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Identification of tissue-specific gene clusters and orthologues of nodulation-related genes in Vigna angularis

Published online by Cambridge University Press:  16 July 2014

Yang Jae Kang ,
Jayern Lee ,
Yong Hwan Kim  and
Suk-Ha Lee
Yang Jae Kang
Affiliation:
Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul151-921, Republic of Korea
Jayern Lee
Affiliation:
Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul151-921, Republic of Korea
Yong Hwan Kim
Affiliation:
Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries, Anyang-si, Republic of Korea
Suk-Ha Lee*
Affiliation:
Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul151-921, Republic of Korea Plant Genomics and Breeding Research Institute, Seoul National University, Seoul151-921, Republic of Korea
*
* Corresponding author. E-mail: sukhalee@snu.ac.kr
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Abstract

Nitrogen fixation in legumes is an important agricultural trait that results from symbiosis between the root and rhizobia. To understand the molecular basis of nodulation, recent research has been focused on the identification of nodulation-related genes by functional analysis using two major model legumes, Medicago truncatula and Lotus japonicus. Thus far, three important processes have been discovered, namely Nod factor (NF) perception, NF signalling and autoregulation of nodulation. Nevertheless, application of the results of these studies is limited for non-model legume crops because a reference genome is unavailable. However, because the cost of whole-transcriptome analysis has dropped dramatically due to the Next generation sequencer (NGS) technology, minor crops for which reference sequences are yet to be constructed can still be studied at the genome level. In this study, we sequenced the leaf and root transcriptomes of Vigna angularis (accession IT213134) and de novo assembled. Our results demonstrate the feasibility of using the transcriptome assembly to effectively identify tissue-specific peptide clusters related to tissue-specific functions and species-specific nodulation-related genes.

Keywords

de novo transcriptome assemblynodulationRNAseqVigna angularis
Type
Research Article
Information
Plant Genetic Resources , Volume 12 , Issue S1: Special issue on the 3rd International Symposium on “Genomics of Plant Genetic Resources” , July 2014 , pp. S21 - S26
Copyright
Copyright © NIAB 2014 

