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Yousefi K, Abdullah SNA, Hatta MAM, Ling KL. Genomics and Transcriptomics Reveal Genetic Contribution to Population Diversity and Specific Traits in Coconut. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091913. [PMID: 37176970 PMCID: PMC10181077 DOI: 10.3390/plants12091913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/15/2023]
Abstract
Coconut is an economically important palm species with a long history of human use. It has applications in various food, nutraceuticals, and cosmetic products, and there has been renewed interest in coconut in recent years due to its unique nutritional and medicinal properties. Unfortunately, the sustainable growth of the coconut industry has been hampered due to a shortage of good quality seedlings. Genetic improvement through the traditional breeding approach faced considerable obstacles due to its perennial nature, protracted juvenile period, and high heterozygosity. Molecular biotechnological tools, including molecular markers and next-generation sequencing (NGS), could expedite genetic improvement efforts in coconut. Researchers have employed various molecular markers to reveal genetic diversity among coconut populations and for the construction of a genetic map for exploitation in coconut breeding programs worldwide. Whole genome sequencing and transcriptomics on the different varieties have generated a massive amount of publicly accessible sequence data, substantially improving the ability to analyze and understand molecular mechanisms affecting crop performance. The production of high-yielding and disease-resilient coconuts and the deciphering of the complex coconut genome's structure can profit tremendously from these technologies. This paper aims to provide a comprehensive review of the progress of coconut research, using genomics, transcriptomics, and molecular markers initiatives.
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Affiliation(s)
- Kobra Yousefi
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Siti Nor Akmar Abdullah
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Laboratory of Sustainable Agronomy and Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Muhammad Asyraf Md Hatta
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Kong Lih Ling
- Laboratory of Sustainable Agronomy and Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
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Arumugam T, Hatta MAM. Improving Coconut Using Modern Breeding Technologies: Challenges and Opportunities. PLANTS (BASEL, SWITZERLAND) 2022; 11:3414. [PMID: 36559524 PMCID: PMC9784122 DOI: 10.3390/plants11243414] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/19/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
Coconut (Cocos nucifera L.) is a perennial palm with a wide range of distribution across tropical islands and coastlines. Multitude use of coconut by nature is important in the socio-economic fabric framework among rural smallholders in producing countries. It is a major source of income for 30 million farmers, while 60 million households rely on the coconut industry directly as farm workers and indirectly through the distribution, marketing, and processing of coconut and coconut-based products. Stagnant production, inadequate planting materials, the effects of climate change, as well as pests and diseases are among the key issues that need to be urgently addressed in the global coconut industry. Biotechnology has revolutionized conventional breeding approaches in creating genetic variation for trait improvement in a shorter period of time. In this review, we highlighted the challenges of current breeding strategies and the potential of biotechnological approaches, such as genomic-assisted breeding, next-generation sequencing (NGS)-based genotyping and genome editing tools in improving the coconut. Also, combining these technologies with high-throughput phenotyping approaches and speed breeding could speed up the rate of genetic gain in coconut breeding to solve problems that have been plaguing the industry for decades.
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Beveridge FC, Kalaipandian S, Yang C, Adkins SW. Fruit Biology of Coconut ( Cocos nucifera L.). PLANTS (BASEL, SWITZERLAND) 2022; 11:3293. [PMID: 36501334 PMCID: PMC9738799 DOI: 10.3390/plants11233293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/24/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Coconut (Cocos nucifera L.) is an important perennial crop adapted to a wide range of habitats. Although global coconut demand has increased sharply over the past few years, its production has been decreasing due to palm senility, as well as abiotic and biotic stresses. In fact, replanting efforts are impeded due to the lack of good quality seedlings. In vitro technologies have a great potential; however, their applications may take time to reach a commercial level. Therefore, traditional seed propagation is still critical to help meet the rising demand and its practice needs to be improved. To achieve an improved propagation via seeds, it is important to understand coconut fruit biology and its related issues. This review aims to provide a comprehensive summary of the existing knowledge on coconut fruit morpho-anatomy, germination biology, seed dispersal, distribution, fruit longevity and storage. This will help to identify gaps where future research efforts should be directed to improve traditional seed propagation.
