The complete mitochondrial genome of the Caulerpa lentillifera (Ulvophyceae, Chlorophyta): Sequence, genome content, organization structure and phylogenetic consideration

Peer Review #1 of "The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns (v0.1)"

“…The overall GC content of the genome is 48.3% (Table 1), which is higher than the average for eukaryotic mitochondrial genomes (38%) (Smith & Lee, 2007) but similar to that of C. lentillifera (50.9%) (Zheng et al, 2018) and not extreme for green algae (Del Vasto et al, 2015).…”

“…The Caulerpa lentillifera mitochondrial genome (Genbank accession KX761577.1) (Zheng et al, 2018) was used as the query in a BLASTn search against the long-read Canu assembly within Geneious version 11.1.2 (Kearse et al, 2012) This contig was used as the query in a BLASTn search against the O. quekettii Spades short-read assembly, within Geneious with default settings. Top hits were aligned with the long-read contig within Geneious.…”

“…Only ORFs that had BLAST results and identified Pfam domains were retained in the final genome annotation. In order to determine relationships between ORFs indicative of common origin, the annotated ORFs along with those from the chloroplast genome of O. quekettii (Marcelino et al, 2016) and the mitochondrial genome of C. lentillifera (Zheng et al, 2018) were clustered based on all-againstall BLAST+ similarities using CLANs (Frickey & Lupas, 2004). This was performed through the MPI Bioinformatics toolkit (Zimmermann et al, 2018), with the BLOSUM62 scoring matrix and extraction of BLAST HSPs up to e-values of 1e-4.…”

“…Within the Bryopsidales, the size and gene arrangement of chloroplast genomes has been found to vary considerably while gene content was much less variable (Cremen et al, 2018). While appreciable short-read sequencing data have been generated for the Bryopsidales, mitochondrial genomes have not been found to assemble well from the sequencing libraries used to assemble chloroplast genomes, and the first bryopsidalean mitochondrial genome was published only very recently for the sea grape Caulerpa lentillifera (Zheng et al, 2018). This 209,034 bp circular-mapping genome is the largest Chlorophyta mitochondrial genome published to date, an order of magnitude larger than the average for Chlorophyta mitochondrial genomes and rich in intergenic sequences and introns, the causes of which have not been examined.…”

“…Furthermore, mitochondrial genome expansion is less frequent in green algae compared with plants (Mower et al, 2012). While Zheng et al (2018) Manuscript to be reviewed 2016). Therefore, the mitochondrial genome of C. lentillifera provides an interesting case in the Chlorophyta to examine the evolution of organellar genomes and, in particular, the processes driving genome expansion.…”