Organization of plastid genomes in the freshwater red algal order Batrachospermales (Rhodophyta)

Abstract

Little is known about genome organization in members of the order Batrachospermales, and the infra‐ordinal relationship remains unresolved. Plastid (cp) genomes of seven members of the freshwater red algal order Batrachospermales were sequenced, with the following aims: (i) to describe the characteristics of cp genomes and compare these with other red algal groups; (ii) to infer the phylogenetic relationships among these members to better understand the infra‐ordinal classification. Cp genomes of Batrachospermales are large, with several cases of gene loss, they are gene‐dense (high gene content for the genome size and short intergenic regions) and have highly conserved gene order. Phylogenetic analyses based on concatenated nucleotide genome data roughly supports the current taxonomic system for the order. Comparative analyses confirm data for members of the class Florideophyceae that cp genomes in Batrachospermales is highly conserved, with little variation in gene composition. However, relevant new features were revealed in our study: genome sizes in members of Batrachospermales are close to the lowest values reported for Florideophyceae; differences in cp genome size within the order are large in comparison with other orders (Ceramiales, Gelidiales, Gracilariales, Hildenbrandiales, and Nemaliales); and members of Batrachospermales have the lowest number of protein‐coding genes among the Florideophyceae. In terms of gene loss, apcF, which encodes the allophycocyanin beta subunit, is absent in all sequenced taxa of Batrachospermales. We reinforce that the interordinal relationships between the freshwater orders Batrachospermales and Thoreales within the Nemaliophycidae is not well resolved due to limited taxon sampling.

Relative expression analysis of light‐harvesting genes in the freshwater alga Lympha mucosa (Batrachospermales, Rhodophyta)

“…, Paiano et al. ). Complete protein synthesis within the plastid makes these transcription factors ideal for activating rapid transcriptional responses of plastid‐encoded genes, and this may contribute to the greater degree of transcriptional regulation in red algal plastids relative to green algal and land plant chloroplasts, which have lost these response regulatory proteins (Minoda et al.…”

Complete mitochondrial genomes of six species of the freshwater red algal order Batrachospermales (Rhodophyta)

“…Algal materials, protocols and analyses were the same applied in a previous study on Batrachospermales plastid genomes (Paiano et al 2017). Only the methods that are specific to this study are described here.…”

“…Yang et al 2016;Salomaki and Lane 2016), only two mt genomes were described for members of Batrachospermales so far: Sheathia arcuata by Nan et al (2017) and Lympha mucosa by Wolf et al (2017). This contrasts with the eight plastid genomes described for species of the order (Lee et al 2016;Nan et al 2017;Paiano et al 2017).…”

Gene‐rich plastid genomes of two parasitic red algal species, Laurencia australis and L. verruciformis (Rhodomelaceae, Ceramiales), and a taxonomic revision of Janczewskia

“…In contrast, ycf46 is predicted to play a role in the uptake and utilization of CO 2 during photosynthesis (Jiang et al, 2015). The loss of ycf46 in the plastid genome is not unusual in free-living red algae and has been observed in the freshwater orders Balbianiales, Batrachospermales, and Thoreales (Cho et al, 2018;Evans et al, 2019;Paiano et al, 2018). This could indicate that the loss of ycf46 is not linked to parasitism but an easily lost function.…”