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Transcriptome analysis reveals key defense-related genes upon SA induction in Cocos nucifera L. Genes Genomics 2021; 44:197-210. [PMID: 34216358 DOI: 10.1007/s13258-021-01068-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 02/17/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Salicylic acid (SA) is an important regulator of genes involved in plant defense and pathogen-triggered systemic acquired resistance (SAR). Coconut is an important crop affected by several pathogens. Reported evidence suggests SA involvement in defense responses, including SAR in coconut. OBJECTIVE To identified differentially expressed genes in leaf and root tissues of coconut plantlets, as a result of SA, that might be involved in coconut defense responses. METHODS Comparative transcriptomic analysis by RNA-Seq of leaf and root tissues from in vitro coconut plantlets unexposed and exposed to SA 2.5 mM for 48 h. And in silico validation of gene expression by qRT-PCR. RESULTS We identified 4615 and 3940 differentially expressed unigenes (DEUs) in leaf and root tissues respectively. Our GO analysis showed functional categories related to the induction of defense responses, such as "systemic acquired resistance" and highly enriched hormone categories, such as abscisic acid. The most abundant KEGG pathway in our results was "Biosynthesis of antibiotics". Our findings support that exogenous application of SA to plantlets induced the activation of PRs, RGAs, ICS2, NLTP2, PER4, TRXM and some WRKYs mediated by NPR1-dependent pathways. Also, we found DEUs, such as BZR1, HSL1, and WHY2 that support that SA could regulate defense-related genes through NPR1-independent pathways. CONCLUSION The present study of massive data analysis carried out on coconut plantlets exposed to SA, generates valuable information that increases our understanding of defense molecular mechanisms in coconut and open new venues for research for the improvement of management of coconut diseases.
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Yang Y, Bocs S, Fan H, Armero A, Baudouin L, Xu P, Xu J, This D, Hamelin C, Iqbal A, Qadri R, Zhou L, Li J, Wu Y, Ma Z, Issali AE, Rivallan R, Liu N, Xia W, Peng M, Xiao Y. Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance. Commun Biol 2021; 4:105. [PMID: 33483627 PMCID: PMC7822834 DOI: 10.1038/s42003-020-01593-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 12/09/2020] [Indexed: 01/30/2023] Open
Abstract
Coconut (Cocos nucifera) is the emblematic palm of tropical coastal areas all around the globe. It provides vital resources to millions of farmers. In an effort to better understand its evolutionary history and to develop genomic tools for its improvement, a sequence draft was recently released. Here, we present a dense linkage map (8402 SNPs) aiming to assemble the large genome of coconut (2.42 Gbp, 2n = 32) into 16 pseudomolecules. As a result, 47% of the sequences (representing 77% of the genes) were assigned to 16 linkage groups and ordered. We observed segregation distortion in chromosome Cn15, which is a signature of strong selection among pollen grains, favouring the maternal allele. Comparing our results with the genome of the oil palm Elaeis guineensis allowed us to identify major events in the evolutionary history of palms. We find that coconut underwent a massive transposable element invasion in the last million years, which could be related to the fluctuations of sea level during the glaciations at Pleistocene that would have triggered a population bottleneck. Finally, to better understand the facultative halophyte trait of coconut, we conducted an RNA-seq experiment on leaves to identify key players of signaling pathways involved in salt stress response. Altogether, our findings represent a valuable resource for the coconut breeding community.
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Affiliation(s)
- Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Stéphanie Bocs
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
- South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398, Montpellier, France
| | - Haikuo Fan
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Alix Armero
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Luc Baudouin
- CIRAD, UMR AGAP, F-34398, Montpellier, France.
