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Qiao X, Li Q, Yin H, Qi K, Li L, Wang R, Zhang S, Paterson AH. Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants. Genome Biol 2019; 20:38. [PMID: 30791939 PMCID: PMC6383267 DOI: 10.1186/s13059-019-1650-2] [Citation(s) in RCA: 469] [Impact Index Per Article: 93.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 02/08/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention. RESULTS We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events-transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in plant self-defense. The rate of gene conversion among WGD-derived gene pairs declined over time, peaking shortly after polyploidization. To provide a platform for accessing duplicated gene pairs in different plants, we constructed the Plant Duplicate Gene Database. CONCLUSIONS We identify a comprehensive landscape of different modes of gene duplication across the plant kingdom by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.
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Affiliation(s)
- Xin Qiao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qionghou Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Hao Yin
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Kaijie Qi
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Leiting Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Runze Wang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605 USA
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152
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Development and validation of whole genome-wide and genic microsatellite markers in oil palm (Elaeis guineensis Jacq.): First microsatellite database (OpSatdb). Sci Rep 2019; 9:1899. [PMID: 30760842 PMCID: PMC6374426 DOI: 10.1038/s41598-018-37737-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 12/11/2018] [Indexed: 01/27/2023] Open
Abstract
The availability of large expressed sequence tag (EST) and whole genome databases of oil palm enabled the development of a data base of microsatellite markers. For this purpose, an EST database consisting of 40,979 EST sequences spanning 27 Mb and a chromosome-wise whole genome databases were downloaded. A total of 3,950 primer pairs were identified and developed from EST sequences. The tri and tetra nucleotide repeat motifs were most prevalent (each 24.75%) followed by di-nucleotide repeat motifs. Whole genome-wide analysis found a total of 245,654 SSR repeats across the 16 chromosomes of oil palm, of which 38,717 were compound microsatellite repeats. A web application, OpSatdb, the first microsatellite database of oil palm, was developed using the PHP and MySQL database ( https://ssr.icar.gov.in/index.php ). It is a simple and systematic web-based search engine for searching SSRs based on repeat motif type, repeat type, and primer details. High synteny was observed between oil palm and rice genomes. The mapping of ESTs having SSRs by Blast2GO resulted in the identification of 19.2% sequences with gene ontology (GO) annotations. Randomly, a set of ten genic SSRs and five genomic SSRs were used for validation and genetic diversity on 100 genotypes belonging to the world oil palm genetic resources. The grouping pattern was observed to be broadly in accordance with the geographical origin of the genotypes. The identified genic and genome-wide SSRs can be effectively useful for various genomic applications of oil palm, such as genetic diversity, linkage map construction, mapping of QTLs, marker-assisted selection, and comparative population studies.
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153
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Xia W, Luo T, Zhang W, Mason AS, Huang D, Huang X, Tang W, Dou Y, Zhang C, Xiao Y. Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis. FRONTIERS IN PLANT SCIENCE 2019; 10:130. [PMID: 30809240 PMCID: PMC6380268 DOI: 10.3389/fpls.2019.00130] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 01/25/2019] [Indexed: 05/28/2023]
Abstract
High-density single nucleotide polymorphisms (SNPs) are used as highly favored makers to analyze genetic diversity and population structure, to construct high-density genetic maps and provide genotypes for genome-wide association analysis. In order to develop genome-wide SNP markers in oil palm (Elaeis guineensis), single locus amplified fragment sequencing (SLAF-seq) technology was performed in a diversity panel of 200 oil palm individuals and 1,261,501 SNPs were identified with minor allele frequency > 0.05 and integrity > 1. Among them, only 17.81% can be mapped within the genic region and the remaining was located into the intergenic region. A positive correlation was detected between the distribution of SNP markers and retrotransposons [transposable elements (TEs)]. Population structure analysis showed that the 200 individuals of oil palm can be divided into five subgroups based on cross-validation errors. However, the subpopulations divided for the 200 oil palm individuals based on the SNP markers were not accurately related to their geographical origins and 80 oil palm individuals from Malaysia showed highest genetic diversity. In addition, the physical distance of linkage disequilibrium (LD) decay in the analyzed oil palm population was 14.516 kb when r2 = 0.1. The LD decay distances for different chromosomes varied from 3.324 (chromosome 15) to 19.983 kb (chromosome 7). Our research provides genome-wide SNPs for future targeted breeding in palm oil.
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Affiliation(s)
- Wei Xia
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Tingting Luo
- National Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wei Zhang
- National Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Annaliese S. Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Dongyi Huang
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Xiaolong Huang
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Wenqi Tang
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Yajing Dou
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Chunyu Zhang
- National Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yong Xiao
- Coconut Research Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
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154
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Ha J, Shim S, Lee T, Kang YJ, Hwang WJ, Jeong H, Laosatit K, Lee J, Kim SK, Satyawan D, Lestari P, Yoon MY, Kim MY, Chitikineni A, Tanya P, Somta P, Srinives P, Varshney RK, Lee S. Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:517-530. [PMID: 30059608 PMCID: PMC6335072 DOI: 10.1111/pbi.12995] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/26/2018] [Indexed: 05/02/2023]
Abstract
Jatropha curcas (physic nut), a non-edible oilseed crop, represents one of the most promising alternative energy sources due to its high seed oil content, rapid growth and adaptability to various environments. We report ~339 Mbp draft whole genome sequence of J. curcas var. Chai Nat using both the PacBio and Illumina sequencing platforms. We identified and categorized differentially expressed genes related to biosynthesis of lipid and toxic compound among four stages of seed development. Triacylglycerol (TAG), the major component of seed storage oil, is mainly synthesized by phospholipid:diacylglycerol acyltransferase in Jatropha, and continuous high expression of homologs of oleosin over seed development contributes to accumulation of high level of oil in kernels by preventing the breakdown of TAG. A physical cluster of genes for diterpenoid biosynthetic enzymes, including casbene synthases highly responsible for a toxic compound, phorbol ester, in seed cake, was syntenically highly conserved between Jatropha and castor bean. Transcriptomic analysis of female and male flowers revealed the up-regulation of a dozen family of TFs in female flower. Additionally, we constructed a robust species tree enabling estimation of divergence times among nine Jatropha species and five commercial crops in Malpighiales order. Our results will help researchers and breeders increase energy efficiency of this important oil seed crop by improving yield and oil content, and eliminating toxic compound in seed cake for animal feed.
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Affiliation(s)
- Jungmin Ha
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoulKorea
| | - Sangrea Shim
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Taeyoung Lee
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Yang J. Kang
- Division of Applied Life Science (BK21 plus program) DepartmentGyeongsang National UniversityPMBBRCJinju‐siKorea
- Division of Life Science DepartmentGyeongsang National UniversityJinju‐siKorea
| | | | - Haneul Jeong
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Kularb Laosatit
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Jayern Lee
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Sue K. Kim
- Department of ChemistryCollege of Natural ScienceDankook UniversityCheonanSouth Korea
| | - Dani Satyawan
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD‐IAARD)BogorIndonesia
| | - Puji Lestari
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD‐IAARD)BogorIndonesia
| | - Min Y. Yoon
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Moon Y. Kim
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoulKorea
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelangana StateIndia
| | - Patcharin Tanya
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Prakit Somta
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Peerasak Srinives
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelangana StateIndia
| | - Suk‐Ha Lee
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoulKorea
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155
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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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156
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Li SF, Guo YJ, Li JR, Zhang DX, Wang BX, Li N, Deng CL, Gao WJ. The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach ( Spinacia oleracea L.). Mob DNA 2019; 10:3. [PMID: 30675191 PMCID: PMC6337768 DOI: 10.1186/s13100-019-0147-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/07/2019] [Indexed: 11/10/2022] Open
Abstract
Background Repetitive sequences, including transposable elements (TEs) and satellite DNAs, occupy a considerable portion of plant genomes. Analysis of the repeat fraction benefits the understanding of genome structure and evolution. Spinach (Spinacia oleracea L.), an important vegetable crop, is also a model dioecious plant species for studying sex determination and sex chromosome evolution. However, the repetitive sequences of the spinach genome have not been fully investigated. Results We extensively analyzed the repetitive components of draft spinach genome, especially TEs and satellites, by different strategies. A total of 16,002 full-length TEs were identified. Among the most abundant long terminal repeat (LTR) retrotransposons (REs), Copia elements were overrepresented compared with Gypsy ones. Angela was the most dominating Copia lineage; Ogre/Tat was the most abundant Gypsy lineage. The mean insertion age of LTR-REs was 1.42 million years; approximately 83.7% of these elements were retrotransposed during the last two million years. RepeatMasker totally masked about 64.05% of the spinach genome, with LTR-REs, non-LTR-REs, and DNA transposons occupying 49.2, 2.4, and 5.6%, respectively. Fluorescence in situ hybridization (FISH) analysis showed that most LTR-REs dispersed all over the chromosomes, by contrast, elements of CRM lineage were distributed at the centromeric region of all chromosomes. In addition, Ogre/Tat lineage mainly accumulated on sex chromosomes, and satellites Spsat2 and Spsat3 were exclusively located at the telomeric region of the short arm of sex chromosomes. Conclusions We reliably annotated the TE fraction of the draft genome of spinach. FISH analysis indicates that Ogre/Tat lineage and the sex chromosome-specific satellites DNAs might participate in sex chromosome formation and evolution. Based on FISH signals of microsatellites, together with 45S rDNA, a fine karyotype of spinach was established. This study improves our knowledge of repetitive sequence organization in spinach genome and aids in accurate spinach karyotype construction. Electronic supplementary material The online version of this article (10.1186/s13100-019-0147-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shu-Fen Li
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Yu-Jiao Guo
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jia-Rong Li
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Dong-Xu Zhang
- 2College of Life Science, Shanxi Datong University, Datong, 037009 China
| | - Bing-Xiao Wang
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Ning Li
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Chuan-Liang Deng
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Wu-Jun Gao
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
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157
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Weckx S, Inzé D, Maene L. Tissue Culture of Oil Palm: Finding the Balance Between Mass Propagation and Somaclonal Variation. FRONTIERS IN PLANT SCIENCE 2019; 10:722. [PMID: 31214232 PMCID: PMC6558080 DOI: 10.3389/fpls.2019.00722] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/16/2019] [Indexed: 05/08/2023]
Abstract
The oil palm (Elaeis guineensis Jacq.) is typically propagated in vitro by indirect somatic embryogenesis, a process in which somatic cells of an explant of choice are, via an intermediate phase of callus growth, induced to differentiate into somatic embryos. The architecture of the oil palm, lacking axillary shoots, does not allow for vegetative propagation. Therefore, somatic embryogenesis is the only alternative to seed propagation, which is hampered by long germination times and low germination rates, for the production of planting material. The current oil palm somatic embryogenesis procedure is associated with several difficulties, which are described in this review. The limited availability of explants, combined with low somatic embryo initiation and regeneration rates, necessitate the proliferation of embryogenic structures, increasing the risk for somaclonal variants such as the mantled phenotype. Several ways to improve the efficiency of the tissue culture method and to reduce the risk of somaclonal variation are described. These include the use of alternative explants and propagation techniques, the introduction of specific embryo maturation treatments and the detection of the mantled abnormality in an early stage. These methods have not yet been fully explored and provide interesting research field for the future. The development of an efficient oil palm micropropagation protocol is needed to keep up with the increasing demand for palm oil in a sustainable way. Mass production of selected, high-yielding palms by tissue culture could raise yields on existing plantations, reducing the need for further expansion of the cultivated area, which is often associated with negative environmental impacts.
