Genomic analyses of unique carbohydrate and phytohormone metabolism in the macroalga Gracilariopsis lemaneiformis (Rhodophyta)

Abstract

Background: Red algae are economically valuable for food and in industry. However, their genomic information is limited, and the genomic data of only a few species of red algae have been sequenced and deposited recently. In this study, we annotated a draft genome of the macroalga Gracilariopsis lemaneiformis (Gracilariales, Rhodophyta).

Results: The entire 88.98 Mb genome of Gp. lemaneiformis 981 was generated from 13,825 scaffolds (≥500 bp) with an N50 length of 30,590 bp, accounting for approximately 91% of this algal genome. A total of 38.73 Mb of scaffold sequences were repetitive, and 9281 protein-coding genes were predicted. A phylogenomic analysis of 20 genomes revealed the relationship among the Chromalveolata, Rhodophyta, Chlorophyta and higher plants. Homology analysis indicated phylogenetic proximity between Gp. lemaneiformis and Chondrus crispus. The number of enzymes related to the metabolism of carbohydrates, including agar, glycoside hydrolases, glycosyltransferases, was abundant. In addition, signaling pathways associated with phytohormones such as auxin, salicylic acid and jasmonates are reported for the first time for this alga.

Conclusion: We sequenced and analyzed a draft genome of the red alga Gp. lemaneiformis, and revealed its carbohydrate metabolism and phytohormone signaling characteristics. This work will be helpful in research on the functional and comparative genomics of the order Gracilariales and will enrich the genomic information on marine algae.

Keywords: Carbohydrate metabolism; Genomic analysis; Gracilariopsis lemaneiformis; Phytohormone signaling.

Fig. 1

Circular diagram depicting the genomic features of the top 20 longest contigs. The outer ring represents the top 20 longest contigs, and the black blocks represent the predicted genes. The middle ring shows the GC content of the corresponding contigs in 1 kb bins. The inner rings show expression of the predicted genes. The blue color indicates low expression, and the red color indicates high expression. The links in the plot represent similarity between the contigs

Fig. 2

Repetitive element distribution in the Gp. lemaneiformis genome. LINEs, long interspersed repeated DNA elements. LTR, long terminal repeat; RC/Helitron, rolling-circle transposon

Fig. 3

Comparative genomic analysis of Gp. lemaneiformis. a The phylogenetic tree was generated using the maximum likelihood method based on single-copy genes shared between algal and plant genomes. b The Venn diagram represents the Gp. lemaneiformis genes shared in the C. crispus, C. merolae and G. sulphuraria genomes. c Gene models of Gp. lemaneiformis are compared with the characterized genomes in the non-redundant protein database using BLASTp. The number of organisms with the top BLASTp hits against Gp. lemaneiformis is indicated

Fig. 4

GO and KEGG analyses of the Gp. lemaneiformis genome. a GO terms derived from the Gp. lemaneiformis gene models. b KEGG pathway lists for Gp. lemaneiformis

Fig. 5

Analysis of genes potentially involved in agar biosynthesis. Gene homologs in the agar biosynthetic pathways in Gp. lemaneiformis compared with those in C. merolae, N. gaditana, E. siliculosus, C. reinhardtii and P. tricornutum. The colored squares denote the number of homologous genes in each species. The step numbers and their representative enzymes are 1. phosphoglucose isomerase; 2. phosphoglucomutase; 3. UTP-glucose-1-phosphate uridylyltransferase; 4. galactose-1-phosphate uridylyltransferase; 5. UDP galactosyltransferase; 6. phosphomannose isomerase; 7. phosphomannomutase; 8. GTP-mannose-1-phosphate guanylyltransferase; 9. GDP-mannose-3,5-epimerase; 10. GDP galactosyltransferase; 11. UDP-glucose pyrophosphorylase; 12. GDP-mannose-3,5-epimerase (the same as 9)