Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA351725 | ENA |
REPOSITORIES: ENA
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Project description:The larvacean, Oikopleura dioica, is a planktonic chordate and belongs to tunicate that is the closest relative to vertebrates. Its simple and transparent body, invariant embryonic cell lineages and short life cycle of five days make it a promising model organism for research in developmental biology. The genome browser, OikoBase, has been established in 2013 using Norwegian O. dioica. However, genome information of other populations is not available, despite that many researchers have used local populations. In the present study, we sequenced genome of O. dioica of a southwestern Japanese population using RNA-Seq data. These RNA-Seq data covers expressions in 8 cell and 12 hours post fertilization (HPF) embryos of Animal(A), Vegetal(V) and whole-embryo regions, as well as whole embryo of 13 stages, including OD_STAGE01 (unfertilized egg), OD_STAGE02 (fertilized egg), OD_STAGE03 (2-cell), OD_STAGE04 (4-cell), OD_STAGE05 (8-cell), OD_STAGE06 (16-cell), OD_STAGE07 (32-cell), OD_STAGE08 (1.5 hours post fertilization), OD_STAGE09 (2.5 hours post fertilization, tadpole larvae), OD_STAGE10 (3 hours post fertilization, hatched larvae), OD_STAGE11 (5 hours post fertilization, early organogenesis), OD_STAGE12 (8 hours post fertilization, late organogenesis), OD_STAGE13 (10 hours post fertilization, juvenile), Adult male and Adult female. These genome assembly, transcript assembly, and transcript models are incorporated into the ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and blast searches. The genome and transcriptome resources will be useful datasets for developmental biology, evolutionary biology and molecular ecology using this model organism.
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Project description:Chickpea (Cicer arietinum L.) seeds are valued for their nutritional scores and limited information on the molecular mechanisms of chickpea fertilization and seed development is available. In the current work, comparative transcriptome analysis was performed on two different stages of chickpea ovules (pre- and post-fertilization) to identify key regulatory transcripts. Two-staged transcriptome sequencing was generated and over 208 million reads were mapped to quantify transcript abundance during fertilization events. Mapping to the reference genome showed that the majority (92.88%) of high-quality illumina reads were aligned to the chickpea genome. Reference-guided genome and transcriptome assembly yielded a total of 28,783 genes. Of these, 3399 genes were differentially expressed after the fertilization event. These involve up-regulated genes including LOC101500970, LOC101506539 and down-regulated genes LOC101493897, LOC101491695 and so on. Transcription factor families including UDP-glucuronyltransferase, NAC transcription factor, heat shock transcription factor, and auxin-responsive transcription factor were also found to be activated after fertilization. Activation of these genes and transcription factors results in the accumulation of carbohydrates and proteins by enhancing their trafficking and biosynthesis. Total 17 differentially expressed genes, were randomly selected for qRT-PCR for validation of transcriptome analysis and showed statistically significant correlations with the transcriptome data. Our findings provide insights into the regulatory mechanisms underlying changes in fertilized chickpea ovules. This work may come closer to a comprehensive understanding of the mechanisms that initiate developmental events in chickpea seeds.
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Project description:shifts of nirS-type denitrifier communities response to long-term different fertilization in the black soils Raw sequence reads
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