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Affiliation(s)
- Sylvie Weckx
- Deroose Plants NV, Evergem, Belgium
- *Correspondence: Sylvie Weckx
| | - Dirk Inzé
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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158
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Santos IR, Maximiano MR, Almeida RF, da Cunha RNV, Lopes R, Scherwinski-Pereira JE, Mehta A. Genotype-dependent changes of gene expression during somatic embryogenesis in oil palm hybrids (Elaeis oleifera x E. guineensis). PLoS One 2018; 13:e0209445. [PMID: 30596686 PMCID: PMC6312368 DOI: 10.1371/journal.pone.0209445] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/05/2018] [Indexed: 11/29/2022] Open
Abstract
To understand the molecular processes triggered during the different steps of somatic embryogenesis (SE) in oil palm, the expression of 19 genes associated to SE identified in proteomic and transcriptomic studies was investigated by qRT-PCR. To evaluate the differential expression of these genes, two interspecific hybrid genotypes (Elaeis oleifera x Elaeis guineensis) contrasting for the acquisition of embryogenic competence were used. Aclorophyllated leaves of both hybrids, one responsive (B351733) and the other non-responsive (B352933) to SE were submitted to callus induction and collected at different time points: 0 (before induction), 14, 30, 90 and 150 days of callus induction (doi). The results obtained showed that all evaluated genes were downregulated at 14 doi in the responsive genotype when compared to the non-responsive. It was also possible to observe that most of the genes changed their expression behavior at 30 doi and were upregulated thereafter until 150 doi, with the exception of the pathogenesis-related PRB1-3-like (PRB1-3) gene, which did not show differential expression at 30 doi and was downregulated at 90 and 150 doi when compared to the non-responsive hybrid. These results indicate that 30 doi is a turning point in gene expression, probably associated to embryogenic competence acquisition. We also show that the expression behavior of the responsive genotype is more stable than that of the non-responsive when the different induction time points are compared to 0 doi (before induction). Moreover, the results obtained in this study corroborate our hypothesis that the regulation of genes involved in the control of oxidative stress and energy metabolism are crucial for the acquisition of embryogenic competence in oil palm.
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Affiliation(s)
- Ivonaldo Reis Santos
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
- Programa de Pós-Graduação em Botânica, Universidade de Brasília, Brasília—DF, Brazil
| | - Mariana Rocha Maximiano
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
- Programa de Pós-Graduação em Ciências Biológicas (Imunologia e DIP/Genética e Biotecnologia), Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Raphael Ferreira Almeida
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
- Programa de Pós-Graduação em Botânica, Universidade de Brasília, Brasília—DF, Brazil
| | | | | | | | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
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159
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Yamazaki T, Konosu E, Takeshita T, Hirata A, Ota S, Kazama Y, Abe T, Kawano S. Independent regulation of the lipid and starch synthesis pathways by sulfate metabolites in the green microalga Parachlorella kessleri under sulfur starvation conditions. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.09.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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160
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Transcriptome Analysis Reveals Dynamic Fat Accumulation in the Walnut Kernel. Int J Genomics 2018; 2018:8931651. [PMID: 30622952 PMCID: PMC6304212 DOI: 10.1155/2018/8931651] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 09/09/2018] [Accepted: 09/16/2018] [Indexed: 01/02/2023] Open
Abstract
Walnut (Juglans regia L.) is an important woody oilseed species cultivated throughout the world. In this study, comparative transcript profiling was performed using high-throughput RNA sequencing technology at the following three stages of walnut fat synthesis in the “Lvling” walnut cultivar: the initial developmental stage (L1), the fast developing stage (L2), and the last developing stage (L3). A total of 68.18 GB of data were obtained on the three developmental stages, and 92% to 94% of clean data were able to be located to the reference genome. Further comparisons of the transcripts in the three libraries revealed that 724, 2027, and 4817 genes were differentially expressed between the L2 and L1 (L2vsL1), L3 and L2 (L3vsL2), and L3 and L1 (L3vsL1) samples, respectively. Through the GO gene enrichment analysis, differentially expressed genes (DEGs) in L2vsL1, L3vsL2, and L3vsL1 were enriched into 3, 0, and 2 functional categories, respectively. According to the KEGG enrichment analysis, DEGs in L2vsL1, L3vsL2, and L3vsL1 were annotated into 77, 110, and 3717 taxonomic metabolic pathways in the KEGG database, respectively. Next, we analyzed expression levels of genes related to fat synthesis. Our results indicated that ACCase, LACS, and FAD7 were the key genes related to fat synthesis. The high-throughput transcriptome sequencing of walnut in different developmental stages has greatly enriched the current genomic available resources. The comparison of DEGs under different developmental stages identified a wealth of candidate genes involved in fat synthesis, which will facilitate further genetic improvement and molecular studies of the walnut.
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161
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Bazzo BR, de Carvalho LM, Carazzolle MF, Pereira GAG, Colombo CA. Development of novel EST-SSR markers in the macaúba palm (Acrocomia aculeata) using transcriptome sequencing and cross-species transferability in Arecaceae species. BMC PLANT BIOLOGY 2018; 18:276. [PMID: 30419831 PMCID: PMC6233587 DOI: 10.1186/s12870-018-1509-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 10/29/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND The macaúba palm is a novel feedstock for oil production suitable for multiple uses, including as biodiesel and in the food and cosmetic industries. As an efficient alternative, the macaúba palm has limited genomic resources, particularly expressed sequence tag (EST) markers. We report a comprehensive set of validated EST-simple sequence repeat (SSR) markers by using transcriptome sequencing, its application in genetic diversity analysis and cross transferability in other palm trees with environmental and economic importance. RESULTS In this study, a total of 418 EST-SSRs were identified to be unique for one transcript and region; 232 EST-SSRs were selected, with trinucleotide repeats being the most frequent motif, representing 380 (90.9%), followed by composited (4.5%), di- (3.6%), and hexanucleotides (3.6%). A total of 145 EST-SSRs (62.5%) were validated for consistent amplification in seventeen macaúba palm samples, and 100 were determined to be polymorphic with PIC values ranging from 0.25 to 0.77. Genetic diversity analysis was performed with the 20 most informative EST-SSR markers showing a distinct separation of the different groups of macaúba palm. Additionally, these 145 markers were transferred in six other palm species resulting in transferability rates of 99% (144) in Acrocomia intumescens, 98% (143) in Acrocomia totai, 80.7% (117 EST-EST) in African oil palm (Elaeis guineensis) and peach palm (Bactris gasipaes) samples, 70% (102) in the juçara palm (Euterpe edulis) and 71.7% (104) in the hat palm (Sabal causiarum). Analysis of genetic distance showed a high separation in accordance with geographic location, establishing distinct groups by genera. CONCLUSIONS The EST markers identified in our study are a valuable resource and provide a genomic tool for genetic mapping and further genetic studies, as well as evaluation of co-location between QTLs and functionally associated markers.
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Affiliation(s)
- Bárbara Regina Bazzo
- Institute of Biology, Laboratory of Genomic and Expression, State University of Campinas, Campinas, Brazil
| | - Lucas Miguel de Carvalho
- Institute of Biology, Laboratory of Genomic and Expression, State University of Campinas, Campinas, Brazil
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162
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Hassan H, Amiruddin MD, Weckwerth W, Ramli US. Deciphering key proteins of oil palm (Elaeis guineensis
Jacq.) fruit mesocarp development by proteomics and chemometrics. Electrophoresis 2018; 40:254-265. [DOI: 10.1002/elps.201800232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/22/2018] [Accepted: 10/25/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Hasliza Hassan
- Advanced Biotechnology and Breeding Centre (ABBC); Malaysian Palm Oil Board (MPOB); Selangor Malaysia
| | - Mohd Din Amiruddin
- Advanced Biotechnology and Breeding Centre (ABBC); Malaysian Palm Oil Board (MPOB); Selangor Malaysia
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology; Faculty of Life Sciences; University of Vienna; Vienna Austria
- Vienna Metabolomics Center (VIME); University of Vienna; Vienna Austria
| | - Umi Salamah Ramli
- Advanced Biotechnology and Breeding Centre (ABBC); Malaysian Palm Oil Board (MPOB); Selangor Malaysia
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163
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de La Harpe M, Hess J, Loiseau O, Salamin N, Lexer C, Paris M. A dedicated target capture approach reveals variable genetic markers across micro‐ and macro‐evolutionary time scales in palms. Mol Ecol Resour 2018; 19:221-234. [DOI: 10.1111/1755-0998.12945] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 08/15/2018] [Accepted: 08/28/2018] [Indexed: 11/29/2022]
Affiliation(s)
| | - Jaqueline Hess
- Department of Botany and Biodiversity Research University of Vienna Vienna Austria
| | - Oriane Loiseau
- Department of Computational Biology, Biophore University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, Biophore University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Christian Lexer
- Department of Botany and Biodiversity Research University of Vienna Vienna Austria
| | - Margot Paris
- Department of Biology, Unit Ecology and Evolution University of Fribourg Fribourg Switzerland
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164
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Lau BYC, Othman A, Ramli US. Application of Proteomics Technologies in Oil Palm Research. Protein J 2018; 37:473-499. [DOI: 10.1007/s10930-018-9802-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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165
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Gao B, Chen M, Li X, Liang Y, Zhu F, Liu T, Zhang D, Wood AJ, Oliver MJ, Zhang J. Evolution by duplication: paleopolyploidy events in plants reconstructed by deciphering the evolutionary history of VOZ transcription factors. BMC PLANT BIOLOGY 2018; 18:256. [PMID: 30367626 PMCID: PMC6204039 DOI: 10.1186/s12870-018-1437-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 09/23/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND Facilitated by the rapid progress of sequencing technology, comparative genomic studies in plants have unveiled recurrent whole genome duplication (i.e. polyploidization) events throughout plant evolution. The evolutionary past of plant genes should be analyzed in a background of recurrent polyploidy events in distinctive plant lineages. The Vascular Plant One Zinc-finger (VOZ) gene family encode transcription factors associated with a number of important traits including control of flowering time and photoperiodic pathways, but the evolutionary trajectory of this gene family remains uncharacterized. RESULTS In this study, we deciphered the evolutionary history of the VOZ gene family by analyses of 107 VOZ genes in 46 plant genomes using integrated methods: phylogenic reconstruction, Ks-based age estimation and genomic synteny comparisons. By scrutinizing the VOZ gene family phylogeny the core eudicot γ event was well circumscribed, and relics of the precommelinid τ duplication event were detected by incorporating genes from oil palm and banana. The more recent T and ρ polyploidy events, closely coincident with the species diversification in Solanaceae and Poaceae, respectively, were also identified. Other important polyploidy events captured included the "salicoid" event in poplar and willow, the "early legume" and "soybean specific" events in soybean, as well as the recent polyploidy event in Physcomitrella patens. Although a small transcription factor gene family, the evolutionary history of VOZ genes provided an outstanding record of polyploidy events in plants. The evolutionary past of VOZ gene family demonstrated a close correlation with critical plant polyploidy events which generated species diversification and provided answer to Darwin's "abominable mystery". CONCLUSIONS We deciphered the evolutionary history of VOZ transcription factor family in plants and ancestral polyploidy events in plants were recapitulated simultaneously. This analysis allowed for the generation of an idealized plant gene tree demonstrating distinctive retention and fractionation patterns following polyploidy events.
