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

Abstract

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.

Figure 1. GC content and average sequencing depth of the genome data used for assembly.

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

Figure 2. Distribution of 17-mer frequency in the 3.5 Gb sequences (3.5 Gb = 18.70 Gb*30X/162X).

Figure 3. GO category comparison among Gp. lemaneiformis, P. yezoensis, Cy. merolae and Ch. crispus.

Figure 4. Frequency of SSR types in the Genome Survey of Gp. lemaneiformis.

Figure 5. Percentage of different motifs in dinucleotide repeats in Gp. lemaneiformis.

Figure 6. Percentage of different motifs in trinucleotide repeats in Gp. lemaneiformis.