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France.
| | - Pengwei Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, P. R. China
| | - Junyang Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, P. R. China
| | - Dominique This
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Chantal Hamelin
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
- South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398, Montpellier, France
| | - Amjad Iqbal
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Rashad Qadri
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Lixia Zhou
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Jing Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Yi Wu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Zilong Ma
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, 571101, Haikou, Hainan, P. R. China
| | - Auguste Emmanuel Issali
- Station Cocotier Marc Delorme, Centre National De Recherche Agronomique (CNRA)07 B.P. 13, Port Bouet, Côte d'Ivoire
| | - Ronan Rivallan
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Na Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, P. R. China
| | - Wei Xia
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China.
| | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, 571101, Haikou, Hainan, P. R. China.
| | - Yong Xiao
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China.
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Mora-Márquez F, Chano V, Vázquez-Poletti JL, López de Heredia U. TOA: A software package for automated functional annotation in non-model plant species. Mol Ecol Resour 2020; 21:621-636. [PMID: 33070442 DOI: 10.1111/1755-0998.13285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 10/01/2020] [Accepted: 10/13/2020] [Indexed: 01/05/2023]
Abstract
The increase of sequencing capacity provided by high-throughput platforms has made it possible to routinely obtain large sets of genomic and transcriptomic sequences from model and non-model organisms. Subsequent genomic analysis and gene discovery in next-generation sequencing experiments are, however, bottlenecked by functional annotation. One common way to perform functional annotation of sets of sequences obtained from next-generation sequencing experiments, is by searching for homologous sequences and accessing the related functional information deposited in genomic databases. Functional annotation is especially challenging for non-model organisms, like many plant species. In such cases, existing free and commercial general-purpose applications may not offer complete and accurate results. We present TOA (Taxonomy-oriented annotation), a Python-based user-friendly open source application designed to establish functional annotation pipelines geared towards non-model plant species that can run in Linux/Mac computers, HPCs and cloud servers. TOA performs homology searches against proteins stored in the PLAZA databases, NCBI RefSeq Plant, Nucleotide Database and Non-Redundant Protein Sequence Database, and outputs functional information from several ontology systems: Gene Ontology, InterPro, EC, KEGG, Mapman and MetaCyc. The software performance was validated by comparing the runtimes, total number of annotated sequences and accuracy of the functional information obtained for several plant benchmark data sets with TOA and other functional annotation solutions. TOA outperformed the other software in terms of number of annotated sequences and accuracy of the annotation and constitutes a good alternative to improve functional annotation in plants. TOA is especially recommended for gymnosperms or for low quality sequence data sets of non-model plants.
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Affiliation(s)
- Fernando Mora-Márquez
- GI Sistemas Naturales e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
| | - Víctor Chano
- GI Sistemas Naturales e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
| | - José Luis Vázquez-Poletti
- GI Arquitectura de Sistemas Distribuidos, Dpto. Arquitectura de Computadores y Automática, Facultad de Informática, Universidad Complutense de Madrid, Madrid, Spain
| | - Unai López de Heredia
- GI Sistemas Naturales e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
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Lantican DV, Strickler SR, Canama AO, Gardoce RR, Mueller LA, Galvez HF. De Novo Genome Sequence Assembly of Dwarf Coconut ( Cocos nucifera L. 'Catigan Green Dwarf') Provides Insights into Genomic Variation Between Coconut Types and Related Palm Species. G3 (BETHESDA, MD.) 2019; 9:2377-2393. [PMID: 31167834 PMCID: PMC6686914 DOI: 10.1534/g3.119.400215] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/31/2019] [Indexed: 11/23/2022]
Abstract
We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, 'Catigan Green Dwarf' (CATD). The genome sequence was generated using the PacBio SMRT sequencing platform at 15X coverage of the expected genome size of 2.15 Gbp, which was corrected with assembled 50X Illumina paired-end MiSeq reads of the same genome. The draft genome was improved through Chicago sequencing to generate a scaffold assembly that results in a total genome size of 2.1 Gbp consisting of 7,998 scaffolds with N50 of 570,487 bp. The final assembly covers around 97.6% of the estimated genome size of coconut 'CATD' based on homozygous k-mer peak analysis. A total of 34,958 high-confidence gene models were predicted and functionally associated to various economically important traits, such as pest/disease resistance, drought tolerance, coconut oil biosynthesis, and putative transcription factors. The assembled genome was used to infer the evolutionary relationship within the palm family based on genomic variations and synteny of coding gene sequences. Data show that at least three (3) rounds of whole genome duplication occurred and are commonly shared by these members of the Arecaceae family. A total of 7,139 unique SSR markers were designed to be used as a resource in marker-based breeding. In addition, we discovered 58,503 variants in coconut by aligning the Hainan Tall (HAT) WGS reads to the non-repetitive regions of the assembled CATD genome. The gene markers and genome-wide SSR markers established here will facilitate the development of varieties with resilience to climate change, resistance to pests and diseases, and improved oil yield and quality.
