Contradiction between Plastid Gene Transcription and Function Due to Complex Posttranscriptional Splicing: An Exemplary Study of ycf15 Function and Evolution in Angiosperms

Plant chloroplast genes are usually co-transcribed while its posttranscriptional splicing is fairly complex and remains largely unsolved. On basis of sequencing the three complete Camellia (Theaceae) chloroplast genomes for the first time, we comprehensively analyzed the evolutionary patterns of ycf15, a plastid gene quite paradoxical in terms of its function and evolution, along the inferred angiosperm phylogeny. Although many species in separate lineages including the three species reported here contained an intact ycf15 gene in their chloroplast genomes, the phylogenetic mixture of both intact and obviously disabled ycf15 genes imply that they are all non-functional. Both intracellular gene transfer (IGT) and horizontal gene transfer (HGT) failed to explain such distributional anomalies. While, transcriptome analyses revealed that ycf15 was transcribed as precursor polycistronic transcript which contained ycf2, ycf15 and antisense trnL-CAA. The transcriptome assembly was surprisingly found to cover near the complete Camellia chloroplast genome. Many non-coding regions including pseudogenes were mapped by multiple transcripts, indicating the generality of pseudogene transcriptions. Our results suggest that plastid DNA posttranscriptional splicing may involve complex cleavage of non-functional genes.

[1]  Patrick J. Biggs,et al.  SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data , 2010, BMC Bioinformatics.

[2]  R. Herrmann,et al.  Comparative analysis of plastid transcription profiles of entire plastid chromosomes from tobacco attributed to wild-type and PEP-deficient transcription machineries. , 2002, The Plant journal : for cell and molecular biology.

[3]  H. Kössel,et al.  RNA editing in maize chloroplasts is a processing step independent of splicing and cleavage to monocistronic mRNAs. , 1993, The Plant journal : for cell and molecular biology.

[4]  Ralph Bock,et al.  Horizontal transfer of chloroplast genomes between plant species , 2012, Proceedings of the National Academy of Sciences.

[5]  Chengying Shi,et al.  Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds , 2011, BMC Genomics.

[6]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[7]  D. Leister,et al.  Generation and evolutionary fate of insertions of organelle DNA in the nuclear genomes of flowering plants. , 2005, Genome research.

[8]  Jeffrey P. Mower,et al.  The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. , 2006, Molecular biology and evolution.

[9]  R. Jansen,et al.  Complete plastid genome sequences of three Rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleus. , 2011, Molecular biology and evolution.

[10]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[11]  Giorgio Valle,et al.  Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing , 2010, Nucleic acids research.

[12]  M. Hasegawa,et al.  Gene transfer to the nucleus and the evolution of chloroplasts , 1998, Nature.

[13]  M. Duvall,et al.  The chloroplast genome of Anomochloa marantoidea (Anomochlooideae; Poaceae) comprises a mixture of grass-like and unique features. , 2010, American journal of botany.

[14]  Konrad U. Förstner,et al.  The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA Polymerase[C][W][OA] , 2012, Plant Cell.

[15]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[16]  Chung-Yen Lin,et al.  The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. , 2006, Molecular biology and evolution.

[17]  M. Hanson,et al.  Chloroplast RNA metabolism. , 2010, Annual review of plant biology.

[18]  Robert K. Jansen,et al.  Automatic annotation of organellar genomes with DOGMA , 2004, Bioinform..

[19]  V. Goremykin,et al.  Analysis of the Amborella trichopoda chloroplast genome sequence suggests that amborella is not a basal angiosperm. , 2003, Molecular biology and evolution.

[20]  Jeffrey D. Palmer,et al.  Widespread horizontal transfer of mitochondrial genes in flowering plants , 2003, Nature.

[21]  W. Martin,et al.  Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes , 2004, Nature Reviews Genetics.

[22]  Linda A. Raubeson,et al.  Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus , 2007, BMC Genomics.

