1
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Chaowongdee S, Vannatim N, Malichan S, Kuncharoen N, Tongyoo P, Siriwan W. Comparative transcriptomics analysis reveals defense mechanisms of Manihot esculenta Crantz against Sri Lanka Cassava MosaicVirus. BMC Genomics 2024; 25:436. [PMID: 38698332 PMCID: PMC11067156 DOI: 10.1186/s12864-024-10315-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/16/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Cassava mosaic disease (CMD), caused by Sri Lankan cassava mosaic virus (SLCMV) infection, has been identified as a major pernicious disease in Manihot esculenta Crantz (cassava) plantations. It is widespread in Southeast Asia, especially in Thailand, which is one of the main cassava supplier countries. With the aim of restricting the spread of SLCMV, we explored the gene expression of a tolerant cassava cultivar vs. a susceptible cassava cultivar from the perspective of transcriptional regulation and the mechanisms underlying plant immunity and adaptation. RESULTS Transcriptomic analysis of SLCMV-infected tolerant (Kasetsart 50 [KU 50]) and susceptible (Rayong 11 [R 11]) cultivars at three infection stages-that is, at 21 days post-inoculation (dpi) (early/asymptomatic), 32 dpi (middle/recovery), and 67 dpi (late infection/late recovery)-identified 55,699 expressed genes. Differentially expressed genes (DEGs) between SLCMV-infected KU 50 and R 11 cultivars at (i) 21 dpi to 32 dpi (the early to middle stage), and (ii) 32 dpi to 67 dpi (the middle stage to late stage) were then identified and validated by real-time quantitative PCR (RT-qPCR). DEGs among different infection stages represent genes that respond to and regulate the viral infection during specific stages. The transcriptomic comparison between the tolerant and susceptible cultivars highlighted the role of gene expression regulation in tolerant and susceptible phenotypes. CONCLUSIONS This study identified genes involved in epigenetic modification, transcription and transcription factor activities, plant defense and oxidative stress response, gene expression, hormone- and metabolite-related pathways, and translation and translational initiation activities, particularly in KU 50 which represented the tolerant cultivar in this study.
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Affiliation(s)
- Somruthai Chaowongdee
- Center of Excellence on Agricultural Biotechnology (AG-BIO/MHESI), Bangkok, 10900, Thailand
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaengsaen Campus, Nakhon Pathom, 73140, Thailand
| | - Nattachai Vannatim
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Srihunsa Malichan
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Nattakorn Kuncharoen
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Pumipat Tongyoo
- Center of Excellence on Agricultural Biotechnology (AG-BIO/MHESI), Bangkok, 10900, Thailand
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaengsaen Campus, Nakhon Pathom, 73140, Thailand
| | - Wanwisa Siriwan
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand.
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2
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Nye DG, Irigoyen ML, Perez-Fons L, Bohorquez-Chaux A, Hur M, Medina-Yerena D, Lopez-Lavalle LAB, Fraser PD, Walling LL. Integrative transcriptomics reveals association of abscisic acid and lignin pathways with cassava whitefly resistance. BMC PLANT BIOLOGY 2023; 23:657. [PMID: 38124051 PMCID: PMC10731783 DOI: 10.1186/s12870-023-04607-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Whiteflies are a global threat to crop yields, including the African subsistence crop cassava (Manihot esculenta). Outbreaks of superabundant whitefly populations throughout Eastern and Central Africa in recent years have dramatically increased the pressures of whitefly feeding and virus transmission on cassava. Whitefly-transmitted viral diseases threaten the food security of hundreds of millions of African farmers, highlighting the need for developing and deploying whitefly-resistant cassava. However, plant resistance to whiteflies remains largely poorly characterized at the genetic and molecular levels. Knowledge of cassava-defense programs also remains incomplete, limiting characterization of whitefly-resistance mechanisms. To better understand the genetic basis of whitefly resistance in cassava, we define the defense hormone- and Aleurotrachelus socialis (whitefly)-responsive transcriptome of whitefly-susceptible (COL2246) and whitefly-resistant (ECU72) cassava using RNA-seq. For broader comparison, hormone-responsive transcriptomes of Arabidopsis thaliana were also generated. RESULTS Whitefly infestation, salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA) transcriptome responses of ECU72 and COL2246 were defined and analyzed. Strikingly, SA responses were largely reciprocal between the two cassava genotypes and we suggest candidate regulators. While susceptibility was associated with SA in COL2246, resistance to whitefly in ECU72 was associated with ABA, with SA-ABA antagonism observed. This was evidenced by expression of genes within the SA and ABA pathways and hormone levels during A. socialis infestation. Gene-enrichment analyses of whitefly- and hormone-responsive genes suggest the importance of fast-acting cell wall defenses (e.g., elicitor recognition, lignin biosynthesis) during early infestation stages in whitefly-resistant ECU72. A surge of ineffective immune and SA responses characterized the whitefly-susceptible COL2246's response to late-stage nymphs. Lastly, in comparison with the model plant Arabidopsis, cassava's hormone-responsive genes showed striking divergence in expression. CONCLUSIONS This study provides the first characterization of cassava's global transcriptome responses to whitefly infestation and defense hormone treatment. Our analyses of ECU72 and COL2246 uncovered possible whitefly resistance/susceptibility mechanisms in cassava. Comparative analysis of cassava and Arabidopsis demonstrated that defense programs in Arabidopsis may not always mirror those in crop species. More broadly, our hormone-responsive transcriptomes will also provide a baseline for the cassava community to better understand global responses to other yield-limiting pests/pathogens.