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Affiliation(s)
- Bei Gao
- School of Life Sciences and the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Moxian Chen
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Xiaoshuang Li
- Key Laboratory of Biogeography and Bioresources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 China
| | - Yuqing Liang
- Key Laboratory of Biogeography and Bioresources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 China
| | - Fuyuan Zhu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu Province, 210037 China
| | - Tieyuan Liu
- School of Life Sciences and the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Daoyuan Zhang
- Key Laboratory of Biogeography and Bioresources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 China
| | - Andrew J. Wood
- Department of Plant Biology, Southern Illinois University-Carbondale, Carbondale, IL 62901-6509 USA
| | - Melvin J. Oliver
- USDA-ARS, Plant Genetic Research Unit, University of Missouri, Columbia, MO 65211 USA
| | - Jianhua Zhang
- School of Life Sciences and the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
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166
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Rosli R, Chan PL, Chan KL, Amiruddin N, Low ETL, Singh R, Harwood JL, Murphy DJ. In silico characterization and expression profiling of the diacylglycerol acyltransferase gene family (DGAT1, DGAT2, DGAT3 and WS/DGAT) from oil palm, Elaeis guineensis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 275:84-96. [PMID: 30107884 DOI: 10.1016/j.plantsci.2018.07.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 07/05/2018] [Accepted: 07/25/2018] [Indexed: 05/14/2023]
Abstract
The diacylglycerol acyltransferases (DGAT) (diacylglycerol:acyl-CoA acyltransferase, EC 2.3.1.20) are a key group of enzymes that catalyse the final and usually the most important rate-limiting step of triacylglycerol biosynthesis in plants and other organisms. Genes encoding four distinct functional families of DGAT enzymes have been characterised in the genome of the African oil palm, Elaeis guineensis. The contrasting features of the various isoforms within the four families of DGAT genes, namely DGAT1, DGAT2, DGAT3 and WS/DGAT are presented both in the oil palm itself and, for comparative purposes, in 12 other oil crop or model/related plants, namely Arabidopsis thaliana, Brachypodium distachyon, Brassica napus, Elaeis oleifera, Glycine max, Gossypium hirsutum, Helianthus annuus, Musa acuminata, Oryza sativa, Phoenix dactylifera, Sorghum bicolor, and Zea mays. The oil palm genome contains respectively three, two, two and two distinctly expressed functional copies of the DGAT1, DGAT2, DGAT3 and WS/DGAT genes. Phylogenetic analyses of the four DGAT families showed that the E. guineensis genes tend to cluster with sequences from P. dactylifera and M. acuminata rather than with other members of the Commelinid monocots group, such as the Poales which include the major cereal crops such as rice and maize. Comparison of the predicted DGAT protein sequences with other animal and plant DGATs was consistent with the E. guineensis DGAT1 being ER located with its active site facing the lumen while DGAT2, although also ER located, had a predicted cytosol-facing active site. In contrast, DGAT3 and some (but not all) WS/DGAT in E. guineensis are predicted to be soluble, cytosolic enzymes. Evaluation of E. guineensis DGAT gene expression in different tissues and developmental stages suggests that the four DGAT groups have distinctive physiological roles and are particularly prominent in developmental processes relating to reproduction, such as flowering, and in fruit/seed formation especially in the mesocarp and endosperm tissues.
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Affiliation(s)
- Rozana Rosli
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF37 1DL, United Kingdom; Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Pek-Lan Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nadzirah Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - John L Harwood
- School of Biosciences, University of Cardiff, Cardiff, CF10 3AX, United Kingdom
| | - Denis J Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF37 1DL, United Kingdom.
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167
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Genus-wide sequencing supports a two-locus model for sex-determination in Phoenix. Nat Commun 2018; 9:3969. [PMID: 30266991 PMCID: PMC6162277 DOI: 10.1038/s41467-018-06375-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 09/03/2018] [Indexed: 11/09/2022] Open
Abstract
The date palm tree is a commercially important member of the genus Phoenix whose 14 species are dioecious with separate male and female individuals. To identify sex determining genes we sequenced the genomes of 15 female and 13 male Phoenix trees representing all 14 species. We identified male-specific sequences and extended them using phased single-molecule sequencing or BAC clones. We observed that only four genes contained sequences conserved in all analyzed Phoenix males. Most of these sequences showed similarity to a single genomic locus in the closely related monoecious oil palm. CYP703 and GPAT3, two single copy genes present in males and critical for male flower development in other monocots, were absent in females. A LOG-like gene appears translocated into the Y-linked region and is suggested to play a role in suppressing female flowers. Our data are consistent with a two-mutation model for the evolution of dioecy in Phoenix. The origin and evolution of separate sexes in plants are long-standing questions. Here, the authors use genus-wide sequencing to identify sex determining candidate genes in the genus Phoenix and demonstrate the consistence with the previously proposed two-mutation model.
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168
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Hodzic J, Gurbeta L, Omanovic-Miklicanin E, Badnjevic A. Overview of Next-generation Sequencing Platforms Used in Published Draft Plant Genomes in Light of Genotypization of Immortelle Plant (Helichrysium Arenarium). Med Arch 2018; 71:288-292. [PMID: 28974852 PMCID: PMC5585786 DOI: 10.5455/medarh.2017.71.288-292] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
INTRODUCTION Major advancements in DNA sequencing methods introduced in the first decade of the new millennium initiated a rapid expansion of sequencing studies, which yielded a tremendous amount of DNA sequence data, including whole sequenced genomes of various species, including plants. A set of novel sequencing platforms, often collectively named as "next-generation sequencing" (NGS) completely transformed the life sciences, by allowing extensive throughput, while greatly reducing the necessary time, labor and cost of any sequencing endeavor. PURPOSE of this paper is to present an overview NGS platforms used to produce the current compendium of published draft genomes of various plants, namely the Roche/454, ABI/SOLiD, and Solexa/Illumina, and to determine the most frequently used platform for the whole genome sequencing of plants in light of genotypization of immortelle plant. MATERIALS AND METHODS 45 papers were selected (with 47 presented plant genome draft sequences), and utilized sequencing techniques and NGS platforms (Roche/454, ABI/SOLiD and Illumina/Solexa) in selected papers were determined. Subsequently, frequency of usage of each platform or combination of platforms was calculated. RESULTS Illumina/Solexa platforms are by used either as sole sequencing tool in 40.42% of published genomes, or in combination with other platforms - additional 48.94% of published genomes, followed by Roche/454 platforms, used in combination with traditional Sanger sequencing method (10.64%), and never as a sole tool. ABI/SOLiD was only used in combination with Illumina/Solexa and Roche/454 in 4.25% of publications. CONCLUSIONS Illumina/Solexa platforms are by far most preferred by researchers, most probably due to most affordable sequencing costs. Taking into consideration the current economic situation in the Balkans region, Illumina Solexa is the best (if not the only) platform choice if the sequencing of immortelle plant (Helichrysium arenarium) is to be performed by the researchers in this region.
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Affiliation(s)
- Jasin Hodzic
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Lejla Gurbeta
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina.,Verlab Ltd, Sarajevo, Bosnia and Herzegovina
| | - Enisa Omanovic-Miklicanin
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina.,Faculty of Agriculture and Food Science, University of Sarajevo, Bosnia and Herzegovina
| | - Almir Badnjevic
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina.,Verlab Ltd, Sarajevo, Bosnia and Herzegovina.,Technical Faculty Bihac, University of Bihac, Bosnia and Herzegovina
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169
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Molecular authentication of Anthemis deserti Boiss. (Asteraceae) based on ITS2 region of nrDNA gene sequence. Saudi J Biol Sci 2018; 26:155-159. [PMID: 30622420 PMCID: PMC6319191 DOI: 10.1016/j.sjbs.2018.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 11/05/2022] Open
Abstract
The dried plant material of medicinally important Anthemis deserti Boiss. (family: Asteraceae) especially when it remains in the powdered form often look similar to Anthemis melampodina Del.; and therefore, difficult to distinguish, finally lead to chances of adulteration. The adulteration in medicinal plants effects on the efficacy of the drugs. The molecular authentication of herbal plant materials such as based on the internal transcribed spacer 2 (ITS2) sequences of nuclear ribosomal DNA (nrDNA) is considered as more reliable method compared to other the biochemical or histological methods. The present study aims to molecular authentication ofA. deserti based on molecular phylogenetic analyses of ITS2 gene sequence of nrDNA region. The ITS2 region of nrDNA of A. deserti were sequenced, and the molecular phylogenetic analyses were performed together with the GenBank sequences. The Maximum Parsimony tree revealed the close relationships of A. deserti with A. melampodina; however, the Neighbor-Joining and Maximum Likelihood tree clearly revealed that A. deserti is distinct from A. melampodina, which is also supported by the differences in nucleotides at five diffident positions (i.e. 22, 28, 87, 175 and 198) in the DNA sequence alignment.
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170
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Almeida AMR, Piñeyro-Nelson A, Yockteng RB, Specht CD. Comparative analysis of whole flower transcriptomes in the Zingiberales. PeerJ 2018; 6:e5490. [PMID: 30155368 PMCID: PMC6110254 DOI: 10.7717/peerj.5490] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 07/30/2018] [Indexed: 01/14/2023] Open
Abstract
The advancement of next generation sequencing technologies (NGS) has revolutionized our ability to generate large quantities of data at a genomic scale. Despite great challenges, these new sequencing technologies have empowered scientists to explore various relevant biological questions on non-model organisms, even in the absence of a complete sequenced reference genome. Here, we analyzed whole flower transcriptome libraries from exemplar species across the monocot order Zingiberales, using a comparative approach in order to gain insight into the evolution of the molecular mechanisms underlying flower development in the group. We identified 4,153 coding genes shared by all floral transcriptomes analyzed, and 1,748 genes that are only retrieved in the Zingiberales. We also identified 666 genes that are unique to the ginger lineage, and 2,001 that are only found in the banana group, while in the outgroup species Dichorisandra thyrsiflora J.C. Mikan (Commelinaceae) we retrieved 2,686 unique genes. It is possible that some of these genes underlie lineage-specific molecular mechanisms of floral diversification. We further discuss the nature of these lineage-specific datasets, emphasizing conserved and unique molecular processes with special emphasis in the Zingiberales. We also briefly discuss the strengths and shortcomings of de novo assembly for the study of developmental processes across divergent taxa from a particular order. Although this comparison is based exclusively on coding genes, with particular emphasis in transcription factors, we believe that the careful study of other regulatory mechanisms, such as non-coding RNAs, might reveal new levels of complexity, which were not explored in this work.
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Affiliation(s)
- Ana Maria R Almeida
- Department of Biological Sciences, California State University, Hayward, Hayward, CA, United States of America
| | - Alma Piñeyro-Nelson
- Department of Food and Animal Production, Autonomous Metropolitan University, Xochimilco, Mexico City, DF, Mexico
| | - Roxana B Yockteng
- Centro de Investigaciones Tibaitatá, Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Tibaitatá, Colombia.,Institut de Systématique, Evolution, Biodiversité-UMR-CNRS, National Museum of Natural History, Paris, France
| | - Chelsea D Specht
- School of Integrative Plant Sciences, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States of America
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171
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Hanifiah FHA, Abdullah SNA, Othman A, Shaharuddin NA, Saud HM, Hasnulhadi HAH, Munusamy U. GCTTCA as a novel motif for regulating mesocarp-specific expression of the oil palm (Elaeis guineensis Jacq.) stearoyl-ACP desaturase gene. PLANT CELL REPORTS 2018; 37:1127-1143. [PMID: 29789886 DOI: 10.1007/s00299-018-2300-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/15/2018] [Indexed: 06/08/2023]
Abstract
TAAAAT and a novel motif, GCTTCA found in the oil palm stearoyl-ACP desaturase (SAD1) promoter are involved in regulating mesocarp-specific expression. Two key fatty acid biosynthetic genes, stearoyl-ACP desaturase (SAD1), and acyl-carrier protein (ACP3) in Elaeis guineensis (oil palm) showed high level of expression during the period of oil synthesis in the mesocarp [12-19 weeks after anthesis (w.a.a.)] and kernel (12-15 w.a.a.). Both genes are expressed in spear leaves at much lower levels and the expression increased by 1.5-fold to 2.5-fold following treatments with ethylene and abscisic acid (ABA). Both SAD1 and ACP3 promoters contain phytohormone-responsive, light-responsive, abiotic factors/wounding-responsive, endosperm specificity and fruit maturation/ripening regulatory motifs. The activities of the full length and six 5' deletion fragments of the SAD1 promoter were analyzed in transiently transformed oil palm tissues by quantitative β-glucuronidase (GUS) fluorometric assay. The highest SAD1 promoter activity was observed in the mesocarp followed by kernel and the least in the leaves. GUS activity in the D3 deletion construct (- 486 to + 108) was the highest, while the D2 (- 535 to + 108) gave the lowest suggesting the presence of negative cis-acting regulatory element(s) in the deleted - 535 to - 486 (49 bp). It was found that the 49-bp region binds to the nuclear protein extract from mesocarp but not from leaves in electrophoretic mobility shift assay (EMSA). Further fine-tuned analysis of this 49-bp region using truncated DNA led to the identification of GCTTCA as a novel motif in the SAD1 promoter. Interestingly, another known fruit ripening-related motif, LECPLEACS2 (TAAAAT) was found to be required for effective binding of the novel motif to the mesocarp nuclear protein extract.