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References

Arrighi, JF, Godfroy, O, de Billy, F, Saurat, O, Jauneau, A and Gough, C (2008) The RPG gene of Medicago truncatula controls Rhizobium-directed polar growth during infection. Proceedings of the National Academy of Sciences of the United States of America 105: 9817–9822.CrossRefGoogle ScholarPubMed
Asamizu, E, Shimoda, Y, Kouchi, H, Tabata, S and Sato, S (2008) A positive regulatory role for LjERF1 in the nodulation process is revealed by systematic analysis of nodule-associated transcription factors of Lotus japonicus . Plant Physiology 147: 2030–2040.Google Scholar
Ferguson, BJ, Indrasumunar, A, Hayashi, S, Lin, MH, Lin, YH, Reid, DE and Gresshoff, PM (2010) Molecular analysis of legume nodule development and autoregulation. Journal of Integrative Plant Biology 52: 61–76.CrossRefGoogle ScholarPubMed
Grabherr, MG, Haas, BJ, Yassour, M, Levin, JZ, Thompson, DA, Amit, I, Adiconis, X, Fan, L, Raychowdhury, R, Zeng, QD, Chen, ZH, Mauceli, E, Hacohen, N, Gnirke, A, Rhind, N, di Palma, F, Birren, BW, Nusbaum, C, Lindblad-Toh, K, Friedman, N and Regev, A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29: 644–652.CrossRefGoogle ScholarPubMed
Imaizumi-Anraku, H, Takeda, N, Charpentier, M, Perry, J, Miwa, H, Umehara, Y, Kouchi, H, Murakami, Y, Mulder, L, Vickers, K, Pike, J, Downie, JA, Wang, T, Sato, S, Asamizu, E, Tabata, S, Yoshikawa, M, Murooka, Y, Wu, GJ, Kawaguchi, M, Kawasaki, S, Parniske, M and Hayashi, M (2005) Plastid proteins crucial for symbiotic fungal and bacterial entry into plant roots. Nature 433: 527–531.CrossRefGoogle ScholarPubMed
Journet, EP, El-Gachtouli, N, Vernoud, V, de Billy, F, Pichon, M, Dedieu, A, Arnould, C, Morandi, D, Barker, DG and Gianinazzi-Pearson, V (2001) Medicago truncatula ENOD11: a novel RPRP-encoding early nodulin gene expressed during mycorrhization in arbuscule-containing cells. Molecular Plant–Microbe Interactions 14: 737–748.Google Scholar
Kalo, P, Gleason, C, Edwards, A, Marsh, J, Mitra, RM, Hirsch, S, Jakab, J, Sims, S, Long, SR, Rogers, J, Kiss, GB, Downie, JA and Oldroyd, GED (2005) Nodulation signaling in legumes requires NSP2, a member of the GRAS family of transcriptional regulators. Science 308: 1786–1789.Google Scholar
Kanamori, N, Madsen, LH, Radutoiu, S, Frantescu, M, Quistgaard, EMH, Miwa, H, Downie, JA, James, EK, Felle, HH, Haaning, LL, Jensen, TH, Sato, S, Nakamura, Y, Tabata, S, Sandal, N and Stougaard, J (2006) A nucleoporin is required for induction of Ca2+ spiking in legume nodule development and essential for rhizobial and fungal symbiosis. Proceedings of the National Academy of Sciences of the United States of America 103: 359–364.Google Scholar
Kevei, Z, Lougnon, G, Mergaert, P, Horvath, GV, Kereszt, A, Jayaraman, D, Zaman, N, Marcel, F, Regulski, K, Kiss, GB, Kondorosi, A, Endre, G, Kondorosi, E and Ane, JM (2007) 3-Hydroxy-3-methylglutaryl coenzyme a reductase 1 interacts with NORK and is crucial for nodulation in Medicago truncatula . Plant Cell 19: 3974–3989.CrossRefGoogle Scholar
Levy, J, Bres, C, Geurts, R, Chalhoub, B, Kulikova, O, Duc, G, Journet, EP, Ane, JM, Lauber, E, Bisseling, T, Denarie, J, Rosenberg, C and Debelle, F (2004) A putative Ca2+ and calmodulin-dependent protein kinase required for bacterial and fungal symbioses. Science 303: 1361–1364.Google Scholar
Li, L, Stoeckert, CJ and Roos, DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Research 13: 2178–2189.CrossRefGoogle ScholarPubMed
Li, DX, Kinkema, M and Gresshoff, PM (2009) Autoregulation of nodulation (AON) in Pisum sativum (pea) involves signalling events associated with both nodule primordia development and nitrogen fixation. Journal of Plant Physiology 166: 955–967.Google Scholar
Mitra, RM, Gleason, CA, Edwards, A, Hadfield, J, Downie, JA, Oldroyd, GED and Long, SR (2004) A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: gene identification by transcript-based cloning. Proceedings of the National Academy of Sciences of the United States of America 101: 4701–4705.Google Scholar
Miyahara, A, Hirani, TA, Oakes, M, Kereszt, A, Kobe, B, Djordjevic, MA and Gresshoff, PM (2008) Soybean nodule autoregulation receptor kinase phosphorylates two kinase-associated protein phosphatases in vitro . Journal of Biological Chemistry 283: 25381–25391.Google Scholar
Miyazawa, H, Oka-Kira, E, Sato, N, Takahashi, H, Wu, GJ, Sato, S, Hayashi, M, Betsuyaku, S, Nakazono, M, Tabata, S, Harada, K, Sawa, S, Fukuda, H and Kawaguchi, M (2010) The receptor-like kinase KLAVIER mediates systemic regulation of nodulation and non-symbiotic shoot development in Lotus japonicus . Development 137: 4317–4325.Google Scholar
Nishimura, R, Hayashi, M, Wu, GJ, Kouchi, H, Imaizumi-Anraku, H, Murakami, Y, Kawasaki, S, Akao, S, Ohmori, M, Nagasawa, M, Harada, K and Kawaguchi, M (2002a) HAR1 mediates systemic regulation of symbiotic organ development. Nature 420: 426–429.CrossRefGoogle ScholarPubMed
Nishimura, R, Ohmori, M, Fujita, H and Kawaguchi, M (2002b) A Lotus basic leucine zipper protein with a RING-finger motif negatively regulates the developmental program of nodulation. Proceedings of the National Academy of Sciences of the United States of America 99: 15206–15210.Google Scholar
Saito, K, Yoshikawa, M, Yano, K, Miwa, H, Uchida, H, Asamizu, E, Sato, S, Tabata, S, Imaizumi-Anraku, H, Umehara, Y, Kouchi, H, Murooka, Y, Szczyglowski, K, Downie, JA, Parniske, M, Hayashi, M and Kawaguchi, M (2007) NUCLEOPORIN85 is required for calcium spiking, fungal and bacterial symbioses, and seed production in Lotus japonicus . Plant Cell 19: 610–624.Google Scholar
Schauser, L, Roussis, A, Stiller, J and Stougaard, J (1999) A plant regulator controlling development of symbiotic root nodules. Nature 402: 191–195.Google Scholar
Schnabel, E, Journet, EP, de Carvalho-Niebel, F, Duc, G and Frugoli, J (2005) The Medicago truncatula SUNN gene encodes a CLV1-like leucine-rich repeat receptor kinase that regulates nodule number and root length. Plant Molecular Biology 58: 809–822.Google Scholar
Searle, IR, Men, AE, Laniya, TS, Buzas, DM, Iturbe-Ormaetxe, I, Carroll, BJ and Gresshoff, PM (2003) Long-distance signaling in nodulation directed by a CLAVATA1-like receptor kinase. Science 299: 109–112.Google Scholar
Shiu, SH and Bleecker, AB (2001) Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proceedings of the National Academy of Sciences of the United States of America 98: 10763–10768.CrossRefGoogle Scholar
Thimm, O, Blasing, O, Gibon, Y, Nagel, A, Meyer, S, Kruger, P, Selbig, J, Muller, LA, Rhee, SY and Stitt, M (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant Journal 37: 914–939.Google Scholar
Zhu, H, Chen, T, Zhu, MS, Fang, Q, Kang, H, Hong, ZL and Zhang, ZM (2008) A novel ARID DNA-binding protein interacts with SymRK and is expressed during early nodule development in Lotus japonicus . Plant Physiology 148: 337–347.Google Scholar
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