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Affiliation(s)
- Danielle G Nye
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Maria L Irigoyen
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Laura Perez-Fons
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Adriana Bohorquez-Chaux
- Alliance Bioversity International and International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Manhoi Hur
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Diana Medina-Yerena
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Luis Augusto Becerra Lopez-Lavalle
- Alliance Bioversity International and International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Present Address: International Center of Biosaline Agriculture, Dubai, United Arab Emirates
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Linda L Walling
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
- Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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3
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Kemfack AM, Hernandez-Morato I, Moayedi Y, Pitman MJ. An optimized method for high-quality RNA extraction from distinctive intrinsic laryngeal muscles in the rat model. Sci Rep 2022; 12:21665. [PMID: 36522411 PMCID: PMC9755529 DOI: 10.1038/s41598-022-25643-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
Challenges related to high-quality RNA extraction from post-mortem tissue have limited RNA-sequencing (RNA-seq) application in certain skeletal muscle groups, including the intrinsic laryngeal muscles (ILMs). The present study identified critical factors contributing to substandard RNA extraction from the ILMs and established a suitable method that permitted high-throughput analysis. Here, standard techniques for tissue processing were adapted, and an effective means to control confounding effects during specimen preparation was determined. The experimental procedure consistently provided sufficient intact total RNA (N = 68) and RIN ranging between 7.0 and 8.6, which was unprecedented using standard RNA purification protocols. This study confirmed the reproducibility of the workflow through repeated trials at different postnatal time points and across the distinctive ILMs. High-throughput diagnostics from 90 RNA samples indicated no sequencing alignment scores below 70%, validating the extraction strategy. Significant differences between the standard and experimental conditions suggest circumvented challenges and broad applicability to other skeletal muscles. This investigation remains ongoing given the prospect of therapeutic insights to voice, swallowing, and airway disorders. The present methodology supports pioneering global transcriptome investigations in the larynx previously unfounded in literature.
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Affiliation(s)
- Angela M Kemfack
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Ignacio Hernandez-Morato
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA.
