Skip to main content
SpringerLink
Log in

Transcriptome Sequencing of a Novel Albino Mutant of Hexaploid Sweetpotato

  • Original Article
  • Published:
Plant Molecular Biology Reporter Aims and scope Submit manuscript

A Correction to this article was published on 13 November 2021

This article has been updated

Abstract

Sweetpotato (Ipomoea batatas L), the herbaceous plant cultivated for its starchy storage roots, has a complex genome (2n = 6x = 90) with the estimated genome size of about 4.5 GB. Albinism, a phenomenon that occurs in plants, is defined as the total pigment loss accompanying with insufficient chloroplast membrane differentiation. For this study, an identified natural albino mutant of Xuzi-8 cultivar was subject to RNA sequencing relative to the green plants of identical cultivar. The results showed that total chlorophyll, chlorophyll a, chlorophyll b, and carotenoids were significantly lower in albino plants than in normal green plants. In addition, the CO2 assimilation rate, intercellular CO2 concentration, conductance level, and transpiration rate were significantly higher in normal green plants than in albino mutants. High-quality reads in the total number of 27,520,273-39,862,794 were obtained following the removal of the potentially contaminated or low-quality reads from the albino-mutant and normal green sweetpotato libraries. Later, sequences were matched with the available online data of Ipomoea batatas, and a very low matching degree (2.22%) was obtained, which indicated the very few available data of Ipomoea batatas genome compared with other plants. Additionally, the obtained unigenes were conducted functional annotations and classification, including GO, KOG, and KEGG analyses. The significance level and DEGs differences between albino-mutant and normal green plants were determined according to the thresholds of FDR ≤ 0.001 and log2 FC ≥ 1. A total of 3000 unigenes were upregulated in albino mutants but normally expressed in normal green plants. These genes were involved in facilitating plant nutrition sources depending on the stored carbohydrates and fats. Furthermore, these unigenes were aligned to the DDP family zinc finger protein, glycerophosphodiester phosphodiesterase, beta-galactosidase, GDE-like, and SELMODRAFT PDDEXK. On the other hand, altogether, 2418 unigenes were downregulated in albino-mutant plants compared with normal green plants, which were responsible for chloroplast differentiation and development, chlorophyll degradation, and synthesis of other pigments. Therefore, they might be related to the defect that caused this mutant.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

Change history

Abbreviations

NGS:

Next-generation sequencing

DEGs:

Differentially expressed genes

GO:

Gene ontology

KOG:

Clusters of orthologous groups of protein

FPKM:

Fragments per kilo base of transcripts per million mapped reads

References

  • Bae C-H et al (2001) Regulation of chloroplast gene expression is affected in ali, a novel tobacco albino mutant. Ann Bot 88:545–553

    Article  CAS  Google Scholar 

  • Bahr JT (2019) Ribulose bisphosphate carboxylase: properties and regulation biochemical basis of plant breeding: Volume 1 Carbon Metabolism:59

  • Bauer MF, Hofmann S, Neupert W, Brunner M (2000) Protein translocation into mitochondria: the role of TIM complexes. Trends Cell Biol 10:25–31

    Article  CAS  Google Scholar 

  • Boyer CD (2019) Synthesis and breakdown of starch. Biochemical Basis of Plant Breeding 1:133–153

    Google Scholar 

  • Brzezowski P, Richter AS, Grimm B (2015) Regulation and function of tetrapyrrole biosynthesis in plants and algae. Biochimica Et Biophysica Acta (BBA)-Bioenergetics 1847:968–985

    Article  CAS  Google Scholar 

  • Cheng CY, Krishnakumar V, Chan AP, Thibaud-Nissen F, Schobel S, Town CD (2017) Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. The Plant Journal : for Cell and Molecular Biology 89:789–804. https://doi.org/10.1111/tpj.13415

    Article  CAS  Google Scholar 

  • Cheng Y, Zhou W, El Sheery NI, Peters C, Li M, Wang X, Huang J (2011) Characterization of the Arabidopsis glycerophosphodiester phosphodiesterase (GDPD) family reveals a role of the plastid-localized AtGDPD1 in maintaining cellular phosphate homeostasis under phosphate starvation. Plant J 66:781–795

    Article  CAS  Google Scholar 

  • Day A, Ellis T (1984) Chloroplast DNA deletions associated with wheat plants regenerated from pollen: possible basis for maternal inheritance of chloroplasts. Cell 39:359–368

    Article  CAS  Google Scholar 

  • DeBlasio SL, Luesse DL, Hangarter RP (2005) A plant-specific protein essential for blue-light-induced chloroplast movements. Plant Physiol 139:101–114

    Article  CAS  Google Scholar 

  • Dunford R, Walden RM (1991) Plastid genome structure and plastid-related transcript levels in albino barley plants derived from anther culture. Curr Genet 20:339–347

    Article  CAS  Google Scholar 

  • Götz S et al (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36:3420–3435

