De novo transcriptome analysis of an albino mutant Pasphiopedilum pacific shamrock reveals reduced expression of genes related to chloroplast biosynthesis and division

Horticulture, Environment, and Biotechnology - Tập 59 - Trang 411-421 - 2018
Han Li1,2,3, Hua Cao1,2,3, Rong-pei Yu1,2,3, Zhen Miao3, Ji-hua Wang1,2,3, Su-Ping Qu1,2,3, Qiang Yuan4, Shen-chong Li1,2,3
1Flower Research Institute Yunnan Agriculture Academy Science, Kunming, China
2National Engineering Research Center For Ornamental Horticulture, Kunming, China
3Key Laboratory of Yunnan Flower Breeding, Kunming, China
4Department Biosciences, University of Helsinki, Helsinki, Finland

Tóm tắt

Paphiopedilum pacific shamrock is an orchid with high ornamental value. Understanding the mechanisms responsible for leaf color in albino mutants is important for ornamental development and breeding. In this study, we compared the leaf photosynthetic pigment content and transcriptome of albino mutants ppa01 and wild-type P. pacific shamrock. Photosynthetic pigment in mutants was less than 2% of the wild type and chl a/b was 60% less than the wild type. Transcriptome sequencing yielded 6.27 Gb and 5.67 Gb clean data from the mutant and wild-type leaves, respectively. De novo assembly yielded 104,763 unigenes with 15,400 greater than 1 kb in length. In unigene expression analysis, 3170 differentially expressed genes (DEGs) were identified with 2231 (70.38% of total DEGs) down-regulated. Results from GO and KEGG enrichment analysis, KEGG pathway analysis and qPCR suggest that the reduction of chloroplast biosynthesis and division in the mutant was due to low expression levels of ppGLK1 and ppFtsz. Mutants were associated with fewer chloroplasts in leaf cells, abnormal chloroplast structures, impaired chlorophyll biosynthesis, and thus reduced total chlorophyll and carotenoid contents. Furthermore, down-regulated expression of ppNYC1 reduced transformation of chlorophyll b into chlorophyll a, leading to a chl a/b decline. The research will guide future studies of leaf pigment mutations and the breeding of P. pacific shamrock.

Tài liệu tham khảo

Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI BLAST: a new generation of protein database search programs. Nucl Acids Res 25:3389–3402 Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11:R106 Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R et al (2004) UniProt: the universal protein knowledgebase. Nucl Acids Res 32:D115-9 Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29 Chang Q, Chen S, Chen Y, Deng Y, Chen F, Zhang F, Wang S (2013) Anatomical and physiological differences and differentially expressed genes between the green and yellow leaf tissue in a variegated chrysanthemum variety. Mol Biotechnol 54:393–411 Chen Y, Goodale UM, Fan XL, Gao JY (2015) Asymbiotic seed germination and in vitro seedling development of Paphiopedilum spicerianum: an orchid with an extremely small population in China. Glob Ecol Conserv 3:367–378 Cox AV, Albert VA, Chase MW (1997) Phylogenetics of the slipper orchids(Cypripedioideae, Orchidaceae): nuclear rDNA ITS sequences. Plant Syst Evol 208:197–223 Fitter DW, Martin DJ, Copley MJ, Scotland RW, Langdale JA (2002) GLK gene pairs regulate chloroplast development in diverse plant species. Plant J 31:713–727 Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R et al (2011) Full length transcriptome assembly from RNA Seq data without a reference genome. Nat Biotechnol 29:644–652 Guo X, Li Y, Li C, Luo H, Wang L, Qian J, Luo X, Xiang L, Song J et al (2013) Analysis of the Dendrobium officinale transcriptome reveals putative alkaloid biosynthetic genes and genetic markers. Gene 527:131–138 Han XJ, Wang YD, Chen YC, Lin LY, Wu QK (2013) Transcriptome sequencing and expression analysis of terpenoid biosynthesis genes in Litsea cubeba. PLoS One 8:e76890 Harmut A, Lichtenthaler K (1987) Chlorophylls and carotenoids: pigments of photosynthetic membranes. Method Enzymol 148:350–383 Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucl Acids Res 32:D277–D280 Ke Y, Tong Z (2013) Construction of customized sub-databases from ncbi-nr database for rapid annotation of huge metagenomic datasets using a combined blast and megan approach. PLoS One 8:e59831 Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:1–10 Li B, Colin ND (2011) RSEM: accurate transcript quantification from RNA Seq data with or without a reference genome. BMC Bioinform 12:323 Liu ZJ, Liu KW, Chen LJ, Lei SP, Li LQ, Shi XC, Huang LQ (2006) Conservation ecology of endangered species Paphiopedilum armeniacum (Orchidaceae). Acta Ecol Sin 26:2791–2799 Liu NT, Jane WN, Tsay HS, Wu H, Chang WC, Lin CS (2007) Chloroplast genome aberration in micropropagation-derived albino Bambusa edulis mutants, ab1 and ab2. Plant Cell Tiss Org 88:147–156 Liu F, Xu Y, Han G, Zhou L, Ali A, Zhu S, Li X (2016a) Molecular evolution and genetic variation of G2-like transcription factor genes in maize. PLoS ONE 11:e0161763 Liu RY, Dong XC, Gu WT, Yu LX, Jin WJ, Qu Y, Zhang F, Li WJ (2016b) Variation in the phenotypic features and transcripts of thermo-sensitive leaf-color mutant induced by carbon ion beam in Green wandering jew (Tradescantia fluminensis). Sci Hortic 213:303–313 Livaka KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-CT method. Method 25:402–408 Ng CY, Saleh NM (2011) In vitro propagation of Paphiopedilum orchid through formation of protocorm-like bodies. Plant Cell Tiss Org 105:193–202 Osteryoung KW, Stokes KD, Rutherford SM, Percival AL, Lee WY (1998) Chloroplast division in higher plants requires members of two functionally divergent gene families with homology to bacterial ftsZ. Plant Cell 10:1991–2004 Qin GJ, Gu HY, Ma LG, Peng YB, Deng XW, Chen Z, Qu LJ (2007) Disruption of phytoene desaturase gene results in albino and dwarf phenotypes in Arabidopsis by impairing chlorophyll, carotenoid, and gibberellin biosynthesis. Cell Res 17:471–482 Sugiura M (1989) The chloroplast chromosomes in land plants. Annu Rev Cell Biol 5:51–70 Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome scale analysis of protein functions and evolution. Nucl Acids Res 28:33–36 Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515 Wang Z, Gerstein M, Snyder M (2009) RNA-seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63 Whiston J (2007) A chlorophyll-deficient rice mutant with impaired chlorophyllide esterification in chlorophyll biosynthesis. Plant Physiol 145:29–40 Yang Y, Chen X, Xu B, Li Y, Ma Y, Wang G (2015) Phenotype and transcriptome analysis reveals chloroplast development and pigment biosynthesis together influenced the leaf color formation in mutants of Anthurium andraeanum ‘sonate’. Front Plant Sci 6:139