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Affiliation(s)
- Farah Hanan Abu Hanifiah
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Siti Nor Akmar Abdullah
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Laboratory of Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
| | - Ashida Othman
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Noor Azmi Shaharuddin
- Laboratory of Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Halimi Mohd Saud
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Hasnul Abdul Hakim Hasnulhadi
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Umaiyal Munusamy
- Laboratory of Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
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Xiao Y, Xu P, Fan H, Baudouin L, Xia W, Bocs S, Xu J, Li Q, Guo A, Zhou L, Li J, Wu Y, Ma Z, Armero A, Issali AE, Liu N, Peng M, Yang Y. The genome draft of coconut (Cocos nucifera). Gigascience 2018; 6:1-11. [PMID: 29048487 PMCID: PMC5714197 DOI: 10.1093/gigascience/gix095] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 09/28/2017] [Indexed: 12/02/2022] Open
Abstract
Coconut palm (Cocos nucifera,2n = 32), a member of genus Cocos and family Arecaceae (Palmaceae), is an important tropical fruit and oil crop. Currently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific Islands, with a total growth area of more than 12 million hectares [1]. Coconut palm is generally classified into 2 main categories: “Tall” (flowering 8–10 years after planting) and “Dwarf” (flowering 4–6 years after planting), based on morphological characteristics and breeding habits. This Palmae species has a long growth period before reproductive years, which hinders conventional breeding progress. In spite of initial successes, improvements made by conventional breeding have been very slow. In the present study, we obtained de novo sequences of the Cocos nucifera genome: a major genomic resource that could be used to facilitate molecular breeding in Cocos nucifera and accelerate the breeding process in this important crop. A total of 419.67 gigabases (Gb) of raw reads were generated by the Illumina HiSeq 2000 platform using a series of paired-end and mate-pair libraries, covering the predicted Cocos nucifera genome length (2.42 Gb, variety “Hainan Tall”) to an estimated ×173.32 read depth. A total scaffold length of 2.20 Gb was generated (N50 = 418 Kb), representing 90.91% of the genome. The coconut genome was predicted to harbor 28 039 protein-coding genes, which is less than in Phoenix dactylifera (PDK30: 28 889), Phoenix dactylifera (DPV01: 41 660), and Elaeis guineensis (EG5: 34 802). BUSCO evaluation demonstrated that the obtained scaffold sequences covered 90.8% of the coconut genome and that the genome annotation was 74.1% complete. Genome annotation results revealed that 72.75% of the coconut genome consisted of transposable elements, of which long-terminal repeat retrotransposons elements (LTRs) accounted for the largest proportion (92.23%). Comparative analysis of the antiporter gene family and ion channel gene families between C. nucifera and Arabidopsis thaliana indicated that significant gene expansion may have occurred in the coconut involving Na+/H+ antiporter, carnitine/acylcarnitine translocase, potassium-dependent sodium-calcium exchanger, and potassium channel genes. Despite its agronomic importance, C. nucifera is still under-studied. In this report, we present a draft genome of C. nucifera and provide genomic information that will facilitate future functional genomics and molecular-assisted breeding in this crop species.
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Affiliation(s)
- Yong Xiao
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Av. Wenqing No. 496, Wenchang, Hainan 571339, P. R. China
| | - Pengwei Xu
- BGI Genomics, BGI-Shenzhen, Building NO.7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Haikuo Fan
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Av. Wenqing No. 496, Wenchang, Hainan 571339, P. R. China
| | - Luc Baudouin
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier Supagro, F-34398, Montpellier, France.,CIRAD, UMR AGAP, F-34398, Montpellier France
| | - Wei Xia
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Av. Wenqing No. 496, Wenchang, Hainan 571339, P. R. China
| | - Stéphanie Bocs
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier Supagro, F-34398, Montpellier, France.,CIRAD, UMR AGAP, F-34398, Montpellier France
| | - Junyang Xu
- BGI Genomics, BGI-Shenzhen, Building NO.7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Qiong Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Rd. Xueyuan No. 4, Haikou, Hainan 571101, P. R. China
| | - Anping Guo
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Rd. Xueyuan No. 4, Haikou, Hainan 571101, P. R. China
| | - Lixia Zhou
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Av. Wenqing No. 496, Wenchang, Hainan 571339, P. R. China
| | - Jing Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Av. Wenqing No. 496, Wenchang, Hainan 571339, P. R. China
| | - Yi Wu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Av. Wenqing No. 496, Wenchang, Hainan 571339, P. R. China
| | - Zilong Ma
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Rd. Xueyuan No. 4, Haikou, Hainan 571101, P. R. China
| | - Alix Armero
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier Supagro, F-34398, Montpellier, France.,Montpellier Supagro, UMR AGAP, F-34398, Montpellier, France
| | - Auguste Emmanuel Issali
- Station Cocotier Marc Delorme, Centre National De Recherche Agronomique (CNRA) 07 B.P. 13, Port Bouet, Côte d'Ivoire
| | - Na Liu
- BGI Genomics, BGI-Shenzhen, Building NO.7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Rd. Xueyuan No. 4, Haikou, Hainan 571101, P. R. China
| | - Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Av. Wenqing No. 496, Wenchang, Hainan 571339, P. R. China
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Vetaryan S, Kwan YY, Namasivayam P, Ho CL, Syed Alwee SSR. Isolation and characterisation of oil palm LEAFY transcripts. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1464949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Sharmilah Vetaryan
- FELDA Global Ventures R&D Sdn Bhd, FGV Innovation Centre, Lengkuk Teknologi, Bandar Enstek, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Yen-Yen Kwan
- FELDA Global Ventures R&D Sdn Bhd, FGV Innovation Centre, Lengkuk Teknologi, Bandar Enstek, Malaysia
| | - Parameswari Namasivayam
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Chai-Ling Ho
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
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174
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Rahman F, Hassan M, Rosli R, Almousally I, Hanano A, Murphy DJ. Evolutionary and genomic analysis of the caleosin/peroxygenase (CLO/PXG) gene/protein families in the Viridiplantae. PLoS One 2018; 13:e0196669. [PMID: 29771926 PMCID: PMC5957377 DOI: 10.1371/journal.pone.0196669] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 03/06/2018] [Indexed: 12/04/2022] Open
Abstract
Bioinformatics analyses of caleosin/peroxygenases (CLO/PXG) demonstrated that these genes are present in the vast majority of Viridiplantae taxa for which sequence data are available. Functionally active CLO/PXG proteins with roles in abiotic stress tolerance and lipid droplet storage are present in some Trebouxiophycean and Chlorophycean green algae but are absent from the small number of sequenced Prasinophyceaen genomes. CLO/PXG-like genes are expressed during dehydration stress in Charophyte algae, a sister clade of the land plants (Embryophyta). CLO/PXG-like sequences are also present in all of the >300 sequenced Embryophyte genomes, where some species contain as many as 10–12 genes that have arisen via selective gene duplication. Angiosperm genomes harbour at least one copy each of two distinct CLO/PX isoforms, termed H (high) and L (low), where H-forms contain an additional C-terminal motif of about 30–50 residues that is absent from L-forms. In contrast, species in other Viridiplantae taxa, including green algae, non-vascular plants, ferns and gymnosperms, contain only one (or occasionally both) of these isoforms per genome. Transcriptome and biochemical data show that CLO/PXG-like genes have complex patterns of developmental and tissue-specific expression. CLO/PXG proteins can associate with cytosolic lipid droplets and/or bilayer membranes. Many of the analysed isoforms also have peroxygenase activity and are involved in oxylipin metabolism. The distribution of CLO/PXG-like genes is consistent with an origin >1 billion years ago in at least two of the earliest diverging groups of the Viridiplantae, namely the Chlorophyta and the Streptophyta, after the Viridiplantae had already diverged from other Archaeplastidal groups such as the Rhodophyta and Glaucophyta. While algal CLO/PXGs have roles in lipid packaging and stress responses, the Embryophyte proteins have a much wider spectrum of roles and may have been instrumental in the colonisation of terrestrial habitats and the subsequent diversification as the major land flora.
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Affiliation(s)
- Farzana Rahman
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
| | - Mehedi Hassan
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
| | - Rozana Rosli
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kuala Lumpur, Malaysia
| | - Ibrahem Almousally
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria, Damascus, Syria
| | - Abdulsamie Hanano
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria, Damascus, Syria
| | - Denis J. Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
- * E-mail:
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175
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Yuan Y, Jin X, Liu J, Zhao X, Zhou J, Wang X, Wang D, Lai C, Xu W, Huang J, Zha L, Liu D, Ma X, Wang L, Zhou M, Jiang Z, Meng H, Peng H, Liang Y, Li R, Jiang C, Zhao Y, Nan T, Jin Y, Zhan Z, Yang J, Jiang W, Huang L. The Gastrodia elata genome provides insights into plant adaptation to heterotrophy. Nat Commun 2018; 9:1615. [PMID: 29691383 PMCID: PMC5915607 DOI: 10.1038/s41467-018-03423-5] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 02/12/2018] [Indexed: 12/22/2022] Open
Abstract
We present the 1.06 Gb sequenced genome of Gastrodia elata, an obligate mycoheterotrophic plant, which contains 18,969 protein-coding genes. Many genes conserved in other plant species have been deleted from the G. elata genome, including most of those for photosynthesis. Additional evidence of the influence of genome plasticity in the adaptation of this mycoheterotrophic lifestyle is evident in the large number of gene families that are expanded in G. elata, including glycoside hydrolases and urease that likely facilitate the digestion of hyphae are expanded, as are genes associated with strigolactone signaling, and ATPases that may contribute to the atypical energy metabolism. We also find that the plastid genome of G. elata is markedly smaller than that of green plant species while its mitochondrial genome is one of the largest observed to date. Our report establishes a foundation for studying adaptation to a mycoheterotrophic lifestyle.
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Affiliation(s)
- Yuan Yuan
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China.
| | - Xiaohua Jin
- Institute of Botany, Chinese Academy of Sciences (IBCAS), 100093, Beijing, China
| | - Juan Liu
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Xing Zhao
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Junhui Zhou
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Xin Wang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Deyi Wang
- Institute of Botany, Chinese Academy of Sciences (IBCAS), 100093, Beijing, China
| | - Changjiangsheng Lai
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Wei Xu
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Jingwen Huang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Liangping Zha
- Anhui University of Chinese Medicine, 230012, Hefei, China
| | - Dahui Liu
- Hubei University of Chinese Medicine, 430065, Wuhan, China
| | - Xiao Ma
- Institute of Botany, Chinese Academy of Sciences (IBCAS), 100093, Beijing, China
| | - Li Wang
- Institute of Medicinal Botany, Yunnan Academy of Agricultural Sciences, 650223, Kunming, China
| | - Menyan Zhou
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Zhi Jiang
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Hubiao Meng
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Huasheng Peng
- Anhui University of Chinese Medicine, 230012, Hefei, China
| | - Yuting Liang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Chao Jiang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Yuyang Zhao
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Tiegui Nan
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Yan Jin
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Zhilai Zhan
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Jian Yang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, 100083, Beijing, China.
| | - Luqi Huang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China.