    Article  Google Scholar 

  • Guo M, Liu J-H, Ma X, Zhai Y-F, Gong Z-H, Lu M-H (2016) Genome-wide analysis of the Hsp70 family genes in pepper (Capsicum annuum L.) and functional identification of CaHsp70-2 involvement in heat stress. Plant Sci 252:246–256

    Article  CAS  Google Scholar 

  • Haas BJ et al (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8:1494

    Article  CAS  Google Scholar 

  • Han C-d, Patrie W, Polacco M, Coe EH (1993) Aberrations in plastid transcripts and deficiency of plastid DNA in striped and albino mutants in maize. Planta 191:552–563

    Article  CAS  Google Scholar 

  • Harada T, Sato T, Asaka D, Matsukawa I (1991) Large-scale deletions of rice plastid DNA in anther culture. Theor Appl Genet 81:157–161

    Article  CAS  Google Scholar 

  • Hatier J-HB, Gould KS (2008) Anthocyanin function in vegetative organs. In: Anthocyanins. Springer, pp 1–19

  • Huamari Z (1992) Systematic botany and morphology of the sweetpotato plant

  • Ilg A, Beyer P, Al-Babili S (2009) Characterization of the rice carotenoid cleavage dioxygenase 1 reveals a novel route for geranial biosynthesis. FEBS J 276:736–747. https://doi.org/10.1111/j.1742-4658.2008.06820.x

    Article  CAS  PubMed  Google Scholar 

  • Jorgensen RA, Dorantes-Acosta AE (2012) Conserved peptide upstream open reading frames are associated with regulatory genes in angiosperms. Front Plant Sci 3:191

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y (2007) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480–D484

    Article  Google Scholar 

  • Kimata-Ariga Y, Chikuma Y, Saitoh T, Miyata M, Yanagihara Y, Yamane K, Hase T (2019) NADP (H) allosterically regulates the interaction between ferredoxin and ferredoxin-NADP+ reductase FEBS open bio

  • Kozgar MI (2014) 4 Chlorophyll Mutations. In: Mutation Breeding in Chickpea:. Sciendo Migration, pp 31–37

  • Lepistö A et al (2009) Chloroplast NADPH-thioredoxin reductase interacts with photoperiodic development in Arabidopsis. Plant Physiol 149:1261–1276. https://doi.org/10.1104/pp.108.133777

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323

    Article  CAS  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCT method. Methods 25:402–408

    Article  CAS  Google Scholar 

  • Luo F et al. (2019) Chlorophyll degradation and carotenoid biosynthetic pathways: gene expression and pigment content in broccoli during yellowing. Food Chemistry:124964

  • Magoon M, Krishnan R, Bai KV (1970) Cytological evidence on the origin of sweet potato. Theor Appl Genet 40:360–366

    Article  CAS  Google Scholar 

  • Mao X, Cai T, Olyarchuk JG, Wei L (2005) Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21:3787–3793

    Article  CAS  Google Scholar 

  • Nikkanen L, Rintamäki E (2019) Chloroplast thioredoxin systems dynamically regulate photosynthesis in plants. Biochem J 476:1159–1172. https://doi.org/10.1042/bcj20180707

    Article  CAS  PubMed  Google Scholar 

  • Oikawa K, Hayashi M, Hayashi Y, Nishimura M (2019) Re-evaluation of physical interaction between plant peroxisomes and other organelles using live-cell imaging techniques. Journal of Integrative Plant Biology

  • Park HL, Cho M-H, Shin D, Bhoo S, Hahn T-R (2012) Molecular characterization of phytochrome-interacting nascent polypeptide associated complex protein in Arabidopsis thaliana. Journal of the Korean Society for Applied Biological Chemistry 55:55–326. https://doi.org/10.1007/s13765-012-1159-9

    Article  CAS  Google Scholar 

  • Porra RJ, Thompson WA, Kriedemann PE (1989) Determination of accurate extinction coefficients and simultaneous equations for assaying chlorophylls a and b extracted with four different solvents: verification of the concentration of chlorophyll standards by atomic absorption spectroscopy. Biochimica et Biophysica Acta (BBA) - Bioenergetics 975:384–394. https://doi.org/10.1016/S0005-2728(89)80347-0

    Article  CAS  Google Scholar 

  • Qin D, Dong J, Xu F, Ge S, Xu Q, Li M (2017) Genome-wide identification and characterization of light harvesting chlorophyll a/b binding protein genes in barley (Hordeum vulgare L). Advances in Crop Science and Technology 05 doi:https://doi.org/10.4172/2329-8863.1000301

  • Sharma A, Sharma R (2014) Crop improvement and mutation breeding. Scientific Publishers,

  • Smith DL, Gross KC (2000) A family of at least seven β-galactosidase genes is expressed during tomato fruit development. Plant Physiol 123:1173–1184. https://doi.org/10.1104/pp.123.3.1173

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Snedecor GW, Cochran WG (1989) Statistical methods, 8thEdn Ames: Iowa State Univ Press Iowa 54:71-82

  • Srisuwan S, Sihachakr D, Siljak-Yakovlev S (2006) The origin and evolution of sweet potato (Ipomoea batatas lam.) and its wild relatives through the cytogenetic approaches. Plant Sci 171:424–433