[23]  A. Barkan,et al.  Site‐specific binding of a PPR protein defines and stabilizes 5′ and 3′ mRNA termini in chloroplasts , 2009, The EMBO journal.

[24]  H. Doddapaneni,et al.  Cyanophora paradoxa Genome Elucidates Origin of Photosynthesis in Algae and Plants , 2012, Science.

[25]  J. Leebens-Mack,et al.  Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids , 2006, BMC Evolutionary Biology.

[26]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[27]  Pamela S Soltis,et al.  Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms , 2007, Proceedings of the National Academy of Sciences.

[28]  A. Hirai,et al.  A transcription map of the chloroplast genome from rice (Oryza sativa) , 1993, Current Genetics.

[29]  M. S. Odintsova,et al.  Plastid Genomes of Higher Plants and Algae: Structure and Functions , 2003, Molecular Biology.

[30]  Alexandros Stamatakis,et al.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..

[31]  K. H. Wolfe,et al.  Complete Chloroplast Genome Sequence of a Major Allogamous Forage Species, Perennial Ryegrass (Lolium perenne L.) , 2009, DNA research : an international journal for rapid publication of reports on genes and genomes.

[32]  R. Mache,et al.  The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization , 2001, Plant Molecular Biology.

[33]  F. Takaiwa,et al.  The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression , 1986, The EMBO journal.

[34]  Ju Gao,et al.  An Improved Chloroplast DNA Extraction Procedure for Whole Plastid Genome Sequencing , 2012, PloS one.

[35]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[36]  J. Palmer,et al.  A transcription map of the pea chloroplast genome , 1988, Current Genetics.

[37]  T. Mondal.  Camellia biotechnology : a bibliographic search , 2001 .

[38]  Dorothy A Steane,et al.  Complete nucleotide sequence of the chloroplast genome from the Tasmanian blue gum, Eucalyptus globulus (Myrtaceae). , 2005, DNA research : an international journal for rapid publication of reports on genes and genomes.

[39]  Lars S. Jermiin,et al.  Many Parallel Losses of infA from Chloroplast DNA during Angiosperm Evolution with Multiple Independent Transfers to the Nucleus , 2001, Plant Cell.

[40]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[41]  Lianming Gao,et al.  Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics. , 2011, Genome.

[42]  M. Sugiura,et al.  Regulation of gene expression in chloroplasts of higher plants , 1996, Plant Molecular Biology.

[43]  Giorgio Valle,et al.  PASS: a program to align short sequences , 2009, Bioinform..

[44]  Ralph Bock,et al.  OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes , 2007, Current Genetics.

[45]  Jun Yu,et al.  The Complete Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L.) , 2010, PloS one.

[46]  James Leebens-Mack,et al.  Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns , 2007, Proceedings of the National Academy of Sciences.

[47]  T. Börner,et al.  The transcription machineries of plant mitochondria and chloroplasts: Composition, function, and regulation. , 2011, Journal of plant physiology.

[48]  G. Schuster,et al.  Evidence for in vivo modulation of chloroplast RNA stability by 3′-UTR homopolymeric tails in Chlamydomonas reinhardtii , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[49]  R. Jansen,et al.  Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage. , 2011, Molecular biology and evolution.

[50]  Sabine Cornelsen,et al.  Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[51]  G. Igloi,et al.  Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. , 1995, Journal of molecular biology.

[52]  U. Klein,et al.  Messenger RNA degradation is initiated at the 5′ end and follows sequence- and condition-dependent modes in chloroplasts , 2011, Nucleic acids research.

[53]  Junichi Obokata,et al.  The Rice Nuclear Genome Continuously Integrates, Shuffles, and Eliminates the Chloroplast Genome to Cause Chloroplast–Nuclear DNA Fluxw⃞ , 2005, The Plant Cell Online.

[54]  João Paulo Kitajima,et al.  Structural features and transcript-editing analysis of sugarcane (Saccharum officinarum L.) chloroplast genome , 2004, Current Genetics.