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Affiliation(s)
- Darlon V Lantican
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
- Philippine Genome Center, University of the Philippines System, Diliman, Quezon City, Philippines
| | | | - Alma O Canama
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
| | - Roanne R Gardoce
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
| | | | - Hayde F Galvez
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
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Reynolds KB, Cullerne DP, El Tahchy A, Rolland V, Blanchard CL, Wood CC, Singh SP, Petrie JR. Identification of Genes Involved in Lipid Biosynthesis through de novo Transcriptome Assembly from Cocos nucifera Developing Endosperm. PLANT & CELL PHYSIOLOGY 2019; 60:945-960. [PMID: 30608545 PMCID: PMC6498750 DOI: 10.1093/pcp/pcy247] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 12/19/2018] [Indexed: 05/07/2023]
Abstract
Cocos nucifera (coconut), a member of the Arecaceae family, is an economically important woody palm that is widely grown in tropical and subtropical regions. The coconut palm is well known for its ability to accumulate large amounts of oil, approximately 63% of the seed weight. Coconut oil varies significantly from other vegetable oils as it contains a high proportion of medium-chain fatty acids (MCFA; 85%). The unique composition of coconut oil raises interest in understanding how the coconut palm produces oil of a high saturated MCFA content, and if such an oil profile could be replicated via biotechnology interventions. Although some gene discovery work has been performed there is still a significant gap in the knowledge associated with coconut's oil production pathways. In this study, a de novo transcriptome was assembled for developing coconut endosperm to identify genes involved in the synthesis of lipids, particularly triacylglycerol. Of particular interest were thioesterases, acyltransferases and oleosins because of their involvement in the processes of releasing fatty acids for assembly, esterification of fatty acids into glycerolipids and protecting oils from degradation, respectively. It is hypothesized that some of these genes may exhibit a strong substrate preference for MCFA and hence may assist the future development of vegetable oils with an enriched MCFA composition. In this study, we identified and confirmed functionality of five candidate genes from the gene families of interest. This study will benefit future work in areas of increasing vegetable oil production and the tailoring of oil fatty acid compositions.