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176
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Yuan Y, Jin X, Liu J, Zhao X, Zhou J, Wang X, Wang D, Lai C, Xu W, Huang J, Zha L, Liu D, Ma X, Wang L, Zhou M, Jiang Z, Meng H, Peng H, Liang Y, Li R, Jiang C, Zhao Y, Nan T, Jin Y, Zhan Z, Yang J, Jiang W, Huang L. The Gastrodia elata genome provides insights into plant adaptation to heterotrophy. Nat Commun 2018. [PMID: 29691383 DOI: 10.1038/s41467-018-03423-3425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
We present the 1.06 Gb sequenced genome of Gastrodia elata, an obligate mycoheterotrophic plant, which contains 18,969 protein-coding genes. Many genes conserved in other plant species have been deleted from the G. elata genome, including most of those for photosynthesis. Additional evidence of the influence of genome plasticity in the adaptation of this mycoheterotrophic lifestyle is evident in the large number of gene families that are expanded in G. elata, including glycoside hydrolases and urease that likely facilitate the digestion of hyphae are expanded, as are genes associated with strigolactone signaling, and ATPases that may contribute to the atypical energy metabolism. We also find that the plastid genome of G. elata is markedly smaller than that of green plant species while its mitochondrial genome is one of the largest observed to date. Our report establishes a foundation for studying adaptation to a mycoheterotrophic lifestyle.
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Affiliation(s)
- Yuan Yuan
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China.
| | - Xiaohua Jin
- Institute of Botany, Chinese Academy of Sciences (IBCAS), 100093, Beijing, China
| | - Juan Liu
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Xing Zhao
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Junhui Zhou
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Xin Wang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Deyi Wang
- Institute of Botany, Chinese Academy of Sciences (IBCAS), 100093, Beijing, China
| | - Changjiangsheng Lai
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Wei Xu
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Jingwen Huang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Liangping Zha
- Anhui University of Chinese Medicine, 230012, Hefei, China
| | - Dahui Liu
- Hubei University of Chinese Medicine, 430065, Wuhan, China
| | - Xiao Ma
- Institute of Botany, Chinese Academy of Sciences (IBCAS), 100093, Beijing, China
| | - Li Wang
- Institute of Medicinal Botany, Yunnan Academy of Agricultural Sciences, 650223, Kunming, China
| | - Menyan Zhou
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Zhi Jiang
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Hubiao Meng
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Huasheng Peng
- Anhui University of Chinese Medicine, 230012, Hefei, China
| | - Yuting Liang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Chao Jiang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Yuyang Zhao
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Tiegui Nan
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Yan Jin
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Zhilai Zhan
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Jian Yang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, 100083, Beijing, China.
| | - Luqi Huang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China.
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177
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Rosli R, Amiruddin N, Ab Halim MA, Chan PL, Chan KL, Azizi N, Morris PE, Leslie Low ET, Ong-Abdullah M, Sambanthamurthi R, Singh R, Murphy DJ. Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm. PLoS One 2018; 13:e0194792. [PMID: 29672525 PMCID: PMC5908059 DOI: 10.1371/journal.pone.0194792] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 03/10/2018] [Indexed: 01/10/2023] Open
Abstract
Comparative genomics and transcriptomic analyses were performed on two agronomically important groups of genes from oil palm versus other major crop species and the model organism, Arabidopsis thaliana. The first analysis was of two gene families with key roles in regulation of oil quality and in particular the accumulation of oleic acid, namely stearoyl ACP desaturases (SAD) and acyl-acyl carrier protein (ACP) thioesterases (FAT). In both cases, these were found to be large gene families with complex expression profiles across a wide range of tissue types and developmental stages. The detailed classification of the oil palm SAD and FAT genes has enabled the updating of the latest version of the oil palm gene model. The second analysis focused on disease resistance (R) genes in order to elucidate possible candidates for breeding of pathogen tolerance/resistance. Ortholog analysis showed that 141 out of the 210 putative oil palm R genes had homologs in banana and rice. These genes formed 37 clusters with 634 orthologous genes. Classification of the 141 oil palm R genes showed that the genes belong to the Kinase (7), CNL (95), MLO-like (8), RLK (3) and Others (28) categories. The CNL R genes formed eight clusters. Expression data for selected R genes also identified potential candidates for breeding of disease resistance traits. Furthermore, these findings can provide information about the species evolution as well as the identification of agronomically important genes in oil palm and other major crops.
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Affiliation(s)
- Rozana Rosli
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Nadzirah Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Mohd Amin Ab Halim
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Pek-Lan Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Norazah Azizi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Priscilla E. Morris
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | | | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Denis J. Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
- * E-mail:
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178
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Unruh SA, McKain MR, Lee YI, Yukawa T, McCormick MK, Shefferson RP, Smithson A, Leebens-Mack JH, Pires JC. Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae). AMERICAN JOURNAL OF BOTANY 2018; 105:631-640. [PMID: 29608785 DOI: 10.1002/ajb2.1047] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/20/2017] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY The slipper orchids (Cypripedioideae) are a morphologically distinct subfamily of Orchidaceae. They also have some of the largest genomes in the orchids, which may be due to polyploidy or some other mechanism of genome evolution. We generated 10 transcriptomes and incorporated existing RNA-seq data to infer a multilocus nuclear phylogeny of the Cypripedioideae and to determine whether a whole-genome duplication event (WGD) correlated with the large genome size of this subfamily. Knowing more about timing of ancient polyploidy events can help us understand the evolution of one of the most species-rich plant families. METHODS Transcriptome data were used to identify low-copy orthologous genes to infer a phylogeny of Orchidaceae and to identify paralogs to place any WGD events on the species tree. KEY RESULTS Our transcriptome phylogeny confirmed relationships published in previous studies that used fewer markers but incorporated more taxa. We did not find a WGD event at the base of the slipper orchids; however, we did identify one on the Orchidaceae stem lineage. We also confirmed the presence of a previously identified WGD event deeper in the monocot phylogeny. CONCLUSIONS Although WGD has played a role in the evolution of Orchidaceae, polyploidy does not appear to be responsible for the large genome size of slipper orchids. The conserved set of 775 largely single-copy nuclear genes identified in this study should prove useful in future studies of orchid evolution.
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Affiliation(s)
- Sarah A Unruh
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Michael R McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Yung-I Lee
- Department of Biology, National Museum of Natural Science, Taichung 404, Taiwan
| | - Tomohisa Yukawa
- Tsukuba Botanical Garden, National Science Museum, Amakubo, Tsukuba, 305-0005, Japan
| | | | - Richard P Shefferson
- Organization for Programs on Environmental Sciences, University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Ann Smithson
- Smithson Environmental Consultancy & DNALabs Environmental Genetics Testing, Bassendean, Western Australia, 6054
| | | | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
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179
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Wang QZ, Downie SR, Chen ZX. Genome-wide searches and molecular analyses highlight the unique evolutionary path of flavone synthase I (FNSI) in Apiaceae. Genome 2018; 61:103-109. [DOI: 10.1139/gen-2017-0117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Flavone synthase is a key enzyme for flavone biosynthesis and is encoded by two gene families: flavone synthase I (FNSI) and flavone synthase II (FNSII). FNSII is widely distributed in plants, while FNSI has been reported in rice (Oryza sativa) and seven species of Apiaceae. FNSI has likely evolved from the duplication of flavanone 3β-hydroxylase (F3H). In this study, we used multiple bioinformatics tools to identify putative FNSI and F3H genes from 42 publicly available genome and transcriptome datasets. Results showed that rice FNSI does not share a common ancestral sequence with other known FNSI genes and that FNSI is absent from species outside of Apiaceae. Positive selection site identification analysis revealed that four sites within the FNSI tree branches of Apiaceae evolved under significant positive selection. The putative F3H genes identified in this study provide a valuable resource for further function analysis of flavone synthase.
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Affiliation(s)
- Qi-Zhi Wang
- Department of Horticulture, Huaqiao University, Xiamen 361021, Fujian, China
| | - Stephen R. Downie
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhen-Xi Chen
- Department of Horticulture, Huaqiao University, Xiamen 361021, Fujian, China
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180
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Bai B, Wang L, Zhang YJ, Lee M, Rahmadsyah R, Alfiko Y, Ye BQ, Purwantomo S, Suwanto A, Chua NH, Yue GH. Developing genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm. Sci Rep 2018; 8:691. [PMID: 29330432 PMCID: PMC5766616 DOI: 10.1038/s41598-017-18613-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 11/28/2017] [Indexed: 12/22/2022] Open
Abstract
Oil palm (Elaeis guineensis Jacq.) is the leading oil-producing crops and the most important edible oil resource worldwide. DNA markers and genetic linkage maps are essential resources for marker-assisted selection to accelerate genetic improvement. We conducted RAD-seq on an Illumina NextSeq500 to discover genome-wide SNPs, and used the SNPs to construct a linkage map for an oil palm (Tenera) population derived from a cross between a Deli Dura and an AVROS Pisifera. The RAD-seq produced 1,076 million single-end reads across the breeding population containing 155 trees. Mining this dataset detected 510,251 loci. After filtering out loci with low accuracy and more than 20% missing data, 11,394 SNPs were retained. Using these SNPs, in combination with 188 anchor SNPs and 123 microsatellites, we constructed a linkage map containing 10,023 markers covering 16 chromosomes. The map length is 2,938.2 cM with an average marker space of 0.29 cM. The large number of SNPs will supply ample choices of DNA markers in analysing the genetic diversity, population structure and evolution of oil palm. This high-density linkage map will contribute to mapping quantitative trait loci (QTL) for important traits, thus accelerating oil palm genetic improvement.
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Affiliation(s)
- Bin Bai
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Le Wang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Ying Jun Zhang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - May Lee
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | | | - Yuzer Alfiko
- Biotech Lab, Wilmar International, Cikarang, Bekasi, 17530, Indonesia
| | - Bao Qing Ye
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Sigit Purwantomo
- Biotech Lab, Wilmar International, Cikarang, Bekasi, 17530, Indonesia
| | - Antonius Suwanto
- Biotech Lab, Wilmar International, Cikarang, Bekasi, 17530, Indonesia.,Bogor Agricultural University, Bogor, Jawa Barat, 16680, Indonesia
| | - Nam-Hai Chua
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.,Laboratory of Plant Molecular Biology, The Rockefeller University, New York, 10065, USA
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore. .,Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore. .,School of Biological Sciences, Nanyang Technological University, 6 Nanyang Drive, Singapore, 637551, Singapore.
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Manimekalai R, Nair S, Naganeeswaran A, Karun A, Malhotra S, Hubbali V. Transcriptome sequencing and de novo assembly in arecanut, Areca catechu L elucidates the secondary metabolite pathway genes. ACTA ACUST UNITED AC 2018; 17:63-69. [PMID: 29321980 PMCID: PMC5755930 DOI: 10.1016/j.btre.2017.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 03/14/2017] [Accepted: 12/05/2017] [Indexed: 11/29/2022]
Abstract
De novo assembly of arecanut transcriptome unfolds the genes involved in carotenoids and alkaloids biosynthetic pathways. High level of transcripts for carotenoid biosynthetic pathway genes implies arecanut as a potential source of carotenoids. First report on arecanut transcriptome reveals microsatellites in areca transcriptome sequence.