| | - Yalda Moayedi
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA
- Department of Neurology, Irving Medical Center, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Michael J Pitman
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA
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4
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Jaramillo AM, Sierra S, Chavarriaga-Aguirre P, Castillo DK, Gkanogiannis A, López-Lavalle LAB, Arciniegas JP, Sun T, Li L, Welsch R, Boy E, Álvarez D. Characterization of cassava ORANGE proteins and their capability to increase provitamin A carotenoids accumulation. PLoS One 2022; 17:e0262412. [PMID: 34995328 PMCID: PMC8741059 DOI: 10.1371/journal.pone.0262412] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 12/23/2021] [Indexed: 11/19/2022] Open
Abstract
Cassava (Manihot esculenta Crantz) biofortification with provitamin A carotenoids is an ongoing process that aims to alleviate vitamin A deficiency. The moderate content of provitamin A carotenoids achieved so far limits the contribution to providing adequate dietary vitamin A levels. Strategies to increase carotenoid content focused on genes from the carotenoids biosynthesis pathway. In recent years, special emphasis was given to ORANGE protein (OR), which promotes the accumulation of carotenoids and their stability in several plants. The aim of this work was to identify, characterize and investigate the role of OR in the biosynthesis and stabilization of carotenoids in cassava and its relationship with phytoene synthase (PSY), the rate-limiting enzyme of the carotenoids biosynthesis pathway. Gene and protein characterization of OR, expression levels, protein amounts and carotenoids levels were evaluated in roots of one white (60444) and two yellow cassava cultivars (GM5309-57 and GM3736-37). Four OR variants were found in yellow cassava roots. Although comparable expression was found for three variants, significantly higher OR protein amounts were observed in the yellow varieties. In contrast, cassava PSY1 expression was significantly higher in the yellow cultivars, but PSY protein amount did not vary. Furthermore, we evaluated whether expression of one of the variants, MeOR_X1, affected carotenoid accumulation in cassava Friable Embryogenic Callus (FEC). Overexpression of maize PSY1 alone resulted in carotenoids accumulation and induced crystal formation. Co-expression with MeOR_X1 led to greatly increase of carotenoids although PSY1 expression was high in the co-expressed FEC. Our data suggest that posttranslational mechanisms controlling OR and PSY protein stability contribute to higher carotenoid levels in yellow cassava. Moreover, we showed that cassava FEC can be used to study the efficiency of single and combinatorial gene expression in increasing the carotenoid content prior to its application for the generation of biofortified cassava with enhanced carotenoids levels.
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Affiliation(s)
- Angélica M. Jaramillo
- HarvestPlus, c/o The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Santiago Sierra
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Paul Chavarriaga-Aguirre
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Diana Katherine Castillo
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Anestis Gkanogiannis
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Juan Pablo Arciniegas
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Tianhu Sun
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, New York, United States of America
| | - Li Li
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, New York, United States of America
| | - Ralf Welsch
- Faculty of Biology II, University of Freiburg, Freiburg, Germany
| | - Erick Boy
- HarvestPlus, International Food Policy Research Institute, Washington, DC, United States of America
| | - Daniel Álvarez
- HarvestPlus, c/o The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
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5
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Jimenez J, Leiva AM, Olaya C, Acosta-Trujillo D, Cuellar WJ. An optimized nucleic acid isolation protocol for virus diagnostics in cassava ( Manihot esculenta Crantz.). MethodsX 2021; 8:101496. [PMID: 34754767 PMCID: PMC8563463 DOI: 10.1016/j.mex.2021.101496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/20/2021] [Indexed: 11/15/2022] Open
Abstract
Our group works on the detection and characterization of cassava viruses, supporting projects that involve large scale pathogen surveillance activities and resistance screening assays in multiple and remote locations. In order to comply with these applications, nucleic acid isolation protocols need to be cost effective, adjusted for samples that will stand long distance transport and harsh storage conditions, while maximizing the yield and quality of the nucleic acid extracts obtained. The method we describe here has been widely used and validated using different downstream tests (including, but not limited to, Rolling Circle Amplification and Illumina and Nanopore sequencing), but is currently unpublished. The protocol begins with milligram amounts of dry leaf samples stored in silica gel, does not require liquid Nitrogen nor phenol extraction and produces an average of 2.11 µg of nucleic acids per mg of dry tissue.•DNA purity estimations reveal OD260/280 ratios above 2.0 and OD260/230 ratios above 1.7, even for samples stored in silica gel for several months.•The high quality of the extracts is suitable for detection of DNA and RNA viruses, with high efficiency.•We suggest this method could be used as part of a gold standard kit for virus detection in cassava.
