The Complete Plastid Genomes of Seven Sargassaceae Species and Their Phylogenetic Analysis

Abstract

Sargassum is one of the most important genera of the family Sargassaceae in brown algae and is used to produce carrageenan, mannitol, iodine, and other economic substances. Here, seven complete plastid genomes of Sargassum ilicifolium var. conduplicatum, S. graminifolium, S. phyllocystum, S. muticum, S. feldmannii, S. mcclurei, and S. henslowianum were assembled using next-generation sequencing. The sizes of the seven circular genomes ranged from 124,258 to 124,563 bp, with two inverted regions and the same set of plastid genes, including 139 protein-coding genes (PCGs), 28 transfer (t)RNAs, and 6 ribosomal (r)RNAs. Compared with the other five available plastid genomes of Fucales, 136 PCGs were conserved, with two common ones shared with Coccophora langsdorfii, and one with S. fusiforme and S. horneri. The co-linear analysis identified two inversions of trnC(gca) and trnN(gtt) in ten Sargassum species, against S. horneri and C. langsdorfii. The phylogenetic analysis based on the plastid genomes of 55 brown algae (Phaeophyceae) showed four clades, whose ancient ancestor lived around 201.42 million years ago (Mya), and the internal evolutionary branches in Fucales started to be formed 92.52 Mya, while Sargassum species were divided into two subclades 14.33 Mya. Our novel plastid genomes provided evidence for the speciation of brown algae and plastid genomic evolution events.

Keywords: Sargassaceae; brown algae; co-linear analysis; comparative analysis; phylogenetic analysis; plastid genome.

FIGURE 1

Gene maps of the plastid genomes of S. ilicifolium var. conduplicatum (A), S. graminifolium (B), S. phyllocystum (C), S. muticum (D), S. feldmannii (E), S. mcclurei (F), and S. henslowianum (G). Genes on the outside of the maps are transcribed in a clockwise direction, whereas those on the inside of the maps are transcribed counterclockwise.

FIGURE 2

Whole-genome multiple alignments of 12 plastid genomes from the order Fucales using the Mauve software. The alignment display is organized into one horizontal “panel” per input genome sequence. Each panel of the genome contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal centerline. When a block lies above the centerline, the aligned region is in the forward orientation relative to the first genome sequence. The blocks below the centerline indicate the regions that align in the reverse complement (inverse) orientation. The colored blocks in the first genome are connected by lines to the similarly colored blocks in other genomes. The area circled in red is the inverted repeat (IR) region, the purple block is the large single-copy (LSC) region, and the yellow block is the small single-copy region (SSC) region.

FIGURE 3

The phylogenetic tree [maximum likelihood (ML) and Bayesian inference (BI)] of 55 species from the class Phaeophyceae based on 73 shared plastid protein-encoding genes (A) and 18 species from the order Fucales based on 125 shared plastid protein-encoding genes (B). The support values for each node are shown from maximum-likelihood bootstrap and Bayesian posterior probabilities. The asterisks indicate newly sequenced S. ilicifolium var. conduplicatum, S. graminifolium, S. phyllocystum, S. muticum, S. feldmannii, S. mcclurei, and S. henslowianum in this study.

FIGURE 4

The chronogram resulting from the relaxed molecular clock analysis performed using the program MCMCtree in PAML. The time unit is 1 Mya.