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Expanding Phaseolus coccineus Genomic Resources: De Novo Transcriptome Assembly and Analysis of Landraces ‘Gigantes’ and ‘Elephantes’ Reveals Rich Functional Variation

  • Aliki Xanthopoulou
  • Christos Kissoudis
  • Ifigeneia Mellidou
  • Maria Manioudaki
  • Irene Bosmali
  • Vasilis Tsakonitis
  • Apostolos Kalivas
  • Maslin Osathanunkul
  • Athanasios Tsaftaris
  • Ioannis GanopoulosEmail author
  • Panagiotis MadesisEmail author
Original Article

Abstract

Beans are one of the most important staple crops in the world. Runner bean (Phaseolus coccineus L.) is a small-scale agriculture crop compared to common bean (Phaseolusvulgaris). Beans have been introduced to Europe from the Central America to Europe and since then they have been scattered to different geographical regions. This has resulted in the generation of numerous local cultivars and landraces with distinguished characters and adaptive potential. To identify and characterize the underlying genomic variation of two very closely related runner bean cultivars, we performed RNA-Seq with de novo transcriptome assembly in two landraces of P. coccineus, ‘Gigantes’ and ‘Elephantes’ phenotypically distinct, differing in seed size and shape. The cleaned reads generated 37,379 and 37,774 transcripts for ‘Gigantes’ and ‘Elephantes,’ respectively. A total of 1896 DEGs were identified between the two cultivars, 1248 upregulated in ‘Elephantes’ and 648 upregulated in ‘Gigantes.’ A significant upregulation of defense-related genes was observed in ‘Elephantes,’ among those, numerous members of the AP2-EREBP, WRKY, NAC, and bHLH transcription factor families. In total, 3956 and 4322 SSRs were identified in ‘Gigantes’ and ‘Elephantes,’ respectively. Trinucleotide repeats were the most dominant repeat motif, accounting for 41.9% in ‘Gigantes’ and 40.1% in ‘Elephantes’ of the SSRs identified, followed by dinucleotide repeats (29.1% in both cultivars). Additionally, 19,281 putative SNPs were identified, among those 3161 were non-synonymous, thus having potential functional implications. High-confidence non-synonymous SNPs were successfully validated with an HRM assay, which can be directly adopted for P. coccineus molecular breeding. These results significantly expand the number of polymorphic markers within P. coccineus genus, enabling the robust identification of runner bean cultivars, the construction of high-resolution genetic maps, potentiating genome-wide association studies. They finally contribute to the genetic reservoir for the improvement of the closely related and intercrossable Phaseolus vulgaris.

Keywords

Phaseolus coccineus RNA-seq Comparative transcriptomics Landraces SNPs 

Notes

Acknowledgements

This research has been co-financed by the European Union and Greek national funds through the Operational Program Competitiveness, Entrepreneurship and Innovation, under the call RESEARCH – CREATE – INNOVATE (Project Code: T1EDK-04718).

Supplementary material

10528_2019_9920_MOESM1_ESM.xlsx (1.6 mb)
Supplementary Table 1 (a) List of the total SNPs identified in the transcriptome of the two landraces, (b) list of SNPs after stringency filtering, (c) primers for selected SNP validation (XLSX 1662 kb)
10528_2019_9920_MOESM2_ESM.xlsx (10 kb)
Supplementary Table 2 List of the HRM validated SSR primers (XLSX 10 kb)
10528_2019_9920_MOESM3_ESM.xlsx (9.6 mb)
Supplementary Table 3 List of transcripts with associated GO terms that have been annotated in‘Gigantes’ and ‘Elephantes’ (XLSX 9794 kb)
10528_2019_9920_MOESM4_ESM.xlsx (144 kb)
Supplementary Table 4 The list of genes differentially expressed between the ‘Gigantes’ and ‘Elephantes’ (XLSX 145 kb)
10528_2019_9920_MOESM5_ESM.xlsx (15 kb)
Supplementary Table 5 The list of top 50 genes differentially expressed between the ‘Gigantes’ and ‘Elephantes’ (corresponding to Fig. 6 heat map) (XLSX 15 kb)
10528_2019_9920_MOESM6_ESM.tif (7.8 mb)
Supplementary Figure 1 Representative seeds from the cultivars 'Gigantes’ and ‘Elephantes’ (TIF 7949 kb)
10528_2019_9920_MOESM7_ESM.tif (2.5 mb)
Supplementary Figure 2 Gene ontology (GO) classification of assembled unigenes in ‘Gigantes’ and ‘Elephantes’using GO slim instances realized with cateGOrizer tool. Genes were classified by biological process, cellular component and molecular function (TIF 2604 kb)
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Supplementary Figure 3 KEGG pathway clustering of DEGs upregulated in a) ‘Gigantes’ and b) ‘Elephantes’ (TIF 2599 kb)
10528_2019_9920_MOESM9_ESM.tif (2.1 mb)
Supplementary Figure 4 DEGs upregulated (green background) in the starch and sucrose metabolism pathway in (a) ‘Gigantes’ and (b) ‘Elephantes’ (TIF 2170 kb)
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Supplementary Figure 5 DEGs upregulated (green background) in the MAPK signaling pathway in (a) ‘Gigantes’ and (b) ‘Elephantes’ (TIF 3279 kb)
10528_2019_9920_MOESM11_ESM.tif (2.5 mb)
Supplementary Figure 6 DEGs upregulated (green background) in the phenylpropanoid metabolic pathway in (a) ‘Gigantes’ and (b) ‘Elephantes’ (TIF 2564 kb)
10528_2019_9920_MOESM12_ESM.tif (2.2 mb)
Supplementary Figure 7 DEGs upregulated (green background) in the plant hormone signaling pathway in (a) ‘Gigantes’ and (b) ‘Elephantes’ (TIF 2303 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Aliki Xanthopoulou
    • 1
  • Christos Kissoudis
    • 2
  • Ifigeneia Mellidou
    • 3
  • Maria Manioudaki
    • 4
  • Irene Bosmali
    • 1
  • Vasilis Tsakonitis
    • 3
  • Apostolos Kalivas
    • 3
  • Maslin Osathanunkul
    • 5
    • 6
  • Athanasios Tsaftaris
    • 2
  • Ioannis Ganopoulos
    • 3
    Email author
  • Panagiotis Madesis
    • 1
    Email author
  1. 1.Institute of Applied BiosciencesCERTHThessalonikiGreece
  2. 2.Perrotis CollegeAmerican Farm SchoolThessalonikiGreece
  3. 3.Institute of Plant Breeding and Genetic ResourcesELGO-DEMETERThessalonikiGreece
  4. 4.Centre for Clinical, Experimental Surgery & Translational ResearchBiomedical Research Foundation Academy of AthensAthensGreece
  5. 5.Department of Biology, Faculty of ScienceChiang Mai UniversityChiang MaiThailand
  6. 6.Center of Excellence in Bioresources for Agriculture, Industry and MedicineChiang Mai UniversityChiang MaiThailand

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