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Affiliation(s)
- Jenyfer Jimenez
- Virology Laboratory, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Ana Maria Leiva
- Virology Laboratory, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | | | - Daniela Acosta-Trujillo
- Virology Laboratory, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Wilmer Jose Cuellar
- Virology Laboratory, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
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6
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Carpinetti PDA, Fioresi VS, Ignez da Cruz T, de Almeida FAN, Canal D, Ferreira A, Ferreira MFDS. Efficient method for isolation of high-quality RNA from Psidium guajava L. tissues. PLoS One 2021; 16:e0255245. [PMID: 34310664 PMCID: PMC8312961 DOI: 10.1371/journal.pone.0255245] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/12/2021] [Indexed: 11/19/2022] Open
Abstract
Acquiring high-quality RNA in sufficient amounts is crucial in plant molecular biology and genetic studies. Several methods for RNA extraction from plants are available in the literature, mainly due to the great biochemical diversity present in each species and tissue, which can complicate or prevent the extraction. Psidium guajava (Myrtaceae family) is a perennial fruit tree of medicinal and economic value; nevertheless, only a few molecular studies are available for the species. One reason is the difficulty in obtaining RNA due to the content of the samples, which are rich in polyphenols, polysaccharides, and secondary metabolites. Furthermore, there are few studies available for the isolation of RNA from guava or Psidium samples, which hampers advances in the study of the genus. Here, quality and yields of RNA isolates were compared using six extraction protocols: two protocols based on the application of cetyltrimethylammonium bromide (CTAB) lysis buffer, one protocol which uses the TRIzol reagent, one which applies guanidine thiocyanate lysis buffer followed by organic phase extraction, and two commercial kits (PureLink RNA Mini Kit and RNeasy Plant Mini Kit). The CTAB-based method provided the highest RNA yields and quality for five different tissues (flower bud, immature leaf, young leaf, mature leaf, and root), genotypes, and stress conditions. For the most efficient protocol, the average yield of RNA from guava leaves was 203.06 μg/g of tissue, and the A260/A280 and A260/A230 ratios were 2.1 and 2.2, respectively. RT-qPCR analysis demonstrated that the purity of the samples was sufficient for molecular biology experiments. CTAB-based methods for RNA isolation were found to be the most efficient, providing the highest RNA yields and quality for tissues from P. guajava. Additionally, they were compatible for downstream RNA-based applications, besides being simple and cost-effective.
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Affiliation(s)
- Paola de Avelar Carpinetti
- Laboratory of Genetics and Plant Improvement, Department of Agronomy, Centre for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alegre, ES, Brazil
| | - Vinicius Sartori Fioresi
- Laboratory of Genetics and Plant Improvement, Department of Agronomy, Centre for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alegre, ES, Brazil
| | - Thais Ignez da Cruz
- Laboratory of Genetics and Plant Improvement, Department of Agronomy, Centre for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alegre, ES, Brazil
| | - Francine Alves Nogueira de Almeida
- Laboratory of Genetics and Plant Improvement, Department of Agronomy, Centre for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alegre, ES, Brazil
| | - Drielli Canal
- Laboratory of Genetics and Plant Improvement, Department of Agronomy, Centre for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alegre, ES, Brazil
| | - Adésio Ferreira
- Laboratory of Genetics and Plant Improvement, Department of Agronomy, Centre for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alegre, ES, Brazil
| | - Marcia Flores da Silva Ferreira
- Laboratory of Genetics and Plant Improvement, Department of Agronomy, Centre for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alegre, ES, Brazil
- * E-mail:
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7
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Behnam B, Higo A, Yamaguchi K, Tokunaga H, Utsumi Y, Selvaraj MG, Seki M, Ishitani M, Ceballos H, Lopez-Lavalle LAB, Tsuji H. Field-transcriptome analyses reveal developmental transitions during flowering in cassava (Manihot esculenta Crantz). PLANT MOLECULAR BIOLOGY 2021; 106:285-296. [PMID: 33855676 DOI: 10.1007/s11103-021-01149-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
We characterized genes that function in the photoperiodic flowering pathway in cassava. Transcriptome analysis of field-grown plants revealed characteristic expression patterns of these genes, demonstrating that field-grown cassava experiences two distinct developmental transitions. Cassava is an important crop for both edible and industrial purposes. Cassava develops storage roots that accumulate starch, providing an important source of staple food in tropical regions. To facilitate cassava breeding, it is important to elucidate how flowering is controlled. Several important genes that control flowering time have been identified in model plants; however, comprehensive characterization of these genes in cassava is still lacking. In this study, we identified genes encoding central flowering time regulators and examined these sequences for the presence or absence of conserved motifs. We found that cassava shares conserved genes for the photoperiodic flowering pathway, including florigen, anti-florigen and its associated transcription factor (GIGANTEA, CONSTANS, FLOWERING LOCUS T, CENTRORADIALIS/TERMINAL FLOWER1 and FD) and florigen downstream genes (SUPRESSOR OF OVEREXPRESSION OF CONSTANS1 and APETALA1/FRUITFUL). We conducted RNA-seq analysis of field-grown cassava plants and characterized the expression of flowering control genes. Finally, from the transcriptome analysis we identified two distinct developmental transitions that occur in field-grown cassava.