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Affiliation(s)
- Kyle B Reynolds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
- Department of Primary Industries, Graham Centre for Agricultural Innovation, Charles Sturt University, Wagga Wagga, NSW, Australia
- ARC Industrial Transformation Training Centre for Functional Grains, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Darren P Cullerne
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, NSW, Australia
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Anna El Tahchy
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Vivien Rolland
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Christopher L Blanchard
- ARC Industrial Transformation Training Centre for Functional Grains, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Craig C Wood
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Surinder P Singh
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - James R Petrie
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
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Xiao Y, Xia W, Mason AS, Cao Z, Fan H, Zhang B, Zhang J, Ma Z, Peng M, Huang D. Genetic control of fatty acid composition in coconut (Cocos nucifera), African oil palm (Elaeis guineensis), and date palm (Phoenix dactylifera). PLANTA 2019; 249:333-350. [PMID: 30194535 DOI: 10.1007/s00425-018-3003-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/03/2018] [Indexed: 05/26/2023]
Abstract
Predominant gene isoforms and expression bias in lipid metabolism pathways are highly conserved between oil-producing Arecaceae crop species coconut and oil palm, but diverge in non-oil-producing species date palm. Coconut (Cocos nucifera), African oil palm (Elaeis guineensis) and date palm (Phoenix dactylifera) are three major crop species in the Arecaceae family for which genome sequences have recently become available. Coconut and African oil palm both store oil in their endosperms, while date palm fruits contain very little oil. We analyzed fatty acid composition in three coconut tissues (leaf, endosperm and embryo) and in two African oil palm tissues (leaf and mesocarp), and identified 806, 840 and 848 lipid-related genes in 22 lipid metabolism pathways from the coconut, African oil palm and date palm genomes, respectively. The majority of lipid-related genes were highly homologous and retained in homologous segments between the three species. Genes involved in the conversion of pyruvate to fatty acid had a five-to-sixfold higher expression in the coconut endosperm and oil palm mesocarp than in the leaf or embryo tissues based on Fragments Per Kilobase of transcript per Million mapped reads values. A close evolutionary relationship between predominant gene isoforms and high conservation of gene expression bias in the lipid and carbohydrate gene metabolism pathways was observed for the two oil-producing species coconut and oil palm, differing from that of date palm, a non-oil-producing species. Our results elucidate the similarities and differences in lipid metabolism between the three major Arecaceae crop species, providing important information for physiology studies as well as breeding for fatty acid composition and oil content in these crops.
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Affiliation(s)
- Yong Xiao
- Coconut Research Institute, CATAS, Wenchang, 571339, Hainan, People's Republic of China
| | - Wei Xia
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, People's Republic of China.
| | - Annaliese S Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Zengying Cao
- MOA Key Laboratory of Tropical Crop Biology and Genetic Resources Utilization, Institute of Tropical Bioscience and Biotechnology, CATAS, Haikou, 571101, Hainan, People's Republic of China
| | - Haikuo Fan
- Coconut Research Institute, CATAS, Wenchang, 571339, Hainan, People's Republic of China
| | - Bo Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, People's Republic of China
| | - Jinlan Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, People's Republic of China
| | - Zilong Ma
- MOA Key Laboratory of Tropical Crop Biology and Genetic Resources Utilization, Institute of Tropical Bioscience and Biotechnology, CATAS, Haikou, 571101, Hainan, People's Republic of China
| | - Ming Peng
- MOA Key Laboratory of Tropical Crop Biology and Genetic Resources Utilization, Institute of Tropical Bioscience and Biotechnology, CATAS, Haikou, 571101, Hainan, People's Republic of China
| | - Dongyi Huang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, People's Republic of China
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Armero A, Baudouin L, Bocs S, This D. Improving transcriptome de novo assembly by using a reference genome of a related species: Translational genomics from oil palm to coconut. PLoS One 2017; 12:e0173300. [PMID: 28334050 PMCID: PMC5363918 DOI: 10.1371/journal.pone.0173300] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 02/17/2017] [Indexed: 01/20/2023] Open
Abstract
The palms are a family of tropical origin and one of the main constituents of the ecosystems of these regions around the world. The two main species of palm represent different challenges: coconut (Cocos nucifera L.) is a source of multiple goods and services in tropical communities, while oil palm (Elaeis guineensis Jacq) is the main protagonist of the oil market. In this study, we present a workflow that exploits the comparative genomics between a target species (coconut) and a reference species (oil palm) to improve the transcriptomic data, providing a proteome useful to answer functional or evolutionary questions. This workflow reduces redundancy and fragmentation, two inherent problems of transcriptomic data, while preserving the functional representation of the target species. Our approach was validated in Arabidopsis thaliana using Arabidopsis lyrata and Capsella rubella as references species. This analysis showed the high sensitivity and specificity of our strategy, relatively independent of the reference proteome. The workflow increased the length of proteins products in A. thaliana by 13%, allowing, often, to recover 100% of the protein sequence length. In addition redundancy was reduced by a factor greater than 3. In coconut, the approach generated 29,366 proteins, 1,246 of these proteins deriving from new contigs obtained with the BRANCH software. The coconut proteome presented a functional profile similar to that observed in rice and an important number of metabolic pathways related to secondary metabolism. The new sequences found with BRANCH software were enriched in functions related to biotic stress. Our strategy can be used as a complementary step to de novo transcriptome assembly to get a representative proteome of a target species. The results of the current analysis are available on the website PalmComparomics (http://palm-comparomics.southgreen.fr/).
