of chromosome 7, the first metacentric chromosome completed so far. The sequence has excellent concordance with previously established physical and genetic maps, and it exhibits an unusual amount of segmentally duplicated sequence (8.2%), with marked differences between the two arms. Our initial analyses have identified 1,150 protein-coding genes, 605 of which have been confirmed by complementary DNA sequences, and an additional 941 pseudogenes. Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame. Title: Complete genome sequence of Salmonella enterica serovar Typhimurium LT2 McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M and Wilson RK <16 more author(s)> McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M, Du F, Hou S, Layman D, Leonard S, Nguyen C, Scott K, Holmes A, Grewal N, Mulvaney E, Ryan E, Sun H, Florea L, Miller W, Stoneking T, Nhan M, Waterston R, Wilson RK (- 16) Ref: Nature, 413:852, 2001 : PubMed ESTHER: McClelland_2001_Nature_413_852 PubMedSearch: McClelland 2001 Nature 413 852 PubMedID: 11677609 Gene_locus related to this paper: salen-OPDB, salti-q8z717, salty-AES, salty-BIOH, salty-ENTF, salty-FES, salty-IROD, salty-IROE, salty-P74847, salty-PLDB, salty-STM0332, salty-STM2547, salty-STM3079, salty-STM4506, salty-STY1441, salty-STY2428, salty-STY3846, salty-yafa, salty-YBFF, salty-ycfp, salty-YFBB, salty-YHET, salty-YJFP, salty-YQIA Abstract Salmonella enterica subspecies I, serovar Typhimurium (S. typhimurium), is a leading cause of human gastroenteritis, and is used as a mouse model of human typhoid fever. The incidence of non-typhoid salmonellosis is increasing worldwide, causing millions of infections and many deaths in the human population each year. Here we sequenced the 4,857-kilobase (kb) chromosome and 94-kb virulence plasmid of S. typhimurium strain LT2. The distribution of close homologues of S. typhimurium LT2 genes in eight related enterobacteria was determined using previously completed genomes of three related bacteria, sample sequencing of both S. enterica serovar Paratyphi A (S. paratyphi A) and Klebsiella pneumoniae, and hybridization of three unsequenced genomes to a microarray of S. typhimurium LT2 genes. Lateral transfer of genes is frequent, with 11% of the S. typhimurium LT2 genes missing from S. enterica serovar Typhi (S. typhi), and 29% missing from Escherichia coli K12. The 352 gene homologues of S. typhimurium LT2 confined to subspecies I of S. enterica-containing most mammalian and bird pathogens-are useful for studies of epidemiology, host specificity and pathogenesis. Most of these homologues were previously unknown, and 50 may be exported to the periplasm or outer membrane, rendering them accessible as therapeutic or vaccine targets. Title: Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana Tabata S, Kaneko T, Nakamura Y, Kotani H, Kato T, Asamizu E, Miyajima N, Sasamoto S, Kimura T and Fransz P <119 more author(s)> Tabata S, Kaneko T, Nakamura Y, Kotani H, Kato T, Asamizu E, Miyajima N, Sasamoto S, Kimura T, Hosouchi T, Kawashima K, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakayama S, Nakazaki N, Naruo K, Okumura S, Shinpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Sato S, de la Bastide M, Huang E, Spiegel L, Gnoj L, O'Shaughnessy A, Preston R, Habermann K, Murray J, Johnson D, Rohlfing T, Nelson J, Stoneking T, Pepin K, Spieth J, Sekhon M, Armstrong J, Becker M, Belter E, Cordum H, Cordes M, Courtney L, Courtney W, Dante M, Du H, Edwards J, Fryman J, Haakensen B, Lamar E, Latreille P, Leonard S, Meyer R, Mulvaney E, Ozersky P, Riley A, Strowmatt C, Wagner-McPherson C, Wollam A, Yoakum M, Bell M, Dedhia N, Parnell L, Shah R, Rodriguez M, See LH, Vil D, Baker J, Kirchoff K, Toth K, King L, Bahret A, Miller B, Marra M, Martienssen R, McCombie WR, Wilson RK, Murphy G, Bancroft I, Volckaert G, Wambutt R, Dusterhoft A, Stiekema W, Pohl T, Entian KD, Terryn N, Hartley N, Bent E, Johnson S, Langham SA, McCullagh B, Robben J, Grymonprez B, Zimmermann W, Ramsperger U, Wedler H, Balke K, Wedler E, Peters S, van Staveren M, Dirkse W, Mooijman P, Lankhorst RK, Weitzenegger T, Bothe G, Rose M, Hauf