Olender T

References (4)

Title : Genome sequence of the pattern-forming social bacterium Paenibacillus dendritiformis C454 chiral morphotype - Sirota-Madi_2012_J.Bacteriol_194_2127
Author(s) : Sirota-Madi A , Olender T , Helman Y , Brainis I , Finkelshtein A , Roth D , Hagai E , Leshkowitz D , Brodsky L , Galatenko V , Nikolaev V , Gutnick DL , Lancet D , Ben-Jacob E
Ref : Journal of Bacteriology , 194 :2127 , 2012
Abstract : Paenibacillus dendritiformis is a Gram-positive, soil-dwelling, spore-forming social microorganism. An intriguing collective faculty of this strain is manifested by its ability to switch between different morphotypes, such as the branching (T) and the chiral (C) morphotypes. Here we report the 6.3-Mb draft genome sequence of the P. dendritiformis C454 chiral morphotype.
ESTHER : Sirota-Madi_2012_J.Bacteriol_194_2127
PubMedSearch : Sirota-Madi_2012_J.Bacteriol_194_2127
PubMedID: 22461558
Gene_locus related to this paper: 9bacl-h3sdn5 , 9bacl-h3sft0 , 9bacl-h3sg17 , 9bacl-h3smu8

Title : Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments - Sirota-Madi_2010_BMC.Genomics_11_710
Author(s) : Sirota-Madi A , Olender T , Helman Y , Ingham C , Brainis I , Roth D , Hagi E , Brodsky L , Leshkowitz D , Galatenko V , Nikolaev V , Mugasimangalam RC , Bransburg-Zabary S , Gutnick DL , Lancet D , Ben-Jacob E
Ref : BMC Genomics , 11 :710 , 2010
Abstract : BACKGROUND: The pattern-forming bacterium Paenibacillus vortex is notable for its advanced social behavior, which is reflected in development of colonies with highly intricate architectures. Prior to this study, only two other Paenibacillus species (Paenibacillus sp. JDR-2 and Paenibacillus larvae) have been sequenced. However, no genomic data is available on the Paenibacillus species with pattern-forming and complex social motility. Here we report the de novo genome sequence of this Gram-positive, soil-dwelling, sporulating bacterium.
RESULTS: The complete P. vortex genome was sequenced by a hybrid approach using 454 Life Sciences and Illumina, achieving a total of 289x coverage, with 99.8% sequence identity between the two methods. The sequencing results were validated using a custom designed Agilent microarray expression chip which represented the coding and the non-coding regions. Analysis of the P. vortex genome revealed 6,437 open reading frames (ORFs) and 73 non-coding RNA genes. Comparative genomic analysis with 500 complete bacterial genomes revealed exceptionally high number of two-component system (TCS) genes, transcription factors (TFs), transport and defense related genes. Additionally, we have identified genes involved in the production of antimicrobial compounds and extracellular degrading enzymes.
CONCLUSIONS: These findings suggest that P. vortex has advanced faculties to perceive and react to a wide range of signaling molecules and environmental conditions, which could be associated with its ability to reconfigure and replicate complex colony architectures. Additionally, P. vortex is likely to serve as a rich source of genes important for agricultural, medical and industrial applications and it has the potential to advance the study of social microbiology within Gram-positive bacteria.
ESTHER : Sirota-Madi_2010_BMC.Genomics_11_710
PubMedSearch : Sirota-Madi_2010_BMC.Genomics_11_710
PubMedID: 21167037
Gene_locus related to this paper: 9bacl-e5yrc1 , 9bacl-e5yu37

