The complete mitochondrial genome sequence of the green microalga Lobosphaera (Parietochloris) incisa reveals a new type of palindromic repetitive repeat

Abstract

BackgroundLobosphaera incisa, formerly known as Myrmecia incisa and then Parietochloris incisa, is an oleaginous unicellular green alga belonging to the class Trebouxiophyceae (Chlorophyta). It is the richest known plant source of arachidonic acid, an ω-6 poly-unsaturated fatty acid valued by the pharmaceutical and baby-food industries. It is therefore an organism of high biotechnological interest, and we recently reported the sequence of its chloroplast genome.ResultsWe now report the complete sequence of the mitochondrial genome of L. incisa from high-throughput Illumina short-read sequencing. The circular chromosome of 69,997 bp is predicted to encode a total of 64 genes, some harboring specific self-splicing group I and group II introns. Overall, the gene content is highly similar to that of the mitochondrial genomes of other Trebouxiophyceae, with 34 protein-coding, 3 rRNA, and 27 tRNA genes. Genes are distributed in two clusters located on different DNA strands, a bipartite arrangement that suggests expression from two divergent promoters yielding polycistronic primary transcripts. The L. incisa mitochondrial genome contains families of intergenic dispersed DNA repeat sequences that are not shared with other known mitochondrial genomes of Trebouxiophyceae. The most peculiar feature of the genome is a repetitive palindromic repeat, the LIMP (L. Incisa Mitochondrial Palindrome), found 19 times in the genome. It is formed by repetitions of an AACCA pentanucleotide, followed by an invariant 7-nt loop and a complementary repeat of the TGGTT motif. Analysis of the genome sequencing reads indicates that the LIMP can be a substrate for large-scale genomic rearrangements. We speculate that LIMPs can act as origins of replication. Deep sequencing of the L. incisa transcriptome also suggests that the LIMPs with long stems are sites of transcript processing. The genome also contains five copies of a related palindromic repeat, the HyLIMP, with a 10-nt motif related to that of the LIMP.ConclusionsThe mitochondrial genome of L. incisa encodes a unique type of repetitive palindromic repeat sequence, the LIMP, which can mediate genome rearrangements and play a role in mitochondrial gene expression. Experimental studies are needed to confirm and further characterize the functional role(s) of the LIMP.

The complete mitochondrial genome of a microalgae Chlamydomonas moewusii strain XJCH-01 from Tarim Basin of Xinjiang, China

“…However, there are two large direct repeat regions that do not appear to encode any functional mitochondrial molecule. The arrangement and composition of the mitochondrial genome are similar to the known microalgae genomes (Wolff et al 1994;Denovan-Wright et al 1998;Smith et al, 2011;Servin-Garciduenas and Martinez-Romero 2012;Tourasse et al 2015;Hu et al 2019;Huang et al 2019). However, it showed a big difference from the vertebrates (Liu et al 2016;Li, Liu, Sui, et al 2019;Li, Kiu, Zhang, 2019) and the Arthropoda (Lavrov et al 2000;Masta and Boore 2004;Choi et al 2007).…”

An optimized method for high quality DNA extraction from microalga Prototheca wickerhamii for genome sequencing

“…More recently, Tourasse et al have reported the complete mitochondrial genome sequence of Lobosphaera ( Parietochloris ) incisa , an oleaginous unicellular green alga belonging to the class Trebouxiophyceae, the same that the Prototheca genus is affiliated with. Here, DNA was extracted following the standard CTAB DNA extraction protocol, whose original description was provided 30 years ago [ 36 ]. Both these methods, under the LN and C designations, respectively, were tested in our study.…”

Characterization of an Oleaginous Unicellular Green Microalga, Lobosphaera incisa (Reisigl, 1964) Strain K-1, Isolated From a Tidal Flat in the Yellow Sea, Republic of Korea

“…Lobosphaera incisa ( Reisigl, 1964 ) comb. nov. is a coccoid, unicellular microalga belonging to the class Trebouxiophyceae (Chlorophyta), which has been isolated from alpine soil, freshwater habitats, and lichen photobionts ( Watanabe et al, 1996 ; Tourasse et al, 2015 ). This species was originally assigned to the genus Myrmecia , and then to Parietochloris , and was subsequently reclassified as Lobosphaera ( Friedl, 1995 ; Watanabe et al, 1996 ; Karsten et al, 2005 ).…”

“…This species was originally assigned to the genus Myrmecia , and then to Parietochloris , and was subsequently reclassified as Lobosphaera ( Friedl, 1995 ; Watanabe et al, 1996 ; Karsten et al, 2005 ). This oleaginous microalga is the richest known plant source of arachidonic acid (AA, C20:4ω6), one of the pharmaceutically valuable ω6 long-chain PUFA, and has, therefore, been biologically and genetically investigated with enormous biotechnological interests ( Bigogno et al, 2002a , b ; Khozin-Goldberg et al, 2002 ; Abu-Ghosh et al, 2015 ; Tourasse et al, 2015 , 2016 ).…”