J, Berneiser S, Hempel S, Feldpausch M, Lamberth S, Villarroel R, Gielen J, Ardiles W, Bents O, Lemcke K, Kolesov G, Mayer K, Rudd S, Schoof H, Schueller C, Zaccaria P, Mewes HW, Bevan M, Fransz P (- 119) Ref: Nature, 408:823, 2000 : PubMed ESTHER: Tabata_2000_Nature_408_823 PubMedSearch: Tabata 2000 Nature 408 823 PubMedID: 11130714 Gene_locus related to this paper: arath-At5g11650, arath-At5g16120, arath-at5g18630, arath-AT5G20520, arath-At5g21950, arath-AT5G27320, arath-CXE15, arath-F1N13.220, arath-F14F8.240, arath-q3e9e4, arath-q8lae9, arath-Q8LFB7, arath-q9ffg7, arath-q9fij5, arath-Q9LVU7, arath-q66gm8, arath-SCPL34, arath-B9DFR3, arath-a0a1p8bcz0 Abstract The genome of the model plant Arabidopsis thaliana has been sequenced by an international collaboration, The Arabidopsis Genome Initiative. Here we report the complete sequence of chromosome 5. This chromosome is 26 megabases long; it is the second largest Arabidopsis chromosome and represents 21% of the sequenced regions of the genome. The sequence of chromosomes 2 and 4 have been reported previously and that of chromosomes 1 and 3, together with an analysis of the complete genome sequence, are reported in this issue. Analysis of the sequence of chromosome 5 yields further insights into centromere structure and the sequence determinants of heterochromatin condensation. The 5,874 genes encoded on chromosome 5 reveal several new functions in plants, and the patterns of gene organization provide insights into the mechanisms and extent of genome evolution in plants. Title: The DNA sequence of human chromosome 22 Dunham I, Hunt AR, Collins JE, Bruskiewich R, Beare DM, Clamp M, Smink LJ, Ainscough R, Almeida JP and O'Brien KP <207 more author(s)> Dunham I, Hunt AR, Collins JE, Bruskiewich R, Beare DM, Clamp M, Smink LJ, Ainscough R, Almeida JP, Babbage AK, Bagguley C, Bailey J, Barlow KF, Bates KN, Beasley OP, Bird CP, Blakey SE, Bridgeman AM, Buck D, Burgess J, Burrill WD, Burton J, Carder C, Carter NP, Chen Y, Clark G, Clegg SM, Cobley VE, Cole CG, Collier RE, Connor R, Conroy D, Corby NR, Coville GJ, Cox AV, Davis J, Dawson E, Dhami PD, Dockree C, Dodsworth SJ, Durbin RM, Ellington AG, Evans KL, Fey JM, Fleming K, French L, Garner AA, Gilbert JGR, Goward ME, Grafham DV, Griffiths MND, Hall C, Hall RE, Hall-Tamlyn G, Heathcott RW, Ho S, Holmes S, Hunt SE, Jones MC, Kershaw J, Kimberley AM, King A, Laird GK, Langford CF, Leversha MA, Lloyd C, Lloyd DM, Martyn ID, Mashreghi-Mohammadi M, Matthews LH, Mccann OT, Mcclay J, Mclaren S, McMurray AA, Milne SA, Mortimore BJ, Odell CN, Pavitt R, Pearce AV, Pearson D, Phillimore BJCT, Phillips SH, Plumb RW, Ramsay H, Ramsey Y, Rogers L, Ross MT, Scott CE, Sehra HK, Skuce CD, Smalley S, Smith ML, Soderlund C, Spragon L, Steward CA, Sulston JE, Swann RM, Vaudin M, Wall M, Wallis JM, Whiteley MN, Willey DL, Williams L, Williams SA, Williamson H, Wilmer TE, Wilming L, Wright CL, Hubbard T, Bentley DR, Beck S, Rogers J, Shimizu N, Minoshima S, Kawasaki K, Sasaki T, Asakawa S, Kudoh J, Shintani A, Shibuya K, Yoshizaki Y, Aoki N, Mitsuyama S, Roe BA, Chen F, Chu L, Crabtree J, Deschamps S, Do A, Do T, Dorman A, Fang F, Fu Y, Hu P, Hua A, Kenton S, Lai H, Lao HI, Lewis J, Lewis S, Lin S-P, Loh P, Malaj E, Nguyen T, Pan H, Phan S, Qi S, Qian Y, Ray L, Ren Q, Shaull S, Sloan D, Song L, Wang Q, Wang Y, Wang Z, White J, Willingham D, Wu H, Yao Z, Zhan M, Zhang G, Chissoe S, Murray J, Miller N, Minx P, Fulton R, Johnson D, Bemis G, Bentley D, Bradshaw H, Bourne S, Cordes M, Du Z, Fulton L, Goela D, Graves T, Hawkins J, Hinds K, Kemp K, Latreille P, Layman D, Ozersky P, Rohlfing T, Scheet P, Walker C, Wamsley A, Wohldmann P, Pepin K, Nelson J, Korf I, Bedell JA, Hillier L, Mardis E, Waterston R, Wilson R, Emanuel BS, Shaikh T, Kurahashi H, Saitta S, Budarf ML, McDermid HE, Johnson A, Wong ACC, Morrow BE, Edelmann L, Kim UJ, Shizuya H, Simon MI, Dumanski JP, Peyrard M, Kedra D, Seroussi E, Fransson I, Tapia I, Bruder CE, O'Brien KP (- 207) Ref: Nature, 402:489, 1999 : PubMed ESTHER: Dunham_1999_Nature_402_489 PubMedSearch: Dunham 1999 Nature 402 489 PubMedID: 10591208 Gene_locus related