The deoxyribonucleic acids of two brown algae: Pylaiella littoralis (L.) Kjellm. and Sphacellaria sp

Genome survey sequencing of Dioscorea zingiberensis

Dioscorea zingiberensis (Dioscoreceae) is the main plant source of diosgenin (steroidal sapogenins), the precursor for the production of steroid hormones in the pharmaceutical industry. Despite its large economic value, genomic information of the genus Dioscorea is currently unavailable. Here, we present an initial survey of the D. zingiberensis genome performed by next-generation sequencing technology together with a genome size investigation inferred by flow cytometry. The whole genome survey of D. zingiberensis generated 31.48 Gb of sequence data with approximately 78.70× coverage. The estimated genome size is 800 Mb, with a high level of heterozygosity based on K-mer analysis. These reads were assembled into 334 288 contigs with a N50 length of 1079 bp, which were further assembled into 92 163 scaffolds with a total length of 173.46 Mb. A total of 4935 genes, 81 tRNAs, 69 rRNAs, and 661 miRNAs were predicted by the genome analysis, and 263 484 repeated sequences were obtained with 419 372 simple sequence repeats (SSRs). Among these SSRs, the mononucleotide repeat type was the most abundant (up to 54.60% of the total SSRs), followed by the dinucleotide (29.60%), trinucleotide (11.37%), tetranucleotide (3.53%), pentanucleotide (0.65%), and hexanucleotide (0.25%) repeat types. The 1C-value of D. zingiberensis was calibrated against Salvia miltiorrhiza and calculated as 0.87 pg (851 Mb) by flow cytometry, which was very close to the result of the genome survey. This is the first report of genome-wide characterization within this taxon.

Genome survey sequencing and genetic background characterization of Gracilariopsis lemaneiformis (Rhodophyta) based on next-generation sequencing

Gracilariopsis lemaneiformis has a high economic value and is one of the most important aquaculture species in China. Despite it is economic importance, it has remained largely unstudied at the genomic level. In this study, we conducted a genome survey of Gp. lemaneiformis using next-generation sequencing (NGS) technologies. In total, 18.70 Gb of high-quality sequence data with an estimated genome size of 97 Mb were obtained by HiSeq 2000 sequencing for Gp. lemaneiformis. These reads were assembled into 160,390 contigs with a N50 length of 3.64 kb, which were further assembled into 125,685 scaffolds with a total length of 81.17 Mb. Genome analysis predicted 3490 genes and a GC% content of 48%. The identified genes have an average transcript length of 1,429 bp, an average coding sequence size of 1,369 bp, 1.36 exons per gene, exon length of 1,008 bp, and intron length of 191 bp. From the initial assembled scaffold, transposable elements constituted 54.64% (44.35 Mb) of the genome, and 7737 simple sequence repeats (SSRs) were identified. Among these SSRs, the trinucleotide repeat type was the most abundant (up to 73.20% of total SSRs), followed by the di- (17.41%), tetra- (5.49%), hexa- (2.90%), and penta- (1.00%) nucleotide repeat type. These characteristics suggest that Gp. lemaneiformis is a model organism for genetic study. This is the first report of genome-wide characterization within this taxon.

Witnessing the evolution of transcription in mitochondria: the mitochondrial genome of the primitive brown alga Pylaiella littoralis (L.) Kjellm. Encodes a T7-like RNA polymerase

A region of the mitochondrial genome of the primitive brown alga Pylaiella littoralis containing a plasmid-like insert which contains a transcribed T7-phage-type RNA polymerase gene is described. This is a first report of a phage-type RNA polymerase gene integrated in a mitochondrial genome. As the mitochondrial genome of this alga also contains sigma-70 proteobacterial promoter regions, i.e. traces of the ancestral alpha2betabeta'sigma-70 proteobacterial RNA polymerase, this genome witnesses two types of RNA polymerases. As such the mitochondrial genome of P. littoralis represents a unique stage in the evolution of transcription in mitochondria, which contrasts with that of the primitive protist Reclinomonas americana, which still retains the ancestral alpha2betabeta'sigma-70 proteobacterial RNA polymerase genes, and with animals, land plants and fungi, which use phage-type polymerases.

The reverse-transcriptase-like proteins encoded by group II introns in the mitochondrial genome of the brown alga Pylaiella littoralis belong to two different lineages which apparently coevolved with the group II ribosyme lineages

The mitochondrial genome of the brown alga Pylaiella littoralis contains two different types of group II introns. They each encode complete complex proteins, i.e., with a reverse transcriptase domain, a maturase or X domain, and an endonuclease or H-N-H/zinc finger domain. To our knowledge, this is the first example of the presence in the same genome of introns belonging to subgroups IIA and IIB which both contain multidomained RT-like proteins. We describe the group IIA introns that interrupt the cox1 gene. The RT-like proteins contained in these introns were compared to those of the LSU rDNA group IIB introns. The phylogenetic relationships of these intron ORFs were investigated and the possible evolution of group II introns is discussed.

The plastome of a brown alga,Dictyota dichotoma : I. Physical properties and the Bam HI/Sal I/Bgl II cleavage site map

Plastids of the brown algaDictyota dichotoma contain a single homogeneous DNA species which bands at a buoyant density of 1.693 g/cm(3) in neutral CsCl equilibrium density gradients. The corresponding nuclear DNA has a density of 1.715 g/cm(3). The molecular size of the plastid DNA is 123 kbp as calculated by both electron microscopy of spread intact circular molecules and gel electrophoresis following single and double digestions with various restriction enzymes. A restriction map has been constructed using the endonucleases Sal I, Bam HI, and Bgl II which cleave theDictyota plastome into 6, 12, and 17 fragments, respectively. No large repeated regions, as found in chlorophycean andEuglena plastid DNAs, were detected.Dictyota dichotoma is the first member from the chlorophyll c-line of the algal pedigree for which a physical map of plastid DNA has been established.