Ulva prolifera is the dominant species of green macroalgal blooms in the Yellow Sea, China. In this study, we sequenced and annotated the complete chloroplast genome of U. prolifera (GenBank accession number: KX342867). The genome of circular chromosomes consists of 93,066 including 66 protein-encoding genes, 26 tRNA genes, and 3 rRNA genes. Compared with the 16 species from Chlorophyta, it has eight genes in expansion and 15 genes in shrink. Phylogenetic analysis shows positioned U. prolifera with U. linza, while Ulva sp.UNA00071828 is closely allied with Ulva fasciata.

Since 2007, the annual green tide disaster in the Yellow Sea has brought serious economic losses to China. There is no research on the genetic similarities of four constituent species of green tide algae at the genomic level. We previously determined the mitochondrial genomes of Ulva prolifera, Ulva linza and Ulva flexuosa. In the present work, the mitochondrial genome of another green tide (Ulva compressa) was sequenced and analyzed. With the length of 62,311 bp, it contained 29 encoding genes, 26 tRNAs and 10 open reading frames. By comparing these four mitochondrial genomes, we found that U. compressa was quite different from the other three types of Ulva species. However, there were similarities between U. prolifera and U. linza in the number, distribution and homology of open reading frames, evolutionary and codon variation of tRNA, evolutionary relationship and selection pressure of coding genes. Repetitive sequence analysis of simple sequence repeats, tandem repeat and forward repeats further supposed that they have evolved from the same origin. In addition, we directly analyzed gene homologies and translocation of four green tide algae by Mauve alignment. There were gene order rearrangements among them. With fast-evolving genomes, these four green algal mitochondria have both conservatism and variation, thus opening another window for the understanding of origin and evolution of Ulva.

Ulva flexuosa, one kind of green tide algae, has outbroken in the Yellow Sea of China during the past ten years. In the present study, we sequenced the chloroplast genome of U. flexuosa followed by annotation and comparative analysis. It indicated that the chloroplast genomes had high conservation among Ulva spp., and high rearrangement outside them. Though U. flexuosa was closer to U. linza than U. fasciata in phylogenetic tree, the average Ka/Ks between U. flexuosa and U. linza assessed by 67 protein-coding genes was higher than those between U. flexuosa and other species in Ulva spp., due to the variation of psbZ, psbM and ycf20. Our results laid the foundation for the future studies on the evolution of chloroplast genomes of Ulva, as well as the molecular identification of U. flexuosa varieties.

Ulva linza is one of the causal species that result in the macroalgal blooms around Yellow Sea, China. The blooms have now become the world's largest green tide, making great disaster for the ecosystem. We analyzed whole genome sequence of chloroplast for the first time (GenBank accession number KX058323). It was found that the annular-shape genome was made up of 86,726 bp, including 67 protein coding genes. We then aligned amino acids of chlorophyta species containing 44 common genes in series as phylogenetic tree, which shows Chlorophyceae and Trebouxiophyceae separately cluster except for Leptosiraterrestri. In the phylogenetic tree of amino acid alignment, Ulvophyceae, Pedinophyceae, Prasinophytes and Chlorophyta incertae sedis are independent cluster respectively, and closer to Trebouxiophyceae in the origin.

Ulva prolifera (U. prolifera), a green macroalgae, is widely known as the dominant species of the world's largest macroalgal blooms in the Yellow Sea, China. In this study, we sequenced and annotated the complete mitochondrial genome of U. prolifera (GenBank accession number: KU161104). The genome consists of circular chromosomes of 61 962 bp and encodes a total of 26 protein-coding genes include nine ribosomal protein genes, five atp genes, three cox genes, eight nad genes and cob gene. Phylogenetic analysis showed U. prolifera clustered into Ulvo phyceae clade and had close genetic relationship with algae Ulva fasciata.