Areca catechu L. belongs to the Arecaceae family which comprises many economically important palms. The palm is a source of alkaloids and carotenoids. The lack of ample genetic information in public databases has been a constraint for the genetic improvement of arecanut. To gain molecular insight into the palm, high throughput RNA sequencing and de novo assembly of arecanut leaf transcriptome was undertaken in the present study. A total 56,321,907 paired end reads of 101 bp length consisting of 11.343 Gb nucleotides were generated. De novo assembly resulted in 48,783 good quality transcripts, of which 67% of transcripts could be annotated against NCBI non – redundant database. The Gene Ontology (GO) analysis with UniProt database identified 9222 biological process, 11268 molecular function and 7574 cellular components GO terms. Large scale expression profiling through Fragments per Kilobase per Million mapped reads (FPKM) showed major genes involved in different metabolic pathways of the plant. Metabolic pathway analysis of the assembled transcripts identified 124 plant related pathways. The transcripts related to carotenoid and alkaloid biosynthetic pathways had more number of reads and FPKM values suggesting higher expression of these genes. The arecanut transcript sequences generated in the study showed high similarity with coconut, oil palm and date palm sequences retrieved from public domains. We also identified 6853 genic SSR regions in the arecanut. The possible primers were designed for SSR detection and this would simplify the future efforts in genetic characterization of arecanut.
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Affiliation(s)
- Ramaswamy Manimekalai
- Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, 641 007, Tamil Nadu, India
| | - Smita Nair
- Central Plantation Crops Research institute, Indian Council of Agricultural Research (ICAR), Kudlu P.O., Kasaragod 671 124, Kerala, India
| | - A Naganeeswaran
- Central Plantation Crops Research institute, Indian Council of Agricultural Research (ICAR), Kudlu P.O., Kasaragod 671 124, Kerala, India
| | - Anitha Karun
- Central Plantation Crops Research institute, Indian Council of Agricultural Research (ICAR), Kudlu P.O., Kasaragod 671 124, Kerala, India
| | - Suresh Malhotra
- Indian Council of Agricultural Research (ICAR), KAB II, New Delhi, India
| | - V Hubbali
- Directorate of Arecanut and Cocoa Development, Kera Bhavan, Kochi, India
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183
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Sanusi NSNM, Rosli R, Halim MAA, Chan KL, Nagappan J, Azizi N, Amiruddin N, Tatarinova TV, Low ETL. PalmXplore: oil palm gene database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5098614. [PMID: 30239681 PMCID: PMC6146135 DOI: 10.1093/database/bay095] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 08/16/2018] [Indexed: 12/20/2022]
Abstract
A set of Elaeis guineensis genes had been generated by combining two gene prediction pipelines: Fgenesh++ developed by Softberry and Seqping by the Malaysian Palm Oil Board. PalmXplore was developed to provide a scalable data repository and a user-friendly search engine system to efficiently store, manage and retrieve the oil palm gene sequences and annotations. Information deposited in PalmXplore includes predicted genes, their genomic coordinates, as well as the annotations derived from external databases, such as Pfam, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Information about genes related to important traits, such as those involved in fatty acid biosynthesis (FAB) and disease resistance, is also provided. The system offers Basic Local Alignment Search Tool homology search, where the results can be downloaded or visualized in the oil palm genome browser (MYPalmViewer). PalmXplore is regularly updated offering new features, improvements to genome annotation and new genomic sequences. The system is freely accessible at http://palmxplore.mpob.gov.my.
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Affiliation(s)
- Nik Shazana Nik Mohd Sanusi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Rozana Rosli
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia.,Genomics and Computational Biology Research Group, University of South Wales,Pontypridd, Wales, UK
| | - Mohd Amin Ab Halim
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Jayanthi Nagappan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Norazah Azizi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Nadzirah Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Tatiana V Tatarinova
- Department of Biology, University of La Verne,1950 Third Street La Verne, CA, USA
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
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184
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Abstract
Functional genomics encompasses diverse disciplines in molecular biology and bioinformatics to comprehend the blueprint, regulation, and expression of genetic elements that define the physiology of an organism. The deluge of sequencing data in the postgenomics era has demanded the involvement of computer scientists and mathematicians to create algorithms, analytical software, and databases for the storage, curation, and analysis of biological big data. In this chapter, we discuss on the concept of functional genomics in the context of systems biology and provide examples of its application in human genetic disease studies, molecular crop improvement, and metagenomics for antibiotic discovery. An overview of transcriptomics workflow and experimental considerations is also introduced. Lastly, we present an in-house case study of transcriptomics analysis of an aromatic herbal plant to understand the effect of elicitation on the biosynthesis of volatile organic compounds.
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Affiliation(s)
- Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia.
| | - Chyan Leong Ng
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Kok-Keong Loke
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
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185
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Genome-wide analysis of SSR and ILP markers in trees: diversity profiling, alternate distribution, and applications in duplication. Sci Rep 2017; 7:17902. [PMID: 29263331 PMCID: PMC5738346 DOI: 10.1038/s41598-017-17203-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/22/2017] [Indexed: 12/15/2022] Open
Abstract
Molecular markers are efficient tools for breeding and genetic studies. However, despite their ecological and economic importance, their development and application have long been hampered. In this study, we identified 524,170 simple sequence repeat (SSR), 267,636 intron length polymorphism (ILP), and 11,872 potential intron polymorphism (PIP) markers from 16 tree species based on recently available genome sequences. Larger motifs, including hexamers and heptamers, accounted for most of the seven different types of SSR loci. Within these loci, A/T bases comprised a significantly larger proportion of sequence than G/C. SSR and ILP markers exhibited an alternative distribution pattern. Most SSRs were monomorphic markers, and the proportions of polymorphic markers were positively correlated with genome size. By verifying with all 16 tree species, 54 SSR, 418 ILP, and four PIP universal markers were obtained, and their efficiency was examined by PCR. A combination of five SSR and six ILP markers were used for the phylogenetic analysis of 30 willow samples, revealing a positive correlation between genetic diversity and geographic distance. We also found that SSRs can be used as tools for duplication analysis. Our findings provide important foundations for the development of breeding and genetic studies in tree species.
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186
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Kwong QB, Teh CK, Ong AL, Chew FT, Mayes S, Kulaveerasingam H, Tammi M, Yeoh SH, Appleton DR, Harikrishna JA. Evaluation of methods and marker Systems in Genomic Selection of oil palm (Elaeis guineensis Jacq.). BMC Genet 2017; 18:107. [PMID: 29228905 PMCID: PMC5725918 DOI: 10.1186/s12863-017-0576-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/29/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Genomic selection (GS) uses genome-wide markers as an attempt to accelerate genetic gain in breeding programs of both animals and plants. This approach is particularly useful for perennial crops such as oil palm, which have long breeding cycles, and for which the optimal method for GS is still under debate. In this study, we evaluated the effect of different marker systems and modeling methods for implementing GS in an introgressed dura family derived from a Deli dura x Nigerian dura (Deli x Nigerian) with 112 individuals. This family is an important breeding source for developing new mother palms for superior oil yield and bunch characters. The traits of interest selected for this study were fruit-to-bunch (F/B), shell-to-fruit (S/F), kernel-to-fruit (K/F), mesocarp-to-fruit (M/F), oil per palm (O/P) and oil-to-dry mesocarp (O/DM). The marker systems evaluated were simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). RR-BLUP, Bayesian A, B, Cπ, LASSO, Ridge Regression and two machine learning methods (SVM and Random Forest) were used to evaluate GS accuracy of the traits. RESULTS The kinship coefficient between individuals in this family ranged from 0.35 to 0.62. S/F and O/DM had the highest genomic heritability, whereas F/B and O/P had the lowest. The accuracies using 135 SSRs were low, with accuracies of the traits around 0.20. The average accuracy of machine learning methods was 0.24, as compared to 0.20 achieved by other methods. The trait with the highest mean accuracy was F/B (0.28), while the lowest were both M/F and O/P (0.18). By using whole genomic SNPs, the accuracies for all traits, especially for O/DM (0.43), S/F (0.39) and M/F (0.30) were improved. The average accuracy of machine learning methods was 0.32, compared to 0.31 achieved by other methods. CONCLUSION Due to high genomic resolution, the use of whole-genome SNPs improved the efficiency of GS dramatically for oil palm and is recommended for dura breeding programs. Machine learning slightly outperformed other methods, but required parameters optimization for GS implementation.
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Affiliation(s)
- Qi Bin Kwong
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, 43400 Serdang, Selangor Malaysia
- Institute of Biological Sciences, University Malaya, 50603 Kuala Lumpur, Malaysia
| | - Chee Keng Teh
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, 43400 Serdang, Selangor Malaysia
| | - Ai Ling Ong
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, 43400 Serdang, Selangor Malaysia
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore, 117543 Singapore
| | - Sean Mayes
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nr, Loughborough, LE12 5RD UK
| | | | - Martti Tammi
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, 43400 Serdang, Selangor Malaysia
| | - Suat Hui Yeoh
- Institute of Biological Sciences, University Malaya, 50603 Kuala Lumpur, Malaysia
| | - David Ross Appleton
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, 43400 Serdang, Selangor Malaysia
| | - Jennifer Ann Harikrishna
- Institute of Biological Sciences, University Malaya, 50603 Kuala Lumpur, Malaysia
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia
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187
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Xiao Y, Zhou L, Lei X, Cao H, Wang Y, Dou Y, Tang W, Xia W. Genome-wide identification of WRKY genes and their expression profiles under different abiotic stresses in Elaeis guineensis. PLoS One 2017; 12:e0189224. [PMID: 29228032 PMCID: PMC5724828 DOI: 10.1371/journal.pone.0189224] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 11/21/2017] [Indexed: 11/18/2022] Open
Abstract
African oil palm (Elaeis guineensis) is an important oil crop grown in tropical region and sensitive to low temperature along with high tolerance to salt and drought stresses. Since the WRKY transcription factor family plays central roles in the regulation of plant stress tolerance, 95 genes belonging to the WRKY family were identified and characterized in oil palm genome. Gene structure analysis showed that EgWRKY genes have considerable variation in intron number (0 to 12) and gene length (477bp to 89,167 bp). Duplicated genes identification indicated 32 EgWRKY genes originated from segmental duplication and two from tandem duplication. Based on transcriptome data, most EgWRKY genes showed tissue-specific expression patterns and their expression could be induced under cold stress. Furthermore, six EgWRKY genes with more than two-folded increased expression level under cold stress were validated by RT-qPCR, which has higher expression level in cold, drought and high salinity treatment. The identification and characterization of WRKY gene family showed that EgWRKY were associated with a wide range of abiotic stress responses in Elaeis guineensis and some EgWRKY members with high expression levels could be selected for further research in analyzing their functions in the stress response in African oil palm.
