Chung-Der Hsiao

Next generation sequencing yields the complete mitochondrial genome of the flathead mullet, Mugil cephalus cryptic species NWP2 (Teleostei: Mugilidae)

Abstract In this study, the complete mitogenome sequence of Northwestern Pacific 2 (NWP2) cryptic species of flathead mullet, Mugil cephalus (Teleostei: Mugilidae) has been amplified by long-range PCR and sequenced by next-generation sequencing method. The assembled mitogenome, consisting of 16,686 bp, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a non-coding control region of D-loop. D-loop was 909 bp length and was located between tRNA-Pro and tRNA-Phe. The overall base composition of NWP2 M. cephalus was 28.4% for A, 29.8% for C, 26.5% for T and 15.3% for G. The complete mitogenome may provide essential and important DNA molecular data for further phylogenetic and evolutionary analysis for flathead mullet species complex.

Next-generation sequencing yields the complete mitogenome of massive coral, Porites lutea (Cnidaria: Poritidae)

Abstract In this study, the complete mitogenome sequence of massive coral, Porites lutea (Cnidaria: Poritidae), has been sequenced by next-generation sequencing method. The overall base composition of Porites lutea mitogenome is 26.0% for A, 13.3% for C, 23.0% for G and 37.8% for T and have high AT content of 63.7%. The assembled mitogenome, consisting of 18 646 bp, has unique 13 protein-coding genes (PCGs), seven transfer RNAs and two ribosomal RNAs genes. The Porites lutea mitogenome has the common mitogenome gene organization and feature of scleractinian coral. Among 13 PCGs, ND5 and COX1 genes are interrupted by group I intron (11 130 and 971 bp, respectively). There are 13 genes embedded in ND5 group I intron (tRNA-Glu, ND1, CYTB, tRNA-Met, ND2, ND6, ATP6, ND4, 12S rRNA, COX3, COX2, ND4L and ND3), and two genes embedded in COX1 group I intron (tRNA-Ile and tRNA-Pro). The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for stony coral.

The complete chloroplast genome of Gracilariopsis lemaneiformis, an important economic red alga of the family Gracilariaceae

Abstract The complete chloroplast DNA (cpDNA) of a famous red alga of the family Gracilariaceae, Gracilariopsis lemaneiformis, was deduced by using next-generation sequencing and de novo assembly technology. The complete cpDNA of G. lemaneiformis consists of 182 505 bp and encodes 230 unique genes consisting 204 protein-coding genes (PCGs), 21 transfer RNA genes, 3 ribosomal RNA genes, 1 transfer-messenger RNA genes and 1 non-coding RNA genes. Among 204 PCGs, ccsA gene is interrupted by a intron. Unlike the typical quadripartite structure (a pair of inverted repeats separated by the small single-copy and large single-copy units) of cpDNA in higher plants, the complete cpDNA of G. lemaneiformis is very compact, containing no inverted repeat and just one copy of rRNA gene cluster consisting of 16S, 23S and 5S rRNA genes. The genic regions account for 83.7% of whole cpDNA genome, and the G + C content of the cpDNA was 27.4%. The low G + C content of G. lemaneiformis cpDNA is largely contributed by high A + T content in the PCGs and non-coding regions. A phylogenetic analysis of the 15 complete cpDNA from rhodophyta shows that G. lemaneiformis is closely related to macroalga Gracilaria salicornia. The complete cpDNA of G. lemaneiformis provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for rhodophyta.

Next generation sequencing yields complete mitogenomes of Leopard whipray (Himantura leoparda) and Blue-spotted stingray (Neotrygon kuhlii) (Chondrichthyes: Dasyatidae)

Abstract The Leopard whipray (Himantura leoparda) and Blue-spotted stingray (Neotrygon kuhlii) are distributed in the Indian and West Pacific Ocean and considered as complex species based on morphological and molecular evidences. In this study, we used the next-generation sequencing method to decode two complete mitogenomes of H. leoparda and N. kuhlii. The assembled mitogenome, consisting lengths of 17,690 bp for H. leoparda and 17,974 bp for N. kuhlii, shows 78% identity to each other. Both mitogenomes follow the typical vertebrate arrangement, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a non-coding control region of D-loop. D-loop with the lengths 1931 bp (H. leoparda) and 2243 bp (N. kuhlii) is located between tRNA-Pro and tRNA-Phe. The overall GC content is 40.3% for H. leoparda and 39.8% for N. kuhlii. The complete mitogenome of H. leoparda and N. kuhlii provides essential and important DNA molecular data for further phylogenetic and evolutionary analyses for stingray species complex.

Low-coverage genome sequencing yields the complete mitogenome of Pyjama Slug, Chromodoris quadricolor (Mollusca: Chromodorididae)

Abstract In this study, the complete mitogenome sequence of Pyjama Slug, Chromodoris quadricolor (Mollusca: Chromodorididae), has been decoded for the first time by low-coverage genome-sequencing method. The overall base composition of C. quadricolor mitogenome is 30.6% for A, 14.4% for C, 17.8% for G and 37.2% for T and has low GC content of 32.2%. The assembled mitogenome, consisting of 14 259 bp, has unique 13 protein-coding genes (PCGs), 22 transfer RNAs and two ribosomal RNAs genes. The C. quadricolor mitogenome has the common mitogenome gene organization and feature of Nudipleura (a clade of sea slugs and sea snails). The complete mitogenome provides essential and important DNA molecular data for further evolutionary analysis for sea slugs and sea snails.

