Chromosome-level genome assembly of agar-producing red seaweed Gracilaria vermiculophylla

TL;DR

This paper presents a high-quality chromosome-level genome assembly for the agar-producing red seaweed Gracilaria vermiculophylla.

Contribution

The study provides the first chromosome-level genome assembly for G. vermiculophylla using a combination of sequencing technologies.

Findings

The genome is 77.5 Mb in size with 22 pseudochromosomes and high contiguity metrics.

Transposable elements make up nearly half the genome, with LTR retrotransposons being the most common.

Over 10,600 protein-coding genes were identified, with most functionally annotated.

Abstract

As an agar-producing red seaweed, Gracilaria vermiculophylla plays a significant role in the food industry as well as in multiple fields, including evolutionary studies, genetic diversity analysis, and ecological research. However, a high-quality chromosome-level genome of G. vermiculophylla is not currently available. In this study, we report a high-quality chromosome-level genome for G. vermiculophylla combining short-read, Nanopore long-read, and Hi-C data. The finally assembled genome size is 77.5 Mb, with Contig N50 of 2.61 Mb and Scaffold N50 of 3.16 Mb, comprising 22 pseudochromosomes. The transposable elements (TEs) constituted 45.93 Mb of the G. vermiculophylla genome, with long terminal repeats (LTRs) accounting for 55.03% of the predominant retrotransposons. The G. vermiculophylla genome contains a total of 10,689 protein-coding genes, of which 86.14% have been functionally annotated. The BUSCO evaluation, GC content and sequencing depth assessment demonstrated the high quality of the assembly and the success of the decontamination process. The high-quality genomic information provides an invaluable resource for agar development, evolution studies, comparative genomics, genetic diversity analysis, and ecological research.

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