Chloroplast Genomes of the Green-Tide Forming Alga Ulva compressa: Comparative Chloroplast Genomics in the Genus Ulva (Ulvophyceae, Chlorophyta)

Feng Liu,James T Melton

doi:10.3389/fmars.2021.668542

Abstract

To understand the evolution of Ulva chloroplast genomes at intraspecific and interspecific levels, in this study, three complete chloroplast genomes of Ulva compressa Linnaeus were sequenced and compared with the available Ulva cpDNA data. Our comparative analyses unveiled many noticeable findings. First, genome size variations of Ulva cpDNAs at intraspecific and interspecific levels were mainly caused by differences in gain or loss of group I/II introns, integration of foreign DNA fragments, and content of non-coding intergenic spacer regions. Second, chloroplast genomes of U. compressa shared the same 100 conserved genes as other Ulva cpDNA, whereas Ulva flexuosa appears to be the only Ulva species with the minD gene retained in its cpDNA. Third, five types of group I introns, most of which carry a LAGLIDADG or GIY-YIG homing endonuclease, and three of group II introns, usually encoding a reverse transcriptase/maturase, were detected at 26 insertion sites of 14 host genes in the 23 Ulva chloroplast genomes, and many intron insertion-sites have been found for the first time in Chlorophyta. Fourth, one degenerate group II intron previously ignored has been detected in the infA genes of all Ulva species, but not in the closest neighbor, Pseudoneochloris marina, and the other chlorophycean taxa, indicating that it should be the result of an independent invasion event that occurred in a common ancestor of Ulva species. Finally, the seven U. compressa cpDNAs represented a novel gene order which was different from that of other Ulva cpDNAs. The structure of Ulva chloroplast genomes is not conserved, but remarkably plastic, due to multiple rearrangement events.

Highlights

The green algal class Ulvophyceae, as one of the five classes of green algae in the core Chlorophyta (Cocquyt et al, 2010; Lang and Nedelcu, 2012; Fucíková et al, 2014), encompasses at least ten orders and more than 1,900 species (Mine et al, 2008; Leliaert et al, 2012; Guiry and Guiry, 2021)
The intron infA62 in U. compressa ranged in size from 728 bp in Uco2 to 761 bp in Uco3, and Uco5-7, which were larger than that in other Ulva species (556-650 bp) (Table 4). This intron was degenerate in all these Ulva cpDNAs and its intronic orf was completely lost, whereas the sequences of splicing sites and domain V were highly conserved. This intron was absent in the closest neighbor of Ulva species, Pseudoneochloris marina (Ulvaceae), and the other chlorophycean taxa, indicating that it should be the result of an independent invasion event occurred in a common ancestor of Ulva species by horizontal transfer
Our study illustrated the remarkable plasticity of Ulva chloroplast genomes among congeneric species, even within the species (e.g., U. compressa and U. australis)

Summary

Introduction

The green algal class Ulvophyceae, as one of the five classes of green algae in the core Chlorophyta (Cocquyt et al, 2010; Lang and Nedelcu, 2012; Fucíková et al, 2014), encompasses at least ten orders and more than 1,900 species (Mine et al, 2008; Leliaert et al, 2012; Guiry and Guiry, 2021). The circular ulvophycean chloroplast genomes range in size from the smallest one with 74.5 kb in Callipsygma wilsonis (Bryopsidales) (Cremen et al, 2018) to the largest with 399.4 kb in Trentepohlia odorata (Trentepohliales) (Zhu et al, 2019). These ulvophycean chloroplast genomes display great variations at the interspecific level in gene content, gene density, content of group I and II intron, gene order, copies of large inverted repeat (IR), and genome architecture (Turmel et al, 2017; Turmel and Lemieux, 2018; Kim et al, 2019). Morphological, anatomical, cytological, mating, and molecular characteristics have been used to evaluate species concepts in this genus (Liu et al, 2013; Hiraoka et al, 2017; Hughey et al, 2019), while molecular data has become a more reliable and commonly used method for species identifications

Methods

Results

Conclusion