Lamerdin J

References (6)

Title : The DNA sequence and biology of human chromosome 19 - Grimwood_2004_Nature_428_529
Author(s) : Grimwood J , Gordon LA , Olsen A , Terry A , Schmutz J , Lamerdin J , Hellsten U , Goodstein D , Couronne O , Tran-Gyamfi M , Aerts A , Altherr M , Ashworth L , Bajorek E , Black S , Branscomb E , Caenepeel S , Carrano A , Caoile C , Chan YM , Christensen M , Cleland CA , Copeland A , Dalin E , Dehal P , Denys M , Detter JC , Escobar J , Flowers D , Fotopulos D , Garcia C , Georgescu AM , Glavina T , Gomez M , Gonzales E , Groza M , Hammon N , Hawkins T , Haydu L , Ho I , Huang W , Israni S , Jett J , Kadner K , Kimball H , Kobayashi A , Larionov V , Leem SH , Lopez F , Lou Y , Lowry S , Malfatti S , Martinez D , McCready P , Medina C , Morgan J , Nelson K , Nolan M , Ovcharenko I , Pitluck S , Pollard M , Popkie AP , Predki P , Quan G , Ramirez L , Rash S , Retterer J , Rodriguez A , Rogers S , Salamov A , Salazar A , She X , Smith D , Slezak T , Solovyev V , Thayer N , Tice H , Tsai M , Ustaszewska A , Vo N , Wagner M , Wheeler J , Wu K , Xie G , Yang J , Dubchak I , Furey TS , DeJong P , Dickson M , Gordon D , Eichler EE , Pennacchio LA , Richardson P , Stubbs L , Rokhsar DS , Myers RM , Rubin EM , Lucas SM
Ref : Nature , 428 :529 , 2004
Abstract : Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high G + C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9% of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in mendelian disorders, including familial hypercholesterolaemia and insulin-resistant diabetes. Nearly one-quarter of these genes belong to tandemly arranged families, encompassing more than 25% of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu.
ESTHER : Grimwood_2004_Nature_428_529
PubMedSearch : Grimwood_2004_Nature_428_529
PubMedID: 15057824

Title : Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis - Chain_2004_Proc.Natl.Acad.Sci.U.S.A_101_13826
Author(s) : Chain PS , Carniel E , Larimer FW , Lamerdin J , Stoutland PO , Regala WM , Georgescu AM , Vergez LM , Land ML , Motin VL , Brubaker RR , Fowler J , Hinnebusch J , Marceau M , Medigue C , Simonet M , Chenal-Francisque V , Souza B , Dacheux D , Elliott JM , Derbise A , Hauser LJ , Garcia E
Ref : Proc Natl Acad Sci U S A , 101 :13826 , 2004
Abstract : Yersinia pestis, the causative agent of plague, is a highly uniform clone that diverged recently from the enteric pathogen Yersinia pseudotuberculosis. Despite their close genetic relationship, they differ radically in their pathogenicity and transmission. Here, we report the complete genomic sequence of Y. pseudotuberculosis IP32953 and its use for detailed genome comparisons with available Y. pestis sequences. Analyses of identified differences across a panel of Yersinia isolates from around the world reveal 32 Y. pestis chromosomal genes that, together with the two Y. pestis-specific plasmids, to our knowledge, represent the only new genetic material in Y. pestis acquired since the the divergence from Y. pseudotuberculosis. In contrast, 149 other pseudogenes (doubling the previous estimate) and 317 genes absent from Y. pestis were detected, indicating that as many as 13% of Y. pseudotuberculosis genes no longer function in Y. pestis. Extensive insertion sequence-mediated genome rearrangements and reductive evolution through massive gene loss, resulting in elimination and modification of preexisting gene expression pathways, appear to be more important than acquisition of genes in the evolution of Y. pestis. These results provide a sobering example of how a highly virulent epidemic clone can suddenly emerge from a less virulent, closely related progenitor.
ESTHER : Chain_2004_Proc.Natl.Acad.Sci.U.S.A_101_13826
PubMedSearch : Chain_2004_Proc.Natl.Acad.Sci.U.S.A_101_13826
PubMedID: 15358858
Gene_locus related to this paper: yerpe-BIOH , yerpe-dlhh , yerpe-IRP1 , yerpe-PIP , yerpe-PLDB , yerpe-PTRB , yerpe-Y0507 , yerpe-Y0644 , yerpe-y1616 , yerpe-y3224 , yerpe-YBTT , yerpe-YPLA , yerpe-YPO0180 , yerpe-YPO0667 , yerpe-YPO0773 , yerpe-YPO0776 , yerpe-YPO0986 , yerpe-YPO1501 , yerpe-YPO1997 , yerpe-YPO2002 , yerpe-YPO2336 , yerpe-YPO2526 , yerpe-YPO2638 , yerpe-YPO2814