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Affiliation(s)
- Babak Behnam
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Asuka Higo
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Kaho Yamaguchi
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Hiroki Tokunaga
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, Japan
- International Laboratory for Cassava Molecular Breeding (ILCMB), AGI, Hanoi, Vietnam
| | - Yoshinori Utsumi
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, Japan
- International Laboratory for Cassava Molecular Breeding (ILCMB), AGI, Hanoi, Vietnam
| | | | - Motoaki Seki
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, Japan
- International Laboratory for Cassava Molecular Breeding (ILCMB), AGI, Hanoi, Vietnam
- Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Manabu Ishitani
- International Laboratory for Cassava Molecular Breeding (ILCMB), AGI, Hanoi, Vietnam
- International Center for Tropical Agriculture (CIAT), Valle del Cauca, Colombia
| | - Hernan Ceballos
- International Center for Tropical Agriculture (CIAT), Valle del Cauca, Colombia
| | | | - Hiroyuki Tsuji
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.
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8
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Garcia T, Duitama J, Zullo SS, Gil J, Ariani A, Dohle S, Palkovic A, Skeen P, Bermudez-Santana CI, Debouck DG, Martínez-Castillo J, Gepts P, Chacón-Sánchez MI. Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean. Nat Commun 2021; 12:702. [PMID: 33514713 PMCID: PMC7846787 DOI: 10.1038/s41467-021-20921-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023] Open
Abstract
Lima bean (Phaseolus lunatus L.), one of the five domesticated Phaseolus bean crops, shows a wide range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations make it a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. In this work, we combine long and short read sequencing technologies with a dense genetic map from a biparental population to obtain the chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models show high diversity among 1917 genes with conserved domains related to disease resistance. Structural comparison across 22,180 orthologs with common bean reveals high genome synteny and five large intrachromosomal rearrangements. Population genomic analyses show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. RNA-seq data reveal 4275 differentially expressed genes, which can be related to pod dehiscence and seed development. We expect the resources presented here to serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide tools and information for breeding for climate change resiliency.
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Affiliation(s)
- Tatiana Garcia
- grid.10689.360000 0001 0286 3748Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia ,grid.17088.360000 0001 2150 1785Present Address: Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI USA
| | - Jorge Duitama
- grid.7247.60000000419370714Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Stephanie Smolenski Zullo
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Juanita Gil
- grid.7247.60000000419370714Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia ,grid.411017.20000 0001 2151 0999Present Address: Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR USA
| | - Andrea Ariani
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA ,Present Address: BASF BBCC - Innovation Center, Gent, Belgium
| | - Sarah Dohle
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Antonia Palkovic
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Paola Skeen
- grid.10689.360000 0001 0286 3748Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia ,Present Address: Nunhems USA, Vegetable Seeds BASF, Acampo, CA USA
| | - Clara Isabel Bermudez-Santana
- grid.10689.360000 0001 0286 3748Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniel G. Debouck
- grid.418348.20000 0001 0943 556XCentro Internacional de Agricultura Tropical, Cali, Colombia
| | - Jaime Martínez-Castillo
- grid.418270.80000 0004 0428 7635Centro de Investigación Científica de Yucatán, Yucatán, Mexico
| | - Paul Gepts
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Maria Isabel Chacón-Sánchez
- grid.10689.360000 0001 0286 3748Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
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9
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Gaafar ARZ, Al-Qurainy F, Alshameri A, Khan S, Nadeem M, Tarroum M, Alansi S, Shaikhaldein HO, Salih AM, Arrak Alenezi N. High RNA quality extracted from the tolerant crop Cyamopsis tetragonoloba (L.) despite possession of low RNA integrity number. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1910567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
| | - Fahad Al-Qurainy
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Aref Alshameri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Salim Khan
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Nadeem
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed Tarroum
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh Alansi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hassan O. Shaikhaldein
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdalrhaman M. Salih