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Affiliation(s)
- Alix Armero
- Montpellier SupAgro, UMR AGAP, Montpellier, France
| | | | - Stéphanie Bocs
- CIRAD, UMR AGAP, Montpellier, France
- South Green Bioinformatics Platform, Montpellier, France
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Saensuk C, Wanchana S, Choowongkomon K, Wongpornchai S, Kraithong T, Imsabai W, Chaichoompu E, Ruanjaichon V, Toojinda T, Vanavichit A, Arikit S. De novo transcriptome assembly and identification of the gene conferring a "pandan-like" aroma in coconut (Cocos nucifera L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:324-334. [PMID: 27717469 DOI: 10.1016/j.plantsci.2016.08.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 08/26/2016] [Accepted: 08/27/2016] [Indexed: 06/06/2023]
Abstract
Thailand's aromatic coconut (Cocos nucifera L.) is a special type of green dwarf coconut, the liquid endosperm of which is characterized by a pleasant "pandan-like" aroma due to the presence of 2-acetyl-1-pyrroline (2AP). The aim of this study was to perform a de novo assembly of transriptome from C. nucifera endosperm and to identify the gene responsible for 2AP biosynthesis. CnAMADH2 was identified as an ortholog of the rice aromatic gene and a G-to-C substitution found in exon 14 was associated with 2AP content in the aromatic green dwarf coconut accessions. The base substitution caused an amino-acid change, alanine-to-proline, at position 442 (P442A). The presence of P at this position might alter the steric conformation at the loop region and subsequently result in an unstabilized dimer conformation that could lower AMADH enzyme activity. Among AMADH/BADH protein sequences in different plant species, the P442A mutation was found exclusively in aromatic coconut. The PCR marker developed based on this sequence variation can perfectly detect the aromatic and non-aromatic alleles of the gene. This study confirms the hypothesis that plants may share a mechanism of 2AP biosynthesis. This is the first identification of the gene associated with 2AP biosynthesis in a tree plant.
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Affiliation(s)
- Chatree Saensuk
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand; Interdisciplinary Graduate Program in Genetic Engineering, Kasetsart University, Bangkok, 10900, Thailand
| | - Samart Wanchana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Sugunya Wongpornchai
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Tippaya Kraithong
- Chumphon Horticultural Research Center, Department of Agriculture, Bangkok, 10900, Thailand
| | - Wachiraya Imsabai
- Department of Horticulture, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
| | - Ekawat Chaichoompu
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
| | - Vinitchan Ruanjaichon
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand
| | - Apichart Vanavichit
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand; Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
| | - Siwaret Arikit
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand; Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.