to this paper: human-CES5A, human-SERHL2 Abstract Knowledge of the complete genomic DNA sequence of an organism allows a systematic approach to defining its genetic components. The genomic sequence provides access to the complete structures of all genes, including those without known function, their control elements, and, by inference, the proteins they encode, as well as all other biologically important sequences. Furthermore, the sequence is a rich and permanent source of information for the design of further biological studies of the organism and for the study of evolution through cross-species sequence comparison. The power of this approach has been amply demonstrated by the determination of the sequences of a number of microbial and model organisms. The next step is to obtain the complete sequence of the entire human genome. Here we report the sequence of the euchromatic part of human chromosome 22. The sequence obtained consists of 12 contiguous segments spanning 33.4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome. Title: Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana Mayer K, Schuller C, Wambutt R, Murphy G, Volckaert G, Pohl T, Dusterhoft A, Stiekema W, Entian KD and McCombie WR <220 more author(s)> Mayer K, Schuller C, Wambutt R, Murphy G, Volckaert G, Pohl T, Dusterhoft A, Stiekema W, Entian KD, Terryn N, Harris B, Ansorge W, Brandt P, Grivell L, Rieger M, Weichselgartner M, de Simone V, Obermaier B, Mache R, Muller M, Kreis M, Delseny M, Puigdomenech P, Watson M, Schmidtheini T, Reichert B, Portatelle D, Perez-Alonso M, Boutry M, Bancroft I, Vos P, Hoheisel J, Zimmermann W, Wedler H, Ridley P, Langham SA, McCullagh B, Bilham L, Robben J, Van der Schueren J, Grymonprez B, Chuang YJ, Vandenbussche F, Braeken M, Weltjens I, Voet M, Bastiaens I, Aert R, Defoor E, Weitzenegger T, Bothe G, Ramsperger U, Hilbert H, Braun M, Holzer E, Brandt A, Peters S, van Staveren M, Dirske W, Mooijman P, Klein Lankhorst R, Rose M, Hauf J, Kotter P, Berneiser S, Hempel S, Feldpausch M, Lamberth S, Van den Daele H, De Keyser A, Buysshaert C, Gielen J, Villarroel R, De Clercq R, van Montagu M, Rogers J, Cronin A, Quail M, Bray-Allen S, Clark L, Doggett J, Hall S, Kay M, Lennard N, McLay K, Mayes R, Pettett A, Rajandream MA, Lyne M, Benes V, Rechmann S, Borkova D, Blocker H, Scharfe M, Grimm M, Lohnert TH, Dose S, de Haan M, Maarse A, Schafer M, Muller-Auer S, Gabel C, Fuchs M, Fartmann B, Granderath K, Dauner D, Herzl A, Neumann S, Argiriou A, Vitale D, Liguori R, Piravandi E, Massenet O, Quigley F, Clabauld G, Mundlein A, Felber R, Schnabl S, Hiller R, Schmidt W, Lecharny A, Aubourg S, Chefdor F, Cooke R, Berger C, Montfort A, Casacuberta E, Gibbons T, Weber N, Vandenbol M, Bargues M, Terol J, Torres A, Perez-Perez A, Purnelle B, Bent E, Johnson S, Tacon D, Jesse T, Heijnen L, Schwarz S, Scholler P, Heber S, Francs P, Bielke C, Frishman D, Haase D, Lemcke K, Mewes HW, Stocker S, Zaccaria P, Bevan M, Wilson RK, de la Bastide M, Habermann K, Parnell L, Dedhia N, Gnoj L, Schutz K, Huang E, Spiegel L, Sehkon M, Murray J, Sheet P, Cordes M, Abu-Threideh J, Stoneking T, Kalicki J, Graves T, Harmon G, Edwards J, Latreille P, Courtney L, Cloud J, Abbott A, Scott K, Johnson D, Minx P, Bentley D, Fulton B, Miller N, Greco T, Kemp K, Kramer J, Fulton L, Mardis E, Dante M, Pepin K, Hillier L, Nelson J, Spieth J, Ryan E, Andrews S, Geisel C, Layman D, Du H, Ali J, Berghoff A, Jones K, Drone K, Cotton M, Joshu C, Antonoiu B, Zidanic M, Strong C, Sun H, Lamar B, Yordan C, Ma P, Zhong J, Preston R, Vil D, Shekher M, Matero A, Shah R, Swaby IK, O'Shaughnessy A, Rodriguez M, Hoffmann J, Till S, Granat S, Shohdy N, Hasegawa A, Hameed A, Lodhi M, Johnson A, Chen E, Marra M, Martienssen R, McCombie WR (- 220) Ref: Nature, 402:769, 1999 : PubMed ESTHER: Mayer_1999_Nature_402_769 PubMedSearch: Mayer 1999 Nature 402 769 PubMedID: 10617198 Gene_locus related to this paper: arath-AT4G00500, arath-AT4G16690, arath-AT4G17480, arath-AT4G24380, arath-AT4g30610, arath-o65513, arath-o65713, arath-LPAAT, arath-f4jt64 Abstract The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins. | |||||||
|
