Study On Organelle Genome And It’s Transcriptome Analysis Of Brasenia Schreberi

Brasenia schreberi J.F.Gmel.is a perennial aquatic plant in Cabombaceae(Nymphaeales),and belongs to the ANA grade in APG IV System.As a reletively primitive angiosperms,B.schreberi is mainly distributed in China,Japan,North America and the East of Oceania,and its wild species are listed as the first-class national key protected plants in China.Moreover,B.schreberi is a traditional Chinese medicinal and food plant,rich in polysaccharides,protein,polyphenols,trace elements,vitamins,and other active ingredients,with antibacterial and anti-inflammatory,anti-tumor,and hypoglycemic effects.Chloroplast(or plastid)and mitochondria,as semi-autonomous organelles in cells,each have a genetic system independent of the nuclear genome in plant.Endosymbiosis hypothesis suggests that mitochondria and chloroplasts originated from aerobic bacteria and photoautotrophic cyanobacteria in prokaryotic cells,respectively,and established a stable regulatory mechanism with nuclear genome during the long evolutionary process.At present,the researches of B.schreberi at domestic and overseas are scattered,mainly focusing on cultivation and management,morphology and anatomy,food,etc.,but there are few basic researches on molecular or genomics.The chloroplast genome of B.schreberi has been reported,but the mitochondrial genome has not,and systematic and comprehensive organelle genome research is still lacking.In this study,the chloroplast genomes of two species of B.schreberi collected from different fields were sequenced and assembled based on Illumina sequencing platform,and they were compared and analyzed with other Nymphaeales plants.Secondly,the mitochondrial genome of B.schreberi was assembled using Oxford nanopore sequencing data,and the comparative genomics of the mitochondrial genome of B.schreberi was studied.Finally,based on transcriptome data,transcripts from organelles were analyzed to identify cotranscriptional units and post-transcriptional RNA editing of organelles encoding genes,and the intron splicing intermediates of organelles’ split genes were also analyzed.The main results are as follows:(1)The chloroplast genome size of the two species of B.schreberi were 158,973 bp and 158,974 bp,respectively.Both were conserved circular molecules with typical tetrad structure and encoded 114 unique genes.The number of repeated sequences in the chloroplast genome of B.schreberi was low,and the Protein-coding Genes(PCGs)have strong codon preference.In terms of structure and sequence characteristics,the chloroplast genome of B.schreberi was highly similar to that of other previously published plants in Nymphaeales,indicating that the chloroplast genome was extremely conserved in structure.(2)The mitochondrial genome of B.schreberi mainly exists in the form of six independent circular molecules,with a length of 628,257 bp,305,975 bp,169,216 bp,159,827 bp,151,102 bp and 110,220 bp,respectively.The total length was about 1.49 Mb.The mitochondrial genome of B.schreberi encodes 60 unique genes,including 39 PCGs,3 Ribosome RNA genes(r RNA)and 18 transfer RNA genes(t RNA).Compared with chloroplast genome,a large number of repeat elements were identified in its mitochondrial genome,but the mitochondrial PCGs were not as good at codon preference as chloroplast genome.Collinearity analysis of the mitochondrial genome of B.schreberi and its related species showed that the mitochondrial genome had highly complex variations in size and structure and had poor collinearity.(3)The homologous sequences among chloroplast and mitochondrial genomes of B.schreberi were identified.The results showed that there were 38 homologous sequences of over 500 bp in length derived from chloroplast in mitochondrial genome,among which the longest sequence was 3,906 bp.These homologous sequences contained 39 chloroplast PCGs fragments and 15 chloroplast t RNA gene fragments.Among them,four t RNA genes(trn A-UAG,trn N-GUU,trn Q-UUG and trn V-GAC)were identical with chloroplast t RNA in sequence,and they were most likely transferred horizontally from chloroplast genome.(4)Based on transcriptome data,there were 496 high-quality RNA editing sites in34 mitochondrial PCGs of B.schreberi were identified.In contrast,a total of 62 RNA editing sites were identified on PCGs of chloroplasts,far fewer than in mitochondria.In terms of editing types,both organelle genomes were dominated by C-U editing,but all11 editing types except A-U editing were identified on mitochondrial genome,while only6 different editing types were identified on chloroplast PCGs.(5)In B.schreberi,there were 15 and 23 Polycistronic Transcription Units(PTU)were identified in mitochondrial and chloroplast genomes,respectively.In addition,only about 1.6 kb region of the chloroplast genome could not be covered by transcripts,that is,more than 98.9% region was observed to be transcribed,indicating that the chloroplast genome of B.schreberi was almost fully transcribed.(6)Transcriptional analysis of split genes from organelles showed that there were abundant intron splicing intermediates in all split genes of organelles in B.schreberi.Among them,it was found that introns near cis-splicing site were always spliced before introns near trans-splicing site on gene rps12.However,introns near some cis-splicing sites were observed to be spliced before introns near trans-splicing sites at gene nad1 and nad2,suggesting that intron splicing intermediates might be more abundant than previously expected.