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Norah Arrak Alenezi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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A universal method for high-quality RNA extraction from plant tissues rich in starch, proteins and fiber. Sci Rep 2020; 10:16887. [PMID: 33037299 PMCID: PMC7547072 DOI: 10.1038/s41598-020-73958-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 09/24/2020] [Indexed: 01/08/2023] Open
Abstract
Using existing protocols, RNA extracted from seeds rich in starch often results in poor quality RNA, making it inappropriate for downstream applications. Though some methods are proposed for extracting RNA from plant tissue rich in starch and other polysaccharides, they invariably yield less and poor quality RNA. In order to obtain high yield and quality RNA from seeds and other plant tissues including roots a modified SDS-LiCl method was compared with existing methods, including TRIZOL kit (Invitrogen), Plant RNeasy mini kit (Qiagen), Furtado (2014) method, and CTAB-LiCl method. Modifications in the extraction buffer and solutions used for RNA precipitation resulted in a robust method for extracting RNA in seeds and roots, where extracting quality RNA is challenging. The modified SDS-LiCl method revealed intense RNA bands through gel electrophoresis and a nanodrop spectrophotometer detected ratios of ≥ 2 and 1.8 for A260/A230 and A260/A280, respectively. The absence of starch co-precipitation during RNA extraction resulted in enhanced yield and quality of RNA with RIN values of 7-9, quantified using a bioanalyzer. The high-quality RNA obtained was demonstrated to be suitable for downstream applications, such as cDNA synthesis, gene amplification, and RT-qPCR. The method was also effective in extracting RNA from seeds of other cereals including field-grown sorghum and corn. The modified SDS-LiCl method is a robust and highly reproducible RNA extraction method for plant tissues rich in starch and other secondary metabolites. The modified SDS-LiCl method successfully extracted high yield and quality RNA from mature, developing, and germinated seeds, leaves, and roots exposed to different abiotic stresses.
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Irigoyen ML, Garceau DC, Bohorquez-Chaux A, Lopez-Lavalle LAB, Perez-Fons L, Fraser PD, Walling LL. Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid. BMC Genomics 2020; 21:93. [PMID: 31996126 PMCID: PMC6990599 DOI: 10.1186/s12864-019-6443-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/29/2019] [Indexed: 11/16/2022] Open
Abstract
Background Whiteflies are a threat to cassava (Manihot esculenta), an important staple food in many tropical/subtropical regions. Understanding the molecular mechanisms regulating cassava’s responses against this pest is crucial for developing control strategies. Pathogenesis-related (PR) protein families are an integral part of plant immunity. With the availability of whole genome sequences, the annotation and expression programs of the full complement of PR genes in an organism can now be achieved. An understanding of the responses of the entire complement of PR genes during biotic stress and to the defense hormones, salicylic acid (SA) and jasmonic acid (JA), is lacking. Here, we analyze the responses of cassava PR genes to whiteflies, SA, JA, and other biotic aggressors. Results The cassava genome possesses 14 of the 17 plant PR families, with a total of 447 PR genes. A cassava PR gene nomenclature is proposed. Phylogenetic relatedness of cassava PR proteins to each other and to homologs in poplar, rice and Arabidopsis identified cassava-specific PR gene family expansions. The temporal programs of PR gene expression in response to the whitefly (Aleurotrachelus socialis) in four whitefly-susceptible cassava genotypes showed that 167 of the 447 PR genes were regulated after whitefly infestation. While the timing of PR gene expression varied, over 37% of whitefly-regulated PR genes were downregulated in all four genotypes. Notably, whitefly-responsive PR genes were largely coordinately regulated by SA and JA. The analysis of cassava PR gene expression in response to five other biotic stresses revealed a strong positive correlation between whitefly and Xanthomonas axonopodis and Cassava Brown Streak Virus responses and negative correlations between whitefly and Cassava Mosaic Virus responses. Finally, certain associations between PR genes in cassava expansions and response to biotic stresses were observed among PR families. Conclusions This study represents the first genome-wide characterization of PR genes in cassava. PR gene responses to six biotic stresses and to SA and JA are demonstrably different to other angiosperms. We propose that our approach could be applied in other species to fully understand PR gene regulation by pathogens, pests and the canonical defense hormones SA and JA.
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Affiliation(s)
- Maria L Irigoyen
- Department of Botany and Plant Sciences and Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Danielle C Garceau
- Department of Botany and Plant Sciences and Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | | | | | - Laura Perez-Fons
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Linda L Walling
- Department of Botany and Plant Sciences and Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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