Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation

Phylogeny and Evolution of Cocconeiopsis (Cocconeidaceae) as Revealed by Complete Chloroplast and Mitochondrial Genomes

The genus Cocconeiopsis was separated from Navicula, but its systematic position is in debate. We sequenced the complete chloroplast and mitochondrial genome of Cocconeidaceae for the first time with Cocconeiopsis kantsiensis and investigated its phylogeny and evolutionary history. Results showed that the plastid genome was 140,415 bp long with 167 genes. The mitochondrial genome was 43,732 bp long with 66 genes. Comparative analysis showed that the plastid genome structure of C. kantsiensis was most similar to those of three Navicula species and Halamphora americana, and its size was significantly smaller than that of a monoraphid species. Its mitochondrial genome was similar to that of related species except for Phaeodactylum tricornutum. The multigene phylogeny reconstruction showed that Cocconeiopsis was sister to Didymosphenia but distant from Naviculaceae. The two-gene phylogenetic analysis containing 255 species showed Cocconeiopsis was sister to Cocconeis, and distant from Naviculaceae as well. Divergence time estimation indicates the common ancestor of cocconeid species occurred about 62.8 Ma and Cocconeiopsis diverged with monoraphid Cocconeis about 58.9 Ma. Our results support the assignment of Cocconeiopsis to Cocconeidaceae and that monoraphid cocconeids were likely evolved from the lineage of Cocconeiopsis.

Evolutionary dynamics of plastomes in coscinodiscophycean diatoms revealed by comparative genomics

To understand the evolution of coscinodiscophycean diatoms, plastome sequences of six coscinodiscophycean diatom species were constructed and analyzed in this study, doubling the number of constructed plastome sequences in Coscinodiscophyceae (radial centrics). The platome sizes varied substantially in Coscinodiscophyceae, ranging from 119.1 kb of Actinocyclus subtilis to 135.8 kb of Stephanopyxis turris. Plastomes in Paraliales and Stephanopyxales tended to be larger than those in Rhizosoleniales and Coscinodiacales, which were due to the expansion of the inverted repeats (IRs) and to the marked increase of the large single copy (LSC). Phylogenomic analysis indicated that Paralia and Stephanopyxis clustered tightly to form the Paraliales-Stephanopyxales complex, which was sister to the Rhizosoleniales-Coscinodiscales complex. The divergence time between Paraliales and Stephanopyxales was estimated at 85 MYA in the middle Upper Cretaceous, indicating that Paraliales and Stephanopyxales appeared later than Coscinodiacales and Rhizosoleniales according to their phylogenetic relationships. Frequent losses of housekeeping protein-coding genes (PCGs) were observed in these coscinodiscophycean plastomes, indicating that diatom plastomes showed an ongoing reduction in gene content during evolution. Two acpP genes (acpP1 and acpP2) detected in diatom plastomes were found to be originated from an early gene duplication event occurred in the common progenitor after diatom emergence, rather than multiple independent gene duplications occurring in different lineages of diatoms. The IRs in Stephanopyxis turris and Rhizosolenia fallax-imbricata exhibited a similar trend of large expansion to the small single copy (SSC) and slightly small contraction from the LSC, which eventually led to the conspicuous increase in IR size. Gene order was highly conserved in Coscinodiacales, while multiple rearrangements were observed in Rhizosoleniales and between Paraliales and Stephanopyxales. Our results greatly expanded the phylogenetic breadth in Coscinodiscophyceae and gained novel insights into the evolution of plastomes in diatoms.