The complete chloroplast genome of Tianshan Snow Lotus (Saussurea involucrata), a famous traditional Chinese medicinal plant of the family Asteraceae

abtract We decoded the complete chloroplast DNA (cpDNA) sequence of the Tianshan Snow Lotus (Saussurea involucrata), a famous traditional Chinese medicinal plant of the family Asteraceae, by using next-generation sequencing technology. The genome consists of 152 490 bp containing a pair of inverted repeats (IRs) of 25 202 bp, which was separated by a large single-copy region and a small single-copy region of 83 446 bp and 18 639 bp, respectively. The genic regions account for 57.7% of whole cpDNA, and the GC content of the cpDNA was 37.7%. The S. involucrata cpDNA encodes 114 unigenes (82 protein-coding genes, 4 rRNA genes, and 28 tRNA genes). There are eight protein-coding genes (atpF, ndhA, ndhB, rpl2, rpoC1, rps16, clpP, and ycf3) and five tRNA genes (trnA-UGC, trnI-GAU, trnK-UUU, trnL-UAA, and trnV-UAC) containing introns. A phylogenetic analysis of the 11 complete cpDNA from Asteracease showed that S. involucrata is closely related to Centaurea diffusa (Diffuse Knapweed). The complete cpDNA of S. involucrata provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for Asteraceae.

De novo assembly and comparison of the ovarian transcriptomes of the common Chinese cuttlefish (Sepiella japonica) with different gonadal development.

The common Chinese cuttlefish (Sepiella japonica) has been considered one of the most economically important marine Cephalopod species in East Asia and seed breeding technology has been established for massive aquaculture and stock enhancement. In the present study, we used Illumina HiSeq2000 to sequence, assemble and annotate the transcriptome of the ovary tissues of S. japonica for the first time. A total of 53,116,650 and 53,446,640 reads were obtained from the immature and matured ovaries, respectively (NCBI SRA database SRX1409472 and SRX1409473), and 70,039 contigs (N50 = 1443 bp) were obtained after de novo assembling with Trinity software. Digital gene expression analysis reveals 47,288 contigs show differential expression profile and 793 contigs are highly expressed in the immature ovary, while 38 contigs are highly expressed in the mature ovary with FPKM > 100. We hope that the ovarian transcriptome and those stage-enriched transcripts of S. japonica can provide some insight into the understanding of genome-wide transcriptome profile of cuttlefish gonad tissue and give useful information in cuttlefish gonad development.

Genome skimming yields the complete mitogenome of Chromodoris annae (Mollusca: Chromodorididae)

Abstract In this study, the complete mitogenome sequence of sea slug, Chromodoris annae (Mollusca: Chromodorididae), has been decoded for the first time by genome skimming method. The overall base composition of C. annae mitogenome is 30.6% for A, 14.5% for C, 17.8% for G, and 37.2% for T, and has GC content of 32.2%. The assembled mitogenome, consisting of 14,260 bp, has unique 13 protein-coding genes (PCGs), 22 transfer RNAs, and two ribosomal RNAs genes. The C. annae has the common mitogenome gene organization and feature of Chromodorididae. The complete mitogenome of C. annae provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for sea slugs.

Next-generation sequencing yields the complete mitochondrial genome of the Redbelly yellowtail fusilier, Caesio cuning (Teleostei: Caesionidae)

Abstract In this study, the complete mitogenome sequence of Redbelly yellowtail fusileer, Caesio cuning (Teleostei: Caesionidae), has been sequenced by the next-generation sequencing method. The assembled mitogenome, consisting of 16 508 bp, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a non-coding control region of D-loop. D-loop contains 826 bp length that is located between tRNA-Pro and tRNA-Phe. The overall base composition of C. cuning is 28.1% for A, 31.1% for C, 16.3% for G and 24.4% for T. The complete mitogenome may provide essential and important DNA molecular data for further phylogenetic and evolutionary analysis for Caesionidae.

A Simple Method to Decode the Complete 18-5.8-28S rRNA Repeated Units of Green Algae by Genome Skimming

Green algae, Chlorella ellipsoidea, Haematococcus pluvialis and Aegagropila linnaei (Phylum Chlorophyta) were simultaneously decoded by a genomic skimming approach within 18-5.8-28S rRNA region. Whole genomic DNAs were isolated from green algae and directly subjected to low coverage genome skimming sequencing. After de novo assembly and mapping, the size of complete 18-5.8-28S rRNA repeated units for three green algae were ranged from 5785 to 6028 bp, which showed high nucleotide diversity (π is around 0.5–0.6) within ITS1 and ITS2 (Internal Transcribed Spacer) regions. Previously, the evolutional diversity of algae has been difficult to decode due to the inability design universal primers that amplify specific marker genes across diverse algal species. In this study, our method provided a rapid and universal approach to decode the 18-5.8-28S rRNA repeat unit in three green algal species. In addition, the completely sequenced 18-5.8-28S rRNA repeated units provided a solid nuclear marker for phylogenetic and evolutionary analysis for green algae for the first time.