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Affiliation(s)
- Yong Xiao
- Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, P.R. China
- * E-mail: (YX); (WX)
| | - Lixia Zhou
- Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, P.R. China
| | - Xintao Lei
- Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, P.R. China
| | - Hongxing Cao
- Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, P.R. China
| | - Yong Wang
- Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, P.R. China
| | - Yajing Dou
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, P.R China
| | - Wenqi Tang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, P.R China
| | - Wei Xia
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, P.R China
- * E-mail: (YX); (WX)
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188
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High density SNP and DArT-based genetic linkage maps of two closely related oil palm populations. J Appl Genet 2017; 59:23-34. [PMID: 29214520 DOI: 10.1007/s13353-017-0420-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/16/2017] [Accepted: 11/23/2017] [Indexed: 12/22/2022]
Abstract
Oil palm (Elaeis guineensis Jacq.) is an outbreeding perennial tree crop with long breeding cycles, typically 12 years. Molecular marker technologies can greatly improve the breeding efficiency of oil palm. This study reports the first use of the DArTseq platform to genotype two closely related self-pollinated oil palm populations, namely AA0768 and AA0769 with 48 and 58 progeny respectively. Genetic maps were constructed using the DArT and SNP markers generated in combination with anchor SSR markers. Both maps consisted of 16 major independent linkage groups (2n = 2× = 32) with 1399 and 1466 mapped markers for the AA0768 and AA0769 populations, respectively, including the morphological trait "shell-thickness" (Sh). The map lengths were 1873.7 and 1720.6 cM with an average marker density of 1.34 and 1.17 cM, respectively. The integrated map was 1803.1 cM long with 2066 mapped markers and average marker density of 0.87 cM. A total of 82% of the DArTseq marker sequence tags identified a single site in the published genome sequence, suggesting preferential targeting of gene-rich regions by DArTseq markers. Map integration of higher density focused around the Sh region identified closely linked markers to the Sh, with D.15322 marker 0.24 cM away from the morphological trait and 5071 bp from the transcriptional start of the published SHELL gene. Identification of the Sh marker demonstrates the robustness of using the DArTseq platform to generate high density genetic maps of oil palm with good genome coverage. Both genetic maps and integrated maps will be useful for quantitative trait loci analysis of important yield traits as well as potentially assisting the anchoring of genetic maps to genomic sequences.
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189
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Li R, Reddy VA, Jin J, Rajan C, Wang Q, Yue G, Lim CH, Chua NH, Ye J, Sarojam R. Comparative transcriptome analysis of oil palm flowers reveals an EAR-motif-containing R2R3-MYB that modulates phenylpropene biosynthesis. BMC PLANT BIOLOGY 2017; 17:219. [PMID: 29169327 PMCID: PMC5701422 DOI: 10.1186/s12870-017-1174-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 11/13/2017] [Indexed: 05/14/2023]
Abstract
BACKGROUND Oil palm is the most productive oil crop and the efficiency of pollination has a direct impact on the yield of oil. Pollination by wind can occur but maximal pollination is mediated by the weevil E. kamerunicus. These weevils complete their life cycle by feeding on male flowers. Attraction of weevils to oil palm flowers is due to the emission of methylchavicol by both male and female flowers. In search for male flowers, the weevils visit female flowers by accident due to methylchavicol fragrance and deposit pollen. Given the importance of methylchavicol emission on pollination, we performed comparative transcriptome analysis of oil palm flowers and leaves to identify candidate genes involved in methylchavicol production in flowers. RESULTS RNA sequencing (RNA-Seq) of male open flowers, female open flowers and leaves was performed using Illumina HiSeq 2000 platform. Analysis of the transcriptome data revealed that the transcripts of methylchavicol biosynthesis genes were strongly up-regulated whereas transcripts encoding genes involved in lignin production such as, caffeic acid O-methyltransferase (COMT) and Ferulate-5-hydroxylase (F5H) were found to be suppressed in oil palm flowers. Among the transcripts encoding transcription factors, an EAR-motif-containing R2R3-MYB transcription factor (EgMYB4) was found to be enriched in oil palm flowers. We determined that EgMYB4 can suppress the expression of a monolignol pathway gene, EgCOMT, in vivo by binding to the AC elements present in the promoter region. EgMYB4 was further functionally characterized in sweet basil which also produces phenylpropenes like oil palm. Transgenic sweet basil plants showed significant reduction in lignin content but produced more phenylpropenes. CONCLUSIONS Our results suggest that EgMYB4 possibly restrains lignin biosynthesis in oil palm flowers thus allowing enhanced carbon flux into the phenylpropene pathway. This study augments our understanding of the diverse roles that EAR-motif-containing MYBs play to fine tune the metabolic flux along the various branches of core phenylpropanoid pathway. This will aid in metabolic engineering of plant aromatic compounds.
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Affiliation(s)
- Ran Li
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
- Present Address: Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Vaishnavi Amarr Reddy
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543 Singapore
| | - Jingjing Jin
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
| | - Chakaravarthy Rajan
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
- Present Address: Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Qian Wang
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
- Present Address: College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, China
| | - Genhua Yue
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
| | - Chin Huat Lim
- R&D Department, Wilmar International Plantation, Palembang, Indonesia
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY 10065 USA
| | - Jian Ye
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Rajani Sarojam
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
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190
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The asparagus genome sheds light on the origin and evolution of a young Y chromosome. Nat Commun 2017; 8:1279. [PMID: 29093472 PMCID: PMC5665984 DOI: 10.1038/s41467-017-01064-8] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 08/16/2017] [Indexed: 12/03/2022] Open
Abstract
Sex chromosomes evolved from autosomes many times across the eukaryote phylogeny. Several models have been proposed to explain this transition, some involving male and female sterility mutations linked in a region of suppressed recombination between X and Y (or Z/W, U/V) chromosomes. Comparative and experimental analysis of a reference genome assembly for a double haploid YY male garden asparagus (Asparagus officinalis L.) individual implicates separate but linked genes as responsible for sex determination. Dioecy has evolved recently within Asparagus and sex chromosomes are cytogenetically identical with the Y, harboring a megabase segment that is missing from the X. We show that deletion of this entire region results in a male-to-female conversion, whereas loss of a single suppressor of female development drives male-to-hermaphrodite conversion. A single copy anther-specific gene with a male sterile Arabidopsis knockout phenotype is also in the Y-specific region, supporting a two-gene model for sex chromosome evolution. Several models have been proposed to explain the emergence of sex chromosomes. Here, through comparative genomics and mutant analysis, Harkess et al. show that linked but separate genes on the Y chromosome are responsible for sex determination in Asparagus, supporting a two-gene model for sex chromosome evolution.
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191
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Sandhu M, Sureshkumar V, Prakash C, Dixit R, Solanke AU, Sharma TR, Mohapatra T, S V AM. RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement. BMC Bioinformatics 2017; 18:432. [PMID: 28964253 PMCID: PMC5622590 DOI: 10.1186/s12859-017-1846-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 09/21/2017] [Indexed: 11/17/2022] Open
Abstract
Background Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to develop a web interface which combines the information from functional genomic studies across different genetic backgrounds with DNA markers so that they can be readily deployed in crop improvement. In the current version of the database, we have included drought and salinity stress studies since these two are the major abiotic stresses in rice. Results RiceMetaSys, a user-friendly and freely available web interface provides comprehensive information on salt responsive genes (SRGs) and drought responsive genes (DRGs) across genotypes, crop development stages and tissues, identified from multiple microarray datasets. ‘Physical position search’ is an attractive tool for those using QTL based approach for dissecting tolerance to salt and drought stress since it can provide the list of SRGs and DRGs in any physical interval. To identify robust candidate genes for use in crop improvement, the ‘common genes across varieties’ search tool is useful. Graphical visualization of expression profiles across genes and rice genotypes has been enabled to facilitate the user and to make the comparisons more impactful. Simple Sequence Repeat (SSR) search in the SRGs and DRGs is a valuable tool for fine mapping and marker assisted selection since it provides primers for survey of polymorphism. An external link to intron specific markers is also provided for this purpose. Bulk retrieval of data without any limit has been enabled in case of locus and SSR search. Conclusions The aim of this database is to facilitate users with a simple and straight-forward search options for identification of robust candidate genes from among thousands of SRGs and DRGs so as to facilitate linking variation in expression profiles to variation in phenotype. Database URL: http://14.139.229.201 Electronic supplementary material The online version of this article (10.1186/s12859-017-1846-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maninder Sandhu
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.,Shobhit University, Modipuram, Meerut, 250110, Uttar Pradesh, India
| | - V Sureshkumar
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.,Department of Plant Molecular Biology and Bioinformatics, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Chandra Prakash
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Rekha Dixit
- Shobhit University, Modipuram, Meerut, 250110, Uttar Pradesh, India.,Current address: Department of biotechnology, Keralverma faculty of science, Swami Vivekanand Subharti University, Meerut, 250005, Uttar Pradesh, India
| | - Amolkumar U Solanke
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Tilak Raj Sharma
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Trilochan Mohapatra
- Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110001, India
| | - Amitha Mithra S V
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.
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192
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Tamiru M, Natsume S, Takagi H, White B, Yaegashi H, Shimizu M, Yoshida K, Uemura A, Oikawa K, Abe A, Urasaki N, Matsumura H, Babil P, Yamanaka S, Matsumoto R, Muranaka S, Girma G, Lopez-Montes A, Gedil M, Bhattacharjee R, Abberton M, Kumar PL, Rabbi I, Tsujimura M, Terachi T, Haerty W, Corpas M, Kamoun S, Kahl G, Takagi H, Asiedu R, Terauchi R. Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination. BMC Biol 2017; 15:86. [PMID: 28927400 PMCID: PMC5604175 DOI: 10.1186/s12915-017-0419-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/10/2017] [Indexed: 11/10/2022] Open
Abstract
Background Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected “orphan” crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop. Results To accelerate marker-assisted breeding of yam, we performed genome analysis of white Guinea yam (Dioscorea rotundata) and assembled a 594-Mb genome, 76.4% of which was distributed among 21 linkage groups. In total, we predicted 26,198 genes. Phylogenetic analyses with 2381 conserved genes revealed that Dioscorea is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana). The entire Dioscorea genus is characterized by the occurrence of separate male and female plants (dioecy), a feature that has limited efficient yam breeding. To infer the genetics of sex determination, we performed whole-genome resequencing of bulked segregants (quantitative trait locus sequencing [QTL-seq]) in F1 progeny segregating for male and female plants and identified a genomic region associated with female heterogametic (male = ZZ, female = ZW) sex determination. We further delineated the W locus and used it to develop a molecular marker for sex identification of Guinea yam plants at the seedling stage. Conclusions Guinea yam belongs to a unique and highly differentiated clade of monocotyledons. The genome analyses and sex-linked marker development performed in this study should greatly accelerate marker-assisted breeding of Guinea yam. In addition, our QTL-seq approach can be utilized in genetic studies of other outcrossing crops and organisms with highly heterozygous genomes. Genomic analysis of orphan crops such as yam promotes efforts to improve food security and the sustainability of tropical agriculture. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0419-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Hiroki Takagi
- Iwate Biotechnology Research Center, Kitakami, Japan
| | | | | | | | | | - Aiko Uemura
- Iwate Biotechnology Research Center, Kitakami, Japan
| | - Kaori Oikawa
- Iwate Biotechnology Research Center, Kitakami, Japan
| | - Akira Abe
- Iwate Biotechnology Research Center, Kitakami, Japan
| | | | | | | | - Shinsuke Yamanaka
- Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
| | - Ryo Matsumoto
- Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
| | - Satoru Muranaka
- Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
| | - Gezahegn Girma
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | - Melaku Gedil
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | - Michael Abberton
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - P Lava Kumar
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Ismail Rabbi
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | | | | | | | | | | | - Hiroko Takagi
- Japan International Research Center for Agricultural Sciences, Tsukuba, Japan.
| | - Robert Asiedu
- International Institute of Tropical Agriculture, Ibadan, Nigeria.
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center, Kitakami, Japan. .,Kyoto University, Kyoto, Japan.
