Chloroplast genome of Sargassum horneri (Sargassaceae, Phaeophyceae): comparative chloroplast genomics of brown algae

Abstract

Sargassum horneri (Turner) C. Agardh is an important canopy-forming seaweed native to the northwestern Pacific coast growing in the upper sublittoral zone. In this study, the chloroplast genome of S. horneri was fully sequenced and compared with three other brown algal chloroplast genomes. The S. horneri chloroplast genome is 124,068 bp in size with an inverted repeat of 5436 bp and is slightly smaller than the other three brown algal chloroplast DNAs (cpDNAs). It contains 173 genes, including 6 ribosomal RNA (rRNA) genes, 28 transfer RNA (tRNA) genes, and 139 protein-coding genes (PCGs). The coding sequence constitutes 86.32 % of the S. horneri cpDNA. The total spacer size was found to be reduced to 16,967 bp with an average length of 101.0 bp, which makes the S. horneri cpDNA more compact than the other three brown algal cpDNAs. Sixteen small inverted and nine tandem repeats were detected in S. horneri chloroplast genomes. Two introns in trnL2 and trnW genes were identified with the size of 209 and 90 bp, respectively. Its gene content and order are identical to those of Fucus vesiculosus cpDNA, indicating that the chloroplast genome organization at the level of the order Fucales is highly conserved.

Comparative mitochondrial and chloroplast genomics of a genetically distinct form of Sargassum contributing to recent “Golden Tides” in the Western Atlantic

“…For chloroplast genomes that were most complete S. natans VIII (C6) and the S. natans I (C2), gene synteny and content were identical to S. horneri with 173 genes (Table S2), including six coding for rRNA genes (two copies each) and 28 coding for tRNA genes (with multiple copies of some, designated with a “1” or a “2” in Table S2). As described extensively in Liu and Pang (), there is a high degree of conservation in chloroplast DNA among the brown algae and our results were consistent with this finding.…”

“…In addition to comparisons between mitogenomes and nuclear marker genes used in other studies targeting Sargassum , we also compared the chloroplast coding regions that we were able to recover from mapping reads from our six representative samples against the full‐length chloroplast genome of S. horneri as a reference (Liu & Pang, ). Near‐complete chloroplast genomes were recovered from one of the S. natans VIII samples (C6) and the S. natans I sample (C2) and included all of the coding regions reported in S. horneri .…”

“…Likewise, differences in chloroplast coding regions are modest at best. In their comparative chloroplast genomics of four brown algae including S. horneri , Fucus vesiculosus , Saccharina japonica , and Ectocarpus siliculosus , Liu and Pang () found that despite a smaller chloroplast genome size, S. horneri shared all the same genes and gene order (synteny) as F . vesiculosus .…”

“…The use of mitogenomes to differentiate between different species of Sargassum has recently provided a bit of traction in terms of offering new sets of genetic markers for population studies of Sargassum species from the Pacific (Bi & Zhou, ; Liu & Pang, ; Liu, Pang, & Chen, ; Liu, Pang, Li, & Li, ; Liu, Pang, & Luo, ). In addition to mitochondrial genomes, the first Sargassum chloroplast genome from the benthic species S. horneri recently became available providing another source of potential marker genes (Liu & Pang, ).…”

Insights on the Sargassum horneri golden tides in the Yellow Sea inferred from morphological and molecular data

“…A sample of sessile S. horneri previously collected from the rocky shores of Xiaohuyu, Nanji Islands, Zhejiang Province, China, was identified to harbor a 34,606 bp mitochondrial genome (mtDNA, Liu et al ) and a 124,068 bp plastid genome (ptDNA, Liu and Pang ). This genomic data provides a valuable source for the exploration of new DNA markers.…”