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Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome. PLoS One 2016; 11:e0163990. [PMID: 27736909 PMCID: PMC5063475 DOI: 10.1371/journal.pone.0163990] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 09/19/2016] [Indexed: 11/19/2022] Open
Abstract
Coconut (Cocos nucifera L.), a member of the palm family (Arecaceae), is one of the most economically important crops in tropics, serving as an important source of food, drink, fuel, medicine, and construction material. Here we report an assembly of the coconut (C. nucifera, Oman local Tall cultivar) mitochondrial (mt) genome based on next-generation sequencing data. This genome, 678,653bp in length and 45.5% in GC content, encodes 72 proteins, 9 pseudogenes, 23 tRNAs, and 3 ribosomal RNAs. Within the assembly, we find that the chloroplast (cp) derived regions account for 5.07% of the total assembly length, including 13 proteins, 2 pseudogenes, and 11 tRNAs. The mt genome has a relatively large fraction of repeat content (17.26%), including both forward (tandem) and inverted (palindromic) repeats. Sequence variation analysis shows that the Ti/Tv ratio of the mt genome is lower as compared to that of the nuclear genome and neutral expectation. By combining public RNA-Seq data for coconut, we identify 734 RNA editing sites supported by at least two datasets. In summary, our data provides the second complete mt genome sequence in the family Arecaceae, essential for further investigations on mitochondrial biology of seed plants.
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Gunn BF, Baudouin L, Beulé T, Ilbert P, Duperray C, Crisp M, Issali A, Konan JL, Rival A. Ploidy and domestication are associated with genome size variation in Palms. AMERICAN JOURNAL OF BOTANY 2015; 102:1625-1633. [PMID: 26437888 DOI: 10.3732/ajb.1500164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 08/24/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY The genome size of a species (C-value) is associated with growth, development and adaptation to environmental changes. Angiosperm C-values range 1200-fold and frequently vary within species, although little is known about the impacts of domestication on genome size. Genome size variation among related species of palms is of evolutionary significance because changes characterize clades and may be associated with polyploidy, transposon amplifications, deletions, or rearrangements. Further knowledge of genome size will provide crucial information needed for planning of whole genome sequencing and accurate annotations. We studied the genome size of Cocos nucifera and its variation among cultivars, and compared it to values for related palms from the Attaleinae subtribe. METHODS Flow cytometric analysis of isolated nuclei from young palm leaves was used to estimate genome sizes of 23 coconut cultivars (Talls, Dwarfs, and hybrids) worldwide and 17 Cocoseae species. Ancestral genome size was reconstructed on a maximum likelihood phylogeny of Attaleinae from seven WRKY loci. KEY RESULTS The coconut genome is large-averaging 5.966 pg-and shows intraspecific variation associated with domestication. Variation among Tall coconuts was significantly greater than among Dwarfs. Attaleinae genomes showed moderate size variation across genera, except polyploids Jubaeopsis caffra, Voanioala gerardii, Beccariophoenix alfredii, and Allagoptera caudescens, which had larger genomes. CONCLUSIONS Our results contribute to the understanding of the relationship between domestication and genome size in long-lived tree crops and provide a basis for whole-genome sequencing of the coconut and other domesticated plants. Polyploidy evolved independently in two clades within Attaleinae.
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Affiliation(s)
- Bee F Gunn
- Research School of Biology, Division of Evolution, Ecology and Genetics, The Australian National University, Acton, ACT 2601, Australia
| | | | | | | | - Christophe Duperray
- Montpellier Rio Imaging, IRB, INSERM U1040, CHU de Montpellier 34295 Montpellier, France
| | - Michael Crisp
- Research School of Biology, Division of Evolution, Ecology and Genetics, The Australian National University, Acton, ACT 2601, Australia
| | - Auguste Issali
- Station de Recherche Marc Delorme, Port Bouët. 07 BP 13 Abidjan, Côte d'Ivoire
| | - Jean-Louis Konan
- Station de Recherche Marc Delorme, Port Bouët. 07 BP 13 Abidjan, Côte d'Ivoire
| | - Alain Rival
- CIRAD, UMR DIADE, F-34398 Montpellier, France
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