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Larix occidentalis

ABSTRACT: Larix occidentalis (western larch) genomic and transcriptomic data

PROVIDER: PRJNA1187655 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR31821237_subreads.fastq.gz	Fastqsanger.gz
	SRR31821238_subreads.fastq.gz	Fastqsanger.gz
	SRR31821239_subreads.fastq.gz	Fastqsanger.gz
	SRR31821240_subreads.fastq.gz	Fastqsanger.gz

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The regulation of synchronism by abscisic acid-responsive small non-coding RNAs during somatic embryogenesis in larch (Larix leptolepis)

Project description:Small non-coding RNAs (sncRNAs) are emerging as key regulators of embryogenesis. To investigate the roles of sRNAs in regulating synchronism of somatic embryogenesis in Larix leptolepis, we deciphered the endogenous "sRNAome" in synchronous and desynchronous embryos. The 24-nt class sRNAs were overrepresented in both synchronous embryos and desynchronous embryos, accounting for 85.29% and 44.79%. A total of 29 miRNAs were upregulated in synchronous embryos, whereas 59 miRNAs were upregulated in desynchronous embryos. We describe the emerging theme for sncRNAs function: inhibiting the precocious expression, thus regulating the synchronism of somatic embryogenesis. These findings indicate that larch and possibly other gymnosperms have complex mechanisms of gene regulation involving sRNAs and miRNAs operating transcriptionally and post-transcriptionally during the regulation of synchronism. One embryogenic cell line of Japanese larch (Larix leptolepis), designated as D878, with a high embryo maturation capacity was used in this study. Embryogenic callus was induced from immature embryos of Japanese larch on induction medium followed by sub-culture. Calli at the proembryogenic mass III stage were cultured on maturation medium in a dark environment at 25 M-BM-1 2M-BM-0C. Samples were cultured on ABA-plus or ABA-minus maturation medium for 45 days. All samples were snap-frozen in liquid nitrogen, and stored in liquid nitrogen until RNA extraction.

2014-07-19 | E-GEOD-49055 | biostudies-arrayexpress

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Project description:Aechmophorus occidentalis (western grebe), bAecOcc1

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Deciphering microRNAs and other small RNAs during the transition of dormant embryo into germinated embryo in larch (Larix leptolepis)

Project description:To investigate the roles of sRNAs in keeping embryo dormancy or germination in Larix leptolepis, we deciphered the endogenous "sRNAome" in dormant and germinated embryos. High-throughput sequencing of the sRNA libraries showed that dormant embryos exhibited a length bias towards 24-nt, while germinated embryos showed a bias towards a 21-nt and/or 22-nt length. Both of proportions for miRNAs to the non-redundant and redundant sRNAs were higher in germinated embryos than those in dormant embryos, while the ratio of unknown sRNAs was higher in dormant embryos than in germinated embryos. The proportion of 21-nt and 22-nt sRNAs increased in germinated embryos, which might attribute to the higher expression level of miRNAs. We identified a total of 160 conserved miRNAs from 39 families, 16 novel miRNAs, and 14 plausible miRNA candidates, of which novel and non-conserved known miRNAs might be the main contributors. These findings indicate that larch and possibly other gymnosperms have complex mechanisms of gene regulation involving sRNAs and miRNAs operating transcriptionally and post-transcriptionally during embryo dormancy and germination. One embryogenic cell line of Japanese larch (Larix leptolepis), designated as D878, with a high embryo maturation capacity was used in this study. Embryogenic callus were induced from immature embryos of larch on induction medium, followed by sub-culture, and culture on ABA-containing mature medium in a dark environment at 25 2 C. After cultured 45 days in mature medium, embryogenic calli developed into mature somatic embryos. In our study, the samples were harvested at day 57, one sample was collected after mature embryos continued to stay for 12 days on ABA-containing medium, and the other one was harvested after cultured for 12 days on ABA-removing medium. All samples were snap-frozen in liquid nitrogen, and stored in liquid nitrogen until RNA extraction.

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