    Article  CAS  Google Scholar 

  • Statistix S (2008) Analytical software. Statistix 9, Tallahassee, FL,

  • Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci 100:9440–9445

    Article  CAS  Google Scholar 

  • Takemiya A, Inoue S-I, Doi M, Kinoshita T, Shimazaki K-I (2005) Phototropins promote plant growth in response to blue light in low light environments. Plant Cell 17:1120–1127. https://doi.org/10.1105/tpc.104.030049

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tanaka Y, Sasaki N, Ohmiya A (2008) Biosynthesis of plant pigments: anthocyanins, betalains and carotenoids. The Plant J 54:733–749

    Article  CAS  Google Scholar 

  • Von Wettstein D, Gough S, Kannangara CG (1995) Chlorophyll biosynthesis. Plant Cell 7:1039–1057. https://doi.org/10.1105/tpc.7.7.1039

    Article  Google Scholar 

  • Wan H, Yuan W, Ruan M, Ye Q, Wang R, Li Z, Zhou G, Yao Z, Zhao J, Liu S, Yang Y (2011) Identification of reference genes for reverse transcription quantitative real-time PCR normalization in pepper (Capsicum annuum L.). Biochem Biophys Res Commun 416:24–30

    Article  CAS  Google Scholar 

  • Wang C et al. (2016) A putative chloroplast-localized Ca<sup>2+</sup>/H<sup>+</sup> antiporter CCHA1 is involved in calcium and pH homeostasis and required for PSII function in <em>Arabidopsis</em> Mol Plant 9:1183-1196 doi:https://doi.org/10.1016/j.molp.2016.05.015

  • Wang L, Yue C, Cao H, Zhou Y, Zeng J, Yang Y, Wang X (2014) Biochemical and transcriptome analyses of a novel chlorophyll-deficient chlorina tea plant cultivar. BMC Plant Biol 14:352

    Article  Google Scholar 

  • Xue Y et al (2019) Comparative transcriptomic and proteomic analyses of the green and white parts of chimeric leaves in Ananas comosus var. bracteatus. PeerJ 7:e7261

    Article  Google Scholar 

  • Yang J et al. (2016) The haplotype-resolved genome sequence of hexaploid Ipomoea batatas reveals its evolutionary history bioRxiv:064428

  • Zhang S et al (2019) Physiological and transcriptomic analysis of yellow leaf coloration in Populus deltoides Marsh. PLoS One 14:e0216879

    Article  CAS  Google Scholar 

  • Zubko MK, Day A (1998) Stable albinism induced without mutagenesis: a model for ribosome-free plastid inheritance. Plant J 15:265–271

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The present study was funded by the National Key R&D Program of China (2019YFD1001300, 2019YFD1001301), Research project of Jiangsu Province (BK20161162), China Agriculture Research System (CARS-10, Sweetpotato) and the fund for the Jiangsu Province Project Number 221727.

Funding

The present study was funded by the earmarked fund for China Agriculture Research System (CARS-10, sweetpotato) and the fund for the Jiangsu Province Project Number 221727.

Author information

Authors and Affiliations

  1. Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China

    Mohamed Hamed Arisha, Yan Hui, Muhammad Qadir Ahmad, Tang Wei, Kou Meng, Liu Yaju, Wang Xin, Zhang Yungang & Li Qiang

  2. Department of Horticulture, Faculty of Agriculture, Zagazig University, Sharkia, 44511, Egypt

    Mohamed Hamed Arisha

  3. Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, 60000, Pakistan

    Muhammad Qadir Ahmad

Authors
  1. Mohamed Hamed Arisha
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yan Hui
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Muhammad Qadir Ahmad
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Tang Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kou Meng
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Liu Yaju
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Wang Xin
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Zhang Yungang
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Li Qiang
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

M.H.A., L.Q. and Y. H. were responsible for study design. M.H.A and Y. H. were in charge of experiment implementation, result analysis, figures drawing and manuscript writing. L. Q., Y. H. and M. Q. A. revised the manuscript. T. W., K. M., L. j., and W. X., Z. G. also participated in carrying out experiments.

Corresponding authors

Correspondence to Mohamed Hamed Arisha or Li Qiang.

Ethics declarations

Competing Interests

All authors declare that they have no competing interest.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Mohamed Hamed Arisha and Yan Hui were equally contributed to this work.

Key message

The present study applied the high-throughput RNA sequencing technique for discovering genes related to albinism in a naturally induced sweetpotato albino mutant that will enrich the sweetpotato genome repertoire and shed more lights on the different physiological and chemical pathways involved in this phenomenon.

Electronic supplementary material

ESM 1

(DOC 161 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Arisha, M.H., Hui, Y., Ahmad, M.Q. et al. Transcriptome Sequencing of a Novel Albino Mutant of Hexaploid Sweetpotato. Plant Mol Biol Rep 39, 473–488 (2021). https://doi.org/10.1007/s11105-020-01239-6

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11105-020-01239-6

Keywords

Search

Navigation