Six Newly Sequenced Chloroplast Genomes From Trentepohliales: The Inflated Genomes, Alternative Genetic Code and Dynamic Evolution

Abstract

Cephaleuros is often known as an algal pathogen with 19 taxonomically valid species, some of which are responsible for red rust and algal spot diseases in vascular plants. No chloroplast genomes have yet been reported in this genus, and the limited genetic information is an obstacle to understanding the evolution of this genus. In this study, we sequenced six new Trentepohliales chloroplast genomes, including four Cephaleuros and two Trentepohlia. The chloroplast genomes of Trentepohliales are large compared to most green algae, ranging from 216 to 408 kbp. They encode between 93 and 98 genes and have a GC content of 26–36%. All new chloroplast genomes were circular-mapping and lacked a quadripartite structure, in contrast to the previously sequenced Trentepohlia odorata, which does have an inverted repeat. The duplicated trnD-GTC, petD, and atpA genes in C. karstenii may be remnants of the IR region and shed light on its reduction. Chloroplast genes of Trentepohliales show elevated rates of evolution, strong rearrangement dynamics and several genes display an alternative genetic code with reassignment of the UGA/UAG codon presumably coding for arginine. Our results present the first whole chloroplast genome of the genus Cephaleuros and enrich the chloroplast genome resources of Trentepohliales.

Novel insights into chloroplast genome evolution in the green macroalgal genus Ulva (Ulvophyceae, Chlorophyta)

“…rpoB , rpoC1 , and rpoC2 ). Unlike those in Sykidiales ( Pseudoneochloris marina ), Ulotrichales, Oltmannsiellopsidales, Ignatiales and Trentepohliales ( Pombert et al., 2005 ; Turmel and Lemieux, 2018 ; Kim et al., 2019 ; Fang et al., 2021 ), most of intergenic regions are relatively short and the rRNA operon-encoding inverted repeat (IR) has been completely lost in Ulva plastomes. The minimum size of overall non-coding intergenic regions was only approximately 11.6 kb, which was observed in U. californica ( Uca ) ( Supplementary Table 2 ).…”

“…The GC composition of ulvophycean plastomes varies significantly among different lineages ( Turmel et al., 2017 ; Zhu et al., 2019 ; Fang et al., 2021 ), but particularly remarkable is that the GC content of Ulva cpDNAs was the lowest among the Ulvophyceae so far, ranging from 23.89 to 26.25% ( Figure 1 ), indicating the strong selection against GC to shape the nucleotide composition in Ulva plastomes. Due to that GC content showed greatly heterogeneity in distinct regions of Ulva plastomes, we analyzed the differences in GC content of overall core-gene coding regions, intronic regions, foreign sequence regions, and non-coding intergenic spacer regions among these 40 Ulva cpDNAs.…”

“…rpl23-rpl2-rps19-rps3-rpl16-rpl14-rpl5-rps8-infA-rpl36-rps11-rpoA-petB-petD , psaC-ycf20-ccsA-trnR1-ycf1-psbA , rns-trnI-trnA-rnl-rrn5-psaA , trnV-rpoB-rpoC1-rpoC2 , ycf3-psbI-psaI-psbN , and psbB-psbT-psbH , were observed to be shared only by plastomes of Ulva and Blidingia ( Figure 9 ), but they did not appear in plastomes of P. marina and other ulvophycean species (e.g. Pombert et al., 2005 ; Pombert et al., 2006 ; Leliaert and Lopez-Bautista, 2015 ; Turmel et al., 2017 ; Fang et al., 2021 ), indicating they have been formed and maintained in their common ancestor after divergence from P. marina . These findings provide important clues for us to understand genome structure and gene order of early IR-lacking plastomes in Ulvales.…”

“…The GC composition of ulvophycean plastomes varies significantly among different lineages (Turmel et al, 2017;Zhu et al, 2019;Fang et al, 2021), but particularly remarkable is that the GC content of Ulva cpDNAs was the lowest among the Ulvophyceae so far, ranging from 23.89 to 26.25% (Figure 1), indicating the strong selection against GC to shape the nucleotide The aligned sequences of trnR2(ucu) and trnR3(ccu) in Ulva plastomes. Shaded nucleotides indicated that bases could be paired.…”

Chloroplast Genome Traits Correlate With Organismal Complexity and Ecological Traits in Chlorophyta

“…One example of a terrestrial green alga with a large chloroplast genome is Floydiella terrestris, which has 521,168 bp cpDNA sequence, with intergenic regions accounting for 77.8% of the total chloroplast genome (Brouard et al, 2010). In the Ulvophyceae, the terrestrial Trentepohliales and Ulotrichales also tend to have relatively large genomes (Fang et al, 2021). A range of reasons could underly this trend.…”