Characterization of the complete mitochondrial genome of Coelastrum_sp.F187

Abstract

Coelastrum is a genus of green algae that belongs to the Scenedesmaceae family. There is little information available about this genus. A phylogenetic analysis of the ITS2 sequences showed that Coelastrum is a paraphyletic group. To better explore the phylogenetic status of this genus, we report the mitochondrial genome sequence of Coelastrum sp. F187 using next-generation sequencing technology. The complete mitochondrial genome is 52,888 bp in size and encodes 43 conventional mitochondrial genes, including 14 protein-coding genes (PCGs), 24 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Most of the PCGs (12/14) and all tRNAs were located in the heavy chain and the light chain, respectively. The phylogenetic analysis based on the complete mitochondrial genome sequences indicated that Coelastrum is closely related to Pectinodesmus pectinatus. The sequenced complete mitochondrial genome of Coelastrum sp. F187 provides fundamental molecular data that will be useful for species identification, population genetics, and evolutionary relationships.

Introduction

Although numerous mitogenomes have been sequenced in recent years (Cameron 2014), little is known about the mitochondrial genome of Coelastrum, a rare genus of green algae belonging to the Scenedesmaceae family. In our previous study, we isolated a microalgae morphologically designated to the Coelastrum genus (Coelastrum sp. F187) from Furong Lake in Fujian, China and deposited in Marine Medicinal Organism Germplasm Resources Bank of Third Institute of Oceanography (MMOGRB 0187F). The ITS analysis results indicated that it was primarily related to the strain Coelastrum astroideum var. rugosum UTEX2442 (Dong et al. 2013). To determine the evolutionary and phylogenetic origin of Coelastrum sp. F187, its complete mitochondrial genome was sequenced.

The mitochondrial genome of Coelastrum sp. F187 was sequenced with the Illumina HiSeq™ 2500 platform at the Beijing Genomic Institute (BGI, Shenzhen, China), by using the PE250 paired-end sequencing strategy. Approximately 3.7 Gb of raw data were generated and finally a total of 14.86 M raw reads were used to construct the genome. All published mitochondrial genome sequences available in NCBI were employed as references for the genome assembly with SOAPdenovo2 (http://soap.genomics.org.cn). Preliminarily gene annotation was conducted using the online program Dual Organellar GenoMe Annotator (DOGMA) (Wyman et al. 2004) and ORF Finder (Cheng et al. 2013) with the Scenedesmus obliquus mitochondrial genetic code and default conditions. To verify the exact gene and exon boundaries, the putative gene sequences and protein sequences were BLAST searched in the Nt and Nr databases. All transfer RNA (tRNA) genes were further confirmed using the online web servers tRNAscan-SE and ARWEN (Griffiths-Jones et al. 2003; Schattner et al. 2005; Abe et al. 2011). Phylogenetic analysis was performed using the maximum likelihood analysis implemented in MEGA6 (Tamura et al. 2013).

The complete mitogenome of Coelastrum sp. F187 has a total length of 52,888 bp, and the GC content of the mitochondrial DNA is 40.91%. The annotated genomic sequence can be obtained with accession number KY984063 in GenBank. The genome sequence contains 43 mitochondrial genes, including 14 protein-coding genes (PCGs), 24 tRNA genes, and 4 rRNA genes. The heavy chain encodes 11 PCGs and 1 tRNA gene, whereas the light chain encodes 2 PCGs, most of the tRNA genes (23/24) and all rRNA genes. The base composition of the Coelastrum sp. F187 mitochondrial genome is as follows: A (28.2%), T (30.8%), C (18.9%), and G (22.1%), with a total A + T content of 59%. To further explore its taxonomic status, maximum likelihood analyses of Coelastrum sp. F187 and 20 other published mitochondrial genomes in Chlorophyceae were reconstructed with the online program RaxML 8.1.5 (Stamatakis 2006). The ML tree suggests that Coelastrum is closely related to Pectinodesmus and forms a sister-group with Scenedesmus (Figure 1). This result is in agreement with previous phylogenetic results constructed using the ITS sequence. However, additional mitochondrial data from Scenedesmaceae are needed to show a clear phylogenetic pattern.

Figure 1.

Phylogeny of Coelastrum sp. F187 and other Chlorophyceae species based on the maximum likelihood (ML) analysis.

Disclosure statement

The authors declared no conflicts of interest to this work.