Title : The genome of a songbird - Warren_2010_Nature_464_757
Author(s) : Warren WC , Clayton DF , Ellegren H , Arnold AP , Hillier LW , Kunstner A , Searle S , White S , Vilella AJ , Fairley S , Heger A , Kong L , Ponting CP , Jarvis ED , Mello CV , Minx P , Lovell P , Velho TA , Ferris M , Balakrishnan CN , Sinha S , Blatti C , London SE , Li Y , Lin YC , George J , Sweedler J , Southey B , Gunaratne P , Watson M , Nam K , Backstrom N , Smeds L , Nabholz B , Itoh Y , Whitney O , Pfenning AR , Howard J , Volker M , Skinner BM , Griffin DK , Ye L , McLaren WM , Flicek P , Quesada V , Velasco G , Lopez-Otin C , Puente XS , Olender T , Lancet D , Smit AF , Hubley R , Konkel MK , Walker JA , Batzer MA , Gu W , Pollock DD , Chen L , Cheng Z , Eichler EE , Stapley J , Slate J , Ekblom R , Birkhead T , Burke T , Burt D , Scharff C , Adam I , Richard H , Sultan M , Soldatov A , Lehrach H , Edwards SV , Yang SP , Li X , Graves T , Fulton L , Nelson J , Chinwalla A , Hou S , Mardis ER , Wilson RK
Ref : Nature , 464 :757 , 2010
Abstract : The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.
ESTHER : Warren_2010_Nature_464_757
PubMedSearch : Warren_2010_Nature_464_757
PubMedID: 20360741
Gene_locus related to this paper: taegu-b5fyu7 , taegu-BCHE , taegu-h0z4h9 , taegu-h0z9w8 , taegu-h0zat6 , taegu-h0ze48 , taegu-h0zha8 , taegu-h0zkr8 , taegu-h0zqp3 , taegu-h0zz82 , taegu-h0zqs1 , taegu-h0yy64 , taegu-h0yv40 , taegu-h0yyt1 , taegu-h0zcc8 , taegu-h0z3k5 , taegu-h0yw95 , taegu-h0zkm7 , taegu-h1a198 , taegu-h0z6w2 , taegu-h0zl93 , taegu-h0zt33 , taegu-h0yp71 , taegu-h0ypu5 , taegu-h1a048 , taegu-h0ztq1 , fical-u3kau2 , 9pass-a0a093qu66 , taegu-h0z7g0 , fical-u3jnn0 , taegu-h0zb80 , taegu-h0zb89 , taegu-h0z994 , taegu-h0ztj6

Title : Genome analysis of the platypus reveals unique signatures of evolution - Warren_2008_Nature_453_175
Author(s) : Warren WC , Hillier LW , Marshall Graves JA , Birney E , Ponting CP , Grutzner F , Belov K , Miller W , Clarke L , Chinwalla AT , Yang SP , Heger A , Locke DP , Miethke P , Waters PD , Veyrunes F , Fulton L , Fulton B , Graves T , Wallis J , Puente XS , Lopez-Otin C , Ordonez GR , Eichler EE , Chen L , Cheng Z , Deakin JE , Alsop A , Thompson K , Kirby P , Papenfuss AT , Wakefield MJ , Olender T , Lancet D , Huttley GA , Smit AF , Pask A , Temple-Smith P , Batzer MA , Walker JA , Konkel MK , Harris RS , Whittington CM , Wong ES , Gemmell NJ , Buschiazzo E , Vargas Jentzsch IM , Merkel A , Schmitz J , Zemann A , Churakov G , Kriegs JO , Brosius J , Murchison EP , Sachidanandam R , Smith C , Hannon GJ , Tsend-Ayush E , McMillan D , Attenborough R , Rens W , Ferguson-Smith M , Lefevre CM , Sharp JA , Nicholas KR , Ray DA , Kube M , Reinhardt R , Pringle TH , Taylor J , Jones RC , Nixon B , Dacheux JL , Niwa H , Sekita Y , Huang X , Stark A , Kheradpour P , Kellis M , Flicek P , Chen Y , Webber C , Hardison R , Nelson J , Hallsworth-Pepin K , Delehaunty K , Markovic C , Minx P , Feng Y , Kremitzki C , Mitreva M , Glasscock J , Wylie T , Wohldmann P , Thiru P , Nhan MN , Pohl CS , Smith SM , Hou S , Nefedov M , de Jong PJ , Renfree MB , Mardis ER , Wilson RK
Ref : Nature , 453 :175 , 2008
Abstract : We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.
ESTHER : Warren_2008_Nature_453_175
PubMedSearch : Warren_2008_Nature_453_175
PubMedID: 18464734
Gene_locus related to this paper: ornan-f6s0q0 , ornan-f6ty74 , ornan-f6u2k2 , ornan-f6uve1 , ornan-f6vpb6 , ornan-f6ybp3 , ornan-f7bgu8 , ornan-f7ct41 , ornan-f7cza1 , ornan-f7ejp8 , ornan-f7exu1 , ornan-f7f392 , ornan-f7f9y6 , ornan-f6ve87 , ornan-f7f1d9 , ornan-f6z3l1 , ornan-f6r3f9 , ornan-f6r3g8 , ornan-f6vs71 , ornan-f7g4v8