Screening and verification of extranuclear genetic markers in green tide algae from the Yellow Sea

Abstract

Over the past decade, Ulva compressa, a cosmopolitan green algal species, has been identified as a component of green tides in the Yellow Sea, China. In the present study, we sequenced and annotated the complete chloroplast genome of U. compressa (alpha-numeric code: RD9023) and focused on the assessment of genome length, homology, gene order and direction, intron size, selection strength, and substitution rate. We compared the chloroplast genome with the mitogenome. The generated phylogenetic tree was analyzed based on single and aligned genes in the chloroplast genome of Ulva compared to mitogenome genes to detect evolutionary trends. U. compressa and U. mutabilis chloroplast genomes had similar gene queues, with individual genes exhibiting high homology levels. Chloroplast genomes were clustered together in the entire phylogenetic tree and shared several forward/palindromic/tandem repetitions, similar to those in U. prolifera and U. linza. However, U. fasciata and U. ohnoi were more divergent, especially in sharing complementary/palindromic repetitions. In addition, phylogenetic analyses of the aligned genes from their chloroplast genomes and mitogenomes confirmed the evolutionary trends of the extranuclear genomes. From phylogenetic analysis, we identified the petA chloroplast genes as potential genetic markers that are similar to the tufA marker. Complementary/forward/palindromic interval repetitions were more abundant in chloroplast genomes than in mitogenomes. Interestingly, a few tandem repetitions were significant for some Ulva subspecies and relatively more evident in mitochondria than in chloroplasts. Finally, the tandem repetition [GAAATATATAATAATA × 3, abbreviated as TRg)] was identified in the mitogenome of U. compressa and the conspecific strain U. mutabilis but not in other algal species of the Yellow Sea. Owing to the high morphological plasticity of U. compressa, the findings of this study have implications for the rapid non-sequencing detection of this species during the occurrence of green tides in the region.

Ulva: An emerging green seaweed model for systems biology

“…Seven chloroplast and five mitochondrial genomes are currently available. Similar to the nuclear genome, intraspecific differences in organelle genome size due to gain or loss of group I/II introns and the integration of foreign DNA fragments and non‐coding intergenic spacer regions have been observed, which is remarkable because most sequenced strains originate from the same geographic area (Yellow Sea; Cai et al, 2018, 2021; Liu et al, 2020; Liu & Melton, 2021; Xia, He, et al, 2021; Xia, Qin, et al, 2021).…”

The unheeded existence of the tubular greens: molecular analyses reveal the distribution of a new Ulva species (Ulvophyceae, Chlorophyta), Ulva capillata sp. nov. in the Atlantic-Baltic Sea transect

“…Ulva species are considered nitrophilic organisms, as they can be indicative of eutrophic environments (Kraft et al 2010) and generally have high metabolic growth rates (Rosenberg and Ramus 1984;Teichberg et al 2010). Due to their ability to proliferate and form blooms (also called green tides) (Blomster et al 1998;Smetacek and Zingone 2013;Cai et al 2021), some Ulva species have attracted interest both from state agencies and policy makers (e.g. driven by the EU´s Water Framework Directive 2000/60/EG) to support biodiversity monitorings, as well as from the emerging aquaculture sector as suitable crop strains (Bolton et al 2009;Carl et al 2014;Califano et al 2020;Olsson et al 2020;Steinhagen et al 2021;2022a;.…”

Complete organellar genomes of six Sargassum species and development of species-specific markers

“…Therefore, it is difficult to classify these species based on morphological characteristics alone.Plastids and mitochondria are organelles that have evolved by endosymbiotic interactions with cyanobacteria and proteobacteria, respectively 12 . These organelles possess independent genomes; thus, the genetic information of these organelles is widely used as molecular markers to infer evolutionary relationships 13,14 . As next-generation sequencing (NGS) technologies have become cheaper and faster, a greater number of complete organellar genome sequences have been published.…”