Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Developmental gene expression of Hymenochirus boettgeri

ABSTRACT: RNA-seq experiments to construct Hymenochirus bettgeri transcripts Collect mRNA from whole eggs/embryos/tadpoles, with poly-A enrichment method

ORGANISM(S): Hymenochirus boettgeri

SUBMITTER: Taejoon Kwon

PROVIDER: E-GEOD-76089 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genome evolution in the allotetraploid frog Xenopus laevis.

Session Adam M AM Uno Yoshinobu Y Kwon Taejoon T Chapman Jarrod A JA Toyoda Atsushi A Takahashi Shuji S Fukui Akimasa A Hikosaka Akira A Suzuki Atsushi A Kondo Mariko M van Heeringen Simon J SJ Quigley Ian I Heinz Sven S Ogino Hajime H Ochi Haruki H Hellsten Uffe U Lyons Jessica B JB Simakov Oleg O Putnam Nicholas N Stites Jonathan J Kuroki Yoko Y Tanaka Toshiaki T Michiue Tatsuo T Watanabe Minoru M Bogdanovic Ozren O Lister Ryan R Georgiou Georgios G Paranjpe Sarita S SS van Kruijsbergen Ila I Shu Shengquiang S Carlson Joseph J Kinoshita Tsutomu T Ohta Yuko Y Mawaribuchi Shuuji S Jenkins Jerry J Grimwood Jane J Schmutz Jeremy J Mitros Therese T Mozaffari Sahar V SV Suzuki Yutaka Y Haramoto Yoshikazu Y Yamamoto Takamasa S TS Takagi Chiyo C Heald Rebecca R Miller Kelly K Haudenschild Christian C Kitzman Jacob J Nakayama Takuya T Izutsu Yumi Y Robert Jacques J Fortriede Joshua J Burns Kevin K Lotay Vaneet V Karimi Kamran K Yasuoka Yuuri Y Dichmann Darwin S DS Flajnik Martin F MF Houston Douglas W DW Shendure Jay J DuPasquier Louis L Vize Peter D PD Zorn Aaron M AM Ito Michihiko M Marcotte Edward M EM Wallingford John B JB Ito Yuzuru Y Asashima Makoto M Ueno Naoto N Matsuda Yoichi Y Veenstra Gert Jan C GJ Fujiyama Asao A Harland Richard M RM Taira Masanori M Rokhsar Daniel S DS

Nature 20161001 7625

To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor ...[more]

PMID: 27762356

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Project description:Oilseed mustard, Brassica juncea, exhibits high levels of genetic variability for salinity tolerance. To obtain the global view of transcriptome and investigate the molecular basis of salinity tolerance in a salt-tolerant variety CS52 of B. juncea, we performed transcriptome sequencing of control and salt-stressed seedlings. De novo assembly of 184 million high-quality paired-end reads yielded 42,327 unique transcripts longer than 300 bp with RPKM ≥1. When compared with non-redundant proteins, we could annotate 67% unigenes obtained in our study. Based on the mapping to expressed sequence tags (ESTs), 52.6% unigenes are novel compared to EST data available for B. juncea and constituent genomes. Differential expression analysis revealed altered expression of 1469 unigenes in response to salinity stress. Of these, 587, mainly associated with ROS detoxification, sulfur assimilation and calcium signaling pathways, are up regulated. Notable of these is RSA1 (SHORT ROOT IN SALT MEDIUM 1) INTERACTING TRANSCRIPTION FACTOR 1 (RITF1) homolog up regulated by >100 folds in response to stress. RITF1, encoding a bHLH transcription factor, is a positive regulator of SOS1 and several key genes involved in scavenging of salt stress-induced reactive oxygen species (ROS). Further, we performed comparative expression profiling of key genes implicated in ion homeostasis and sequestration (SOS1, SOS2, SOS3, ENH1, NHX1), calcium sensing pathway (RITF1) and ROS detoxification in contrasting cultivars, B. juncea and B. nigra, for salinity tolerance. The results revealed higher transcript accumulation of most of these genes in B. juncea var. CS52 compared to salt-sensitive cultivar even under normal growth conditions. Together, these findings reveal key pathways and signaling components that contribute to salinity tolerance in B. juncea var. CS52. We report transcriptome sequencing of two-weeks-old seedlings of B. juncea var. CS52 under normal growth conditions (CTRL) and in response to salinity stress (SS) using Illumina paired-end sequencing

Dataset Information

Developmental gene expression of Hymenochirus boettgeri

Publications

Genome evolution in the allotetraploid frog Xenopus laevis.

Similar Datasets

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