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Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei.

ABSTRACT: Chondrichthyans (cartilaginous fishes) exhibit highly variable reproductive styles, categorized as viviparity and oviparity. Among these, species with oviparity provide an enormous potential of molecular experimentation with stable sample supply which does not demand the sacrifices of live mothers. Cartilaginous fishes are divided into two subclasses, chimaeras (Holocephali) and elasmobranchs (Elasmobranchii), and the latter consists of two monophyletic groups, Batoidea (rays, skates and torpedoes) and Selachimorpha (sharks). Here we report transcriptome assemblies of the ocellate spot skate Okamejei kenojei, produced by strand-specific RNA-seq of its embryonic tissues. We obtained a total of 325 million illumina short reads from libraries prepared using four different tissue domains and assembled them all together. Our assembly result confirmed the species authenticity and high continuity of contig sequences. Also, assessment of its coverage of pre-selected one-to-one orthologs supported high diversity of transcripts in the assemblies. Our products are expected to provide a basis of comparative molecular studies encompassing other chondrichthyan species with emerging genomic and transcriptomic sequence information.

SUBMITTER: Tanegashima C

PROVIDER: S-EPMC6174922 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei.

Tanegashima Chiharu C Nishimura Osamu O Motone Fumio F Tatsumi Kaori K Kadota Mitsutaka M Kuraku Shigehiro S

Scientific data 20181008

Chondrichthyans (cartilaginous fishes) exhibit highly variable reproductive styles, categorized as viviparity and oviparity. Among these, species with oviparity provide an enormous potential of molecular experimentation with stable sample supply which does not demand the sacrifices of live mothers. Cartilaginous fishes are divided into two subclasses, chimaeras (Holocephali) and elasmobranchs (Elasmobranchii), and the latter consists of two monophyletic groups, Batoidea (rays, skates and torpedo ...[more]

PMID: 30295675

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Project description:BackgroundMaize is one of the primary crops of genetic manipulation, which provides an excellent means of promoting stress resistance and increasing yield. However, the differences in induction and regeneration capacity of embryonic callus (EC) among various genotypes result in genotypic dependence in genetic transformation.ResultsIn this study, embryonic calli of two maize inbred lines with strong redifferentiation capacity and two lines with weak redifferentiation capability were separately subjected to transcriptome sequencing analysis during the early redifferentiation stages (stage I, 1-3 d; stage II, 4-6 d; stage III, 7-9 d) along with their corresponding controls. A total of ~ 654.72 million cDNA clean reads were yielded, and 62.64%~ 69.21% clean reads were mapped to the reference genome for each library. In comparison with the control, the numbers of differentially expressed genes (DEGs) for the four inbred lines identified in the three stages ranged from 1694 to 7193. By analyzing the common and specific DEGs of the four materials, we found that there were 321 upregulated genes and 386 downregulated genes identified in the high-regeneration lines (141 and DH40), whereas 611 upregulated genes and 500 downregulated genes were specifically expressed in the low-regeneration lines (ZYDH381-1 and DH3732). Analysis of the DEG expression patterns indicated a sharp change at stage I in both the high- and low-regeneration lines, which suggested that stage I constitutes a crucial period for EC regeneration. Notably, the specific common DEGs of 141 and DH40 were mainly associated with photosynthesis, porphyrin and chlorophyll metabolism, ribosomes, and plant hormone signal transduction. In contrast, the DEGs in ZYDH381-1 and DH3732 were mainly related to taurine and hypotaurine metabolism, nitrogen metabolism, fatty acid elongation, starch and sucrose metabolism, phenylpropanoid biosynthesis, and plant circadian rhythm. More importantly, WOX genes, which have an ancestral role in embryo development in seed plants and promote the regeneration of transformed calli, were specifically upregulated in the two high-regeneration lines.ConclusionsOur research contributes to the elucidation of molecular regulation during early redifferentiation in the maize embryonic callus.

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Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei.

Publications

Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei.

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