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Quasipaa boulengeri and Amolops chunganensis

ABSTRACT: Raw reads from total genomic libraries of frogs by Illumina MiSeq Raw sequence reads

PROVIDER: PRJNA329172 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
	SRR3929655_1.fastq.gz	Fastqsanger.gz
	SRR3929655_2.fastq.gz	Fastqsanger.gz
	SRR3929656_1.fastq.gz	Fastqsanger.gz
	SRR3929656_2.fastq.gz	Fastqsanger.gz

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Project description:Methods: The cDNA libraries from 3 pooled samples of liver tissues for each group were sequenced to generate RNA profiles using Illumina Miseq platform Results: The sequencing runs yielded a total of 22.67 M reads with an average length of 100 bp. The high-throughput sequencing performed for liver samples with different treatments showed similar numbers of yielded reads ranged from 5.57 to 5.74 M and the same average length. The Strand NGS software (version 2.1) was used using default parameters for pre-alignment and post-alignment quality control analysis and 100% of the raw reads remained in the dataset. Of these, 19.02 M reads (84%) were mapped into contigs of the rat genome (rn5) and identified 31457 transcripts in liver samples.

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Project description:Methods: The cDNA libraries from 3 pooled samples of cultured cells for each group were sequenced to generate RNA profiles using Illumina Miseq platform Results: The sequencing runs yielded a total of 95.01 M reads with an average length of 73-74 bp. The high-throughput sequencing performed for liver samples with different treatments showed similar numbers of yielded reads ranged from 5.57 to 5.74 M and the same average length. The Strand NGS software (version 2.1) was used using default parameters for pre-alignment and post-alignment quality control analysis and 100% of the raw reads remained in the dataset. Of these, 19.02 M reads (84%) were mapped into contigs of the rat genome (rn5) and identified 31457 transcripts in liver samples.

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Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in <i>Amolops chunganensis</i> and <i>Quasipaa boulengeri</i>.

Project description:Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, Amolops chunganensis and Quasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome of A. chunganensis and Q. boulengeri are typical neobatrachian pattern except for rearrangements at the position of "WANCY" tRNA genes cluster. Further, the mitogenome of Q. boulengeri is characterized with a tandem duplication of trnM. Moreover, we utilize 13 protein-coding genes of A. chunganensis, Q. boulengeri and other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity of A. chunganensis and Q. boulengeri. In this work, we provide nearly complete mitochondrial genomes of A. chunganensis and Q. boulengeri.

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Quasipaa boulengeri

Project description:Quasipaa boulengeri Transcriptome or Gene expression

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Quasipaa boulengeri

Project description:Quasipaa boulengeri Transcriptome or Gene expression

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Quasipaa boulengeri

Project description:Quasipaa boulengeri overview

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A draft genome sequence of the elusive giant squid, Architeuthis dux

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2019-12-16 | PXD016522 | Pride

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