Title : Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris - Larimer_2004_Nat.Biotechnol_22_55
Author(s) : Larimer FW , Chain P , Hauser L , Lamerdin J , Malfatti S , Do L , Land ML , Pelletier DA , Beatty JT , Lang AS , Tabita FR , Gibson JL , Hanson TE , Bobst C , Torres JL , Peres C , Harrison FH , Gibson J , Harwood CS
Ref : Nat Biotechnol , 22 :55 , 2004
Abstract : Rhodopseudomonas palustris is among the most metabolically versatile bacteria known. It uses light, inorganic compounds, or organic compounds, for energy. It acquires carbon from many types of green plant-derived compounds or by carbon dioxide fixation, and it fixes nitrogen. Here we describe the genome sequence of R. palustris, which consists of a 5,459,213-base-pair (bp) circular chromosome with 4,836 predicted genes and a plasmid of 8,427 bp. The sequence reveals genes that confer a remarkably large number of options within a given type of metabolism, including three nitrogenases, five benzene ring cleavage pathways and four light harvesting 2 systems. R. palustris encodes 63 signal transduction histidine kinases and 79 response regulator receiver domains. Almost 15% of the genome is devoted to transport. This genome sequence is a starting point to use R. palustris as a model to explore how organisms integrate metabolic modules in response to environmental perturbations.
ESTHER : Larimer_2004_Nat.Biotechnol_22_55
PubMedSearch : Larimer_2004_Nat.Biotechnol_22_55
PubMedID: 14704707
Gene_locus related to this paper: rhopa-3873 , rhopa-metx , rhopa-q6n0d1 , rhopa-q6n0w4 , rhopa-q6n3c2 , rhopa-q6n3g3 , rhopa-q6n3r3 , rhopa-q6n4a9 , rhopa-q6n4k0 , rhopa-q6n4n9 , rhopa-q6n4x3 , rhopa-q6n5y2 , rhopa-q6n6i9 , rhopa-q6n6w3 , rhopa-q6n7z8 , rhopa-q6n7z9 , rhopa-q6n9a2 , rhopa-q6n9h9 , rhopa-q6n9i1 , rhopa-q6n9m9 , rhopa-q6n9n0 , rhopa-q6n209 , rhopa-q6n255 , rhopa-q6n530 , rhopa-q6n645 , rhopa-q6n684 , rhopa-q6n701 , rhopa-q6n738 , rhopa-q6n920 , rhopa-q6naa8 , rhopa-q6nah3 , rhopa-q6naj1 , rhopa-q6nam1 , rhopa-q6nb34 , rhopa-q6nb93 , rhopa-q6nbe0 , rhopa-q6nbx2 , rhopa-q6nc00 , rhopa-q6nc97 , rhopa-q6ncc5 , rhopa-q6ncw9 , rhopa-q6ncx2 , rhopa-q6ncx3 , rhopa-RPA3893 , rhops-q131c1

Title : Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea - Chain_2003_J.Bacteriol_185_2759
Author(s) : Chain P , Lamerdin J , Larimer F , Regala W , Lao V , Land M , Hauser L , Hooper A , Klotz M , Norton J , Sayavedra-Soto L , Arciero D , Hommes N , Whittaker Mark , Arp D
Ref : Journal of Bacteriology , 185 :2759 , 2003
Abstract : Nitrosomonas europaea (ATCC 19718) is a gram-negative obligate chemolithoautotroph that can derive all its energy and reductant for growth from the oxidation of ammonia to nitrite. Nitrosomonas europaea participates in the biogeochemical N cycle in the process of nitrification. Its genome consists of a single circular chromosome of 2,812,094 bp. The GC skew analysis indicates that the genome is divided into two unequal replichores. Genes are distributed evenly around the genome, with approximately 47% transcribed from one strand and approximately 53% transcribed from the complementary strand. A total of 2,460 protein-encoding genes emerged from the modeling effort, averaging 1,011 bp in length, with intergenic regions averaging 117 bp. Genes necessary for the catabolism of ammonia, energy and reductant generation, biosynthesis, and CO(2) and NH(3) assimilation were identified. In contrast, genes for catabolism of organic compounds are limited. Genes encoding transporters for inorganic ions were plentiful, whereas genes encoding transporters for organic molecules were scant. Complex repetitive elements constitute ca. 5% of the genome. Among these are 85 predicted insertion sequence elements in eight different families. The strategy of N. europaea to accumulate Fe from the environment involves several classes of Fe receptors with more than 20 genes devoted to these receptors. However, genes for the synthesis of only one siderophore, citrate, were identified in the genome. This genome has provided new insights into the growth and metabolism of ammonia-oxidizing bacteria.
ESTHER : Chain_2003_J.Bacteriol_185_2759
PubMedSearch : Chain_2003_J.Bacteriol_185_2759
PubMedID: 12700255
Gene_locus related to this paper: niteu-BIOH , niteu-METX , niteu-NE0456 , niteu-NE0850 , niteu-NE0879 , niteu-NE0908 , niteu-NE1027 , niteu-NE1289 , niteu-NE1875 , niteu-NE2161 , niteu-NE2162 , niteu-NE2295 , niteu-NE2346 , niteu-q82u14 , niteu-TGL2

