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.
Highlights
Green algae extranuclear genomes date back at least one billion years [1] and account for 0.1% of the nuclear genome
Pseudendoclonium cpDNA features a large inverted repeat, its quadripartite structure is unusual in that it displays an ribosomal RNA (rRNA) operon transcribed toward the large singlecopy region and a small single-copy region containing 14 genes that are normally found in the large single-copy region [12]
The chloroplast genome clustered with peer-reviewed sequences previously identified as U. compressa (S1 Fig in S1 File)
Summary
Green algae extranuclear genomes date back at least one billion years [1] and account for 0.1% of the nuclear genome They are used to forecast the evolutionary trends of various species [2, 3]. Ulvophyceae evolution was studied using phylogenetic analysis of seven nuclear genes, small subunit nuclear rDNA, and the plastid genes rbcL and atpB [10], whereas Ulvales evolution was studied using rbcL and small subunit nuclear rDNA [11]. Results from these studies revealed a few unusual structural features based on the chloroplast genomes of individual species. A few studies have investigated chloroplast genome-based phylogeny within the genus Ulva, and no comparisons have been made with their corresponding mitogenomes [13, 14]
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