Table_2_First insight into H3K4me3 modification in the rapid growth of Alexandrium pacificum (dinoflagellates).docx

BackgroundAlexandrium pacificum is a dinoflagellate species notorious for its rapid growth resulting in large-scale blooms. This study aimed to investigate the molecular mechanisms of A. pacificum under laboratory-simulated rapid growth conditions from the perspective of H3K4me3 modification regulation.Methods and resultsWestern blot was used to detect the modification abundance of H3K4me3 in A. pacificum cultured under different conditions, including high light (HL), high nitrogen (HN), and f/2 medium (control, CT), in the rapid growth exponential phase. The results showed that the modification abundance of H3K4me3 under HL or HN was greater than that under CT. Chromatin immunoprecipitation-sequencing was used to explore the acting genes of H3K4me3 under different conditions for the first time. Nitrogen metabolism and endocytosis were significantly associated with H3K4me3 regulation under HL. Furthermore, H3K4me3 was also significantly associated with the vitamin metabolism pathway under HN.ConclusionsThese findings demonstrate that H3K4me3 plays a potentially important role in the regulation of the rapid growth of A. pacificum. Such knowledge of a histone modification regulatory network in this dinoflagellate, lays a necessary foundation for future research in related fields.</p

Table_1_First insight into H3K4me3 modification in the rapid growth of Alexandrium pacificum (dinoflagellates).docx

BackgroundAlexandrium pacificum is a dinoflagellate species notorious for its rapid growth resulting in large-scale blooms. This study aimed to investigate the molecular mechanisms of A. pacificum under laboratory-simulated rapid growth conditions from the perspective of H3K4me3 modification regulation.Methods and resultsWestern blot was used to detect the modification abundance of H3K4me3 in A. pacificum cultured under different conditions, including high light (HL), high nitrogen (HN), and f/2 medium (control, CT), in the rapid growth exponential phase. The results showed that the modification abundance of H3K4me3 under HL or HN was greater than that under CT. Chromatin immunoprecipitation-sequencing was used to explore the acting genes of H3K4me3 under different conditions for the first time. Nitrogen metabolism and endocytosis were significantly associated with H3K4me3 regulation under HL. Furthermore, H3K4me3 was also significantly associated with the vitamin metabolism pathway under HN.ConclusionsThese findings demonstrate that H3K4me3 plays a potentially important role in the regulation of the rapid growth of A. pacificum. Such knowledge of a histone modification regulatory network in this dinoflagellate, lays a necessary foundation for future research in related fields.</p

Genome Survey Sequencing and Genetic Background Characterization of <i>Gracilariopsis lemaneiformis</i> (Rhodophyta) Based on Next-Generation Sequencing

<div><p><i>Gracilariopsis lemaneiformis</i> 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 <i>Gp. lemaneiformis</i> 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 <i>Gp. lemaneiformis</i>. 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%.</p><p>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 <i>Gp. lemaneiformis</i> is a model organism for genetic study. This is the first report of genome-wide characterization within this taxon.</p></div

GC content and average sequencing depth of the genome data used for assembly.

<p>(The x-axis was GC content percent across every 10-kb non-overlapping sliding window).</p

Frequency of SSR types in the Genome Survey of <i>Gp. lemaneiformis</i>.

<p>Frequency of SSR types in the Genome Survey of <i>Gp. lemaneiformis</i>.</p

Summary of two paired-end libraries used for HiSeq 2000 Sequencing and paired-end sequencing datasets.

<p>Summary of two paired-end libraries used for HiSeq 2000 Sequencing and paired-end sequencing datasets.</p

Comparison of general genome characteristics from four red algae.

<p>Comparison of general genome characteristics from four red algae.</p

Percentage of the genome masked as each class of transposable elements.

<p>Note: RepBase TEs and TE proteins were obtained, using RepeatMasker and RepeatProteinMask respectively, based on the RepBase library; De novo repeat prediction identified repetitive DNA using RepeatMasker against the <i>de novo</i> repeat library of <i>Gp. lemaneiformis</i>, which was constructed by the programs LTR-FINDER, Piler and RepeatScout; Combined TEs were the integration and filtering redundancies of the above three methods.</p

Summary of match sequence between <i>Gracilariopsis lemaneiformis</i> and <i>Chlorella variabili</i>.

<p>Summary of match sequence between <i>Gracilariopsis lemaneiformis</i> and <i>Chlorella variabili</i>.</p

Statistics of the genome assembly.

<p>Statistics of the genome assembly.</p