Title : The genome of a motile marine Synechococcus - Palenik_2003_Nature_424_1037
Author(s) : Palenik B , Brahamsha B , Larimer FW , Land M , Hauser L , Chain P , Lamerdin J , Regala W , Allen EE , McCarren J , Paulsen I , Dufresne A , Partensky F , Webb EA , Waterbury J
Ref : Nature , 424 :1037 , 2003
Abstract : Marine unicellular cyanobacteria are responsible for an estimated 20-40% of chlorophyll biomass and carbon fixation in the oceans. Here we have sequenced and analysed the 2.4-megabase genome of Synechococcus sp. strain WH8102, revealing some of the ways that these organisms have adapted to their largely oligotrophic environment. WH8102 uses organic nitrogen and phosphorus sources and more sodium-dependent transporters than a model freshwater cyanobacterium. Furthermore, it seems to have adopted strategies for conserving limited iron stores by using nickel and cobalt in some enzymes, has reduced its regulatory machinery (consistent with the fact that the open ocean constitutes a far more constant and buffered environment than fresh water), and has evolved a unique type of swimming motility. The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages. The genetic material contributed by horizontal gene transfer includes genes involved in the modification of the cell surface and in swimming motility. On the basis of its genome, WH8102 is more of a generalist than two related marine cyanobacteria.
ESTHER : Palenik_2003_Nature_424_1037
PubMedSearch : Palenik_2003_Nature_424_1037
PubMedID: 12917641
Gene_locus related to this paper: synpx-q7u3b1 , synpx-q7u3f4 , synpx-q7u3l2 , synpx-q7u7h0 , synpx-q7u8c6 , synpx-q7u8i5 , synpx-q7u9d5 , synpx-q7u9k7 , synpx-q7u648 , synpx-q7u656 , synpx-q7ua09 , synsp-SYNW0105 , synsp-SYNW0159 , synsp-SYNW0681 , synsp-SYNW0940

Title : Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation - Rocap_2003_Nature_424_1042
Author(s) : Rocap G , Larimer FW , Lamerdin J , Malfatti S , Chain P , Ahlgren NA , Arellano A , Coleman M , Hauser L , Hess WR , Johnson ZI , Land M , Lindell D , Post AF , Regala W , Shah M , Shaw SL , Steglich C , Sullivan MB , Ting CS , Tolonen A , Webb EA , Zinser ER , Chisholm SW
Ref : Nature , 424 :1042 , 2003
Abstract : The marine unicellular cyanobacterium Prochlorococcus is the smallest-known oxygen-evolving autotroph. It numerically dominates the phytoplankton in the tropical and subtropical oceans, and is responsible for a significant fraction of global photosynthesis. Here we compare the genomes of two Prochlorococcus strains that span the largest evolutionary distance within the Prochlorococcus lineage and that have different minimum, maximum and optimal light intensities for growth. The high-light-adapted ecotype has the smallest genome (1,657,990 base pairs, 1,716 genes) of any known oxygenic phototroph, whereas the genome of its low-light-adapted counterpart is significantly larger, at 2,410,873 base pairs (2,275 genes). The comparative architectures of these two strains reveal dynamic genomes that are constantly changing in response to myriad selection pressures. Although the two strains have 1,350 genes in common, a significant number are not shared, and these have been differentially retained from the common ancestor, or acquired through duplication or lateral transfer. Some of these genes have obvious roles in determining the relative fitness of the ecotypes in response to key environmental variables, and hence in regulating their distribution and abundance in the oceans.
ESTHER : Rocap_2003_Nature_424_1042
PubMedSearch : Rocap_2003_Nature_424_1042
PubMedID: 12917642
Gene_locus related to this paper: prom3-a2c804 , proma-PMM0356 , proma-PMM1153 , proma-PMM1599 , proma-PMM1628 , proma-PMT0128 , proma-PMT1063 , proma-PMT1175 , proma-PMT1943 , proma-TODF , promm-q7v4t5 , promm-q7v5f8 , promm-q7v6l0 , promm-q7v6v8 , promm-q7v8b7 , promm-q7v8c5 , promm-q7v8g2 , promp-q7v0v8 , promp-q7v3k6 , promp-q7v139 , promp-q7v266 , promp-q7v291 , promp-q7v298 , promp-q7v327 , promm-q7v8g5 , prom3-a2ce38