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193
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Chan KL, Tatarinova TV, Rosli R, Amiruddin N, Azizi N, Halim MAA, Sanusi NSNM, Jayanthi N, Ponomarenko P, Triska M, Solovyev V, Firdaus-Raih M, Sambanthamurthi R, Murphy D, Low ETL. Evidence-based gene models for structural and functional annotations of the oil palm genome. Biol Direct 2017; 12:21. [PMID: 28886750 PMCID: PMC5591544 DOI: 10.1186/s13062-017-0191-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/07/2017] [Indexed: 11/13/2022] Open
Abstract
Background Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes. Classification and characterization of genes associated with traits of interest, such as those for fatty acid biosynthesis and disease resistance, were also limited. Lipid-, especially fatty acid (FA)-related genes are of particular interest for the oil palm as they specify oil yields and quality. This paper presents the characterization of the oil palm genome using different gene prediction methods and comparative genomics analysis, identification of FA biosynthesis and disease resistance genes, and the development of an annotation database and bioinformatics tools. Results Using two independent gene-prediction pipelines, Fgenesh++ and Seqping, 26,059 oil palm genes with transcriptome and RefSeq support were identified from the oil palm genome. These coding regions of the genome have a characteristic broad distribution of GC3 (fraction of cytosine and guanine in the third position of a codon) with over half the GC3-rich genes (GC3 ≥ 0.75286) being intronless. In comparison, only one-seventh of the oil palm genes identified are intronless. Using comparative genomics analysis, characterization of conserved domains and active sites, and expression analysis, 42 key genes involved in FA biosynthesis in oil palm were identified. For three of them, namely EgFABF, EgFABH and EgFAD3, segmental duplication events were detected. Our analysis also identified 210 candidate resistance genes in six classes, grouped by their protein domain structures. Conclusions We present an accurate and comprehensive annotation of the oil palm genome, focusing on analysis of important categories of genes (GC3-rich and intronless), as well as those associated with important functions, such as FA biosynthesis and disease resistance. The study demonstrated the advantages of having an integrated approach to gene prediction and developed a computational framework for combining multiple genome annotations. These results, available in the oil palm annotation database (http://palmxplore.mpob.gov.my), will provide important resources for studies on the genomes of oil palm and related crops. Reviewers This article was reviewed by Alexander Kel, Igor Rogozin, and Vladimir A. Kuznetsov. Electronic supplementary material The online version of this article (doi:10.1186/s13062-017-0191-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.,Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Tatiana V Tatarinova
- Department of Biology, University of La Verne, La Verne, California, 91750, USA.,Spatial Sciences Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Rozana Rosli
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.,Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF371DL, UK
| | - Nadzirah Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Norazah Azizi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Mohd Amin Ab Halim
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nik Shazana Nik Mohd Sanusi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nagappan Jayanthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Petr Ponomarenko
- Spatial Sciences Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Martin Triska
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, 90089, USA
| | - Victor Solovyev
- Softberry Inc., 116 Radio Circle, Suite 400, Mount Kisco, NY, 10549, USA
| | - Mohd Firdaus-Raih
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ravigadevi Sambanthamurthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Denis Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF371DL, UK
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
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194
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Ruzlan N, Low YSJ, Win W, Azizah Musa N, Ong AL, Chew FT, Appleton D, Mohd Yusof H, Kulaveerasingam H. Key glycolytic branch influences mesocarp oil content in oil palm. Sci Rep 2017; 7:9626. [PMID: 28852058 PMCID: PMC5575415 DOI: 10.1038/s41598-017-10195-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/22/2017] [Indexed: 11/08/2022] Open
Abstract
The fructose-1,6-bisphosphate aldolase catalyzed glycolysis branch that forms dihydroxyacetone phosphate and glyceraldehyde-3-phosphate was identified as a key driver of increased oil synthesis in oil palm and was validated in Saccharomyces cerevisiae. Reduction in triose phosphate isomerase (TPI) activity in a yeast knockdown mutant resulted in 19% increase in lipid content, while yeast strains overexpressing oil palm fructose-1,6-bisphosphate aldolase (EgFBA) and glycerol-3-phosphate dehydrogenase (EgG3PDH) showed increased lipid content by 16% and 21%, respectively. Genetic association analysis on oil palm SNPs of EgTPI SD_SNP_000035801 and EgGAPDH SD_SNP_000041011 showed that palms harboring homozygous GG in EgTPI and heterozygous AG in EgGAPDH exhibited higher mesocarp oil content based on dry weight. In addition, AG genotype of the SNP of EgG3PDH SD_SNP_000008411 was associated with higher mean mesocarp oil content, whereas GG genotype of the EgFBA SNP SD_SNP_000007765 was favourable. Additive effects were observed with a combination of favourable alleles in TPI and FBA in Nigerian x AVROS population (family F7) with highest allele frequency GG.GG being associated with a mean increase of 3.77% (p value = 2.3E-16) oil content over the Family 1. An analogous effect was observed in yeast, where overexpressed EgFBA in TPI - resulted in a 30% oil increment. These results provide insights into flux balances in glycolysis leading to higher yield in mesocarp oil-producing fruit.
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Affiliation(s)
- Nurliyana Ruzlan
- Sime Darby Renewables, Sime Darby Plantation Sdn Bhd, Selangor, Malaysia.
| | - Yoke Sum Jaime Low
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, Malaysia
| | - Wilonita Win
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, Malaysia
| | - Noor Azizah Musa
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, Malaysia
| | - Ai-Ling Ong
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, Malaysia
| | - Fook-Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - David Appleton
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, Malaysia
| | - Hirzun Mohd Yusof
- Sime Darby Renewables, Sime Darby Plantation Sdn Bhd, Selangor, Malaysia
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195
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Evolutionarily Conserved Alternative Splicing Across Monocots. Genetics 2017; 207:465-480. [PMID: 28839042 DOI: 10.1534/genetics.117.300189] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/11/2017] [Indexed: 12/22/2022] Open
Abstract
One difficulty when identifying alternative splicing (AS) events in plants is distinguishing functional AS from splicing noise. One way to add confidence to the validity of a splice isoform is to observe that it is conserved across evolutionarily related species. We use a high throughput method to identify junction-based conserved AS events from RNA-Seq data across nine plant species, including five grass monocots (maize, sorghum, rice, Brachpodium, and foxtail millet), plus two nongrass monocots (banana and African oil palm), the eudicot Arabidopsis, and the basal angiosperm Amborella In total, 9804 AS events were found to be conserved between two or more species studied. In grasses containing large regions of conserved synteny, the frequency of conserved AS events is twice that observed for genes outside of conserved synteny blocks. In plant-specific RS and RS2Z subfamilies of the serine/arginine (SR) splice-factor proteins, we observe both conservation and divergence of AS events after the whole genome duplication in maize. In addition, plant-specific RS and RS2Z splice-factor subfamilies are highly connected with R2R3-MYB in STRING functional protein association networks built using genes exhibiting conserved AS. Furthermore, we discovered that functional protein association networks constructed around genes harboring conserved AS events are enriched for phosphatases, kinases, and ubiquitylation genes, which suggests that AS may participate in regulating signaling pathways. These data lay the foundation for identifying and studying conserved AS events in the monocots, particularly across grass species, and this conserved AS resource identifies an additional layer between genotype to phenotype that may impact future crop improvement efforts.
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196
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The Discovery of Wild Date Palms in Oman Reveals a Complex Domestication History Involving Centers in the Middle East and Africa. Curr Biol 2017; 27:2211-2218.e8. [DOI: 10.1016/j.cub.2017.06.045] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 05/10/2017] [Accepted: 06/19/2017] [Indexed: 11/22/2022]
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197
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Identification of Ganoderma Disease Resistance Loci Using Natural Field Infection of an Oil Palm Multiparental Population. G3-GENES GENOMES GENETICS 2017; 7:1683-1692. [PMID: 28592650 PMCID: PMC5473749 DOI: 10.1534/g3.117.041764] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Multi-parental populations are promising tools for identifying quantitative disease resistance loci. Stem rot caused by Ganoderma boninense is a major threat to palm oil production, with yield losses of up to 80% prompting premature replantation of palms. There is evidence of genetic resistance sources, but the genetic architecture of Ganoderma resistance has not yet been investigated. This study aimed to identify Ganoderma resistance loci using an oil palm multi-parental population derived from nine major founders of ongoing breeding programs. A total of 1200 palm trees of the multi-parental population was planted in plots naturally infected by Ganoderma, and their health status was assessed biannually over 25 yr. The data were treated as survival data, and modeled using the Cox regression model, including a spatial effect to take the spatial component in the spread of Ganoderma into account. Based on the genotypes of 757 palm trees out of the 1200 planted, and on pedigree information, resistance loci were identified using a random effect with identity-by-descent kinship matrices as covariance matrices in the Cox model. Four Ganoderma resistance loci were identified, two controlling the occurrence of the first Ganoderma symptoms, and two the death of palm trees, while favorable haplotypes were identified among a major gene pool for ongoing breeding programs. This study implemented an efficient and flexible QTL mapping approach, and generated unique valuable information for the selection of oil palm varieties resistant to Ganoderma disease.
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198
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Kwong QB, Ong AL, Teh CK, Chew FT, Tammi M, Mayes S, Kulaveerasingam H, Yeoh SH, Harikrishna JA, Appleton DR. Genomic Selection in Commercial Perennial Crops: Applicability and Improvement in Oil Palm (Elaeis guineensis Jacq.). Sci Rep 2017; 7:2872. [PMID: 28588233 PMCID: PMC5460275 DOI: 10.1038/s41598-017-02602-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/13/2017] [Indexed: 12/24/2022] Open
Abstract
Genomic selection (GS) uses genome-wide markers to select individuals with the desired overall combination of breeding traits. A total of 1,218 individuals from a commercial population of Ulu Remis x AVROS (UR x AVROS) were genotyped using the OP200K array. The traits of interest included: shell-to-fruit ratio (S/F, %), mesocarp-to-fruit ratio (M/F, %), kernel-to-fruit ratio (K/F, %), fruit per bunch (F/B, %), oil per bunch (O/B, %) and oil per palm (O/P, kg/palm/year). Genomic heritabilities of these traits were estimated to be in the range of 0.40 to 0.80. GS methods assessed were RR-BLUP, Bayes A (BA), Cπ (BC), Lasso (BL) and Ridge Regression (BRR). All methods resulted in almost equal prediction accuracy. The accuracy achieved ranged from 0.40 to 0.70, correlating with the heritability of traits. By selecting the most important markers, RR-BLUP B has the potential to outperform other methods. The marker density for certain traits can be further reduced based on the linkage disequilibrium (LD). Together with in silico breeding, GS is now being used in oil palm breeding programs to hasten parental palm selection.
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Affiliation(s)
- Qi Bin Kwong
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, 43400 Malaysia
| | - Ai Ling Ong
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, 43400 Malaysia
| | - Chee Keng Teh
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, 43400 Malaysia
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore, 117543 Singapore
| | - Martti Tammi
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, 43400 Malaysia
| | - Sean Mayes
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | | | - Suat Hui Yeoh
- Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jennifer Ann Harikrishna
- Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - David Ross Appleton
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, 43400 Malaysia
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199
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Nic-Matos G, Narváez M, Peraza-Echeverría S, Sáenz L, Oropeza C. Molecular cloning of two novel NPR1 homologue genes in coconut palm and analysis of their expression in response to the plant defense hormone salicylic acid. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0566-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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200
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Bai B, Wang L, Lee M, Zhang Y, Alfiko Y, Ye BQ, Wan ZY, Lim CH, Suwanto A, Chua NH, Yue GH. Genome-wide identification of markers for selecting higher oil content in oil palm. BMC PLANT BIOLOGY 2017; 17:93. [PMID: 28558657 PMCID: PMC5450198 DOI: 10.1186/s12870-017-1045-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/22/2017] [Indexed: 05/28/2023]
Abstract
BACKGROUND Oil palm (Elaeis guineensis, Jacq.) is the most important source of edible oil. The improvement of oil yield is currently slow in conventional breeding programs due to long generation intervals. Marker-assisted selection (MAS) has the potential to accelerate genetic improvement. To identify DNA markers associated with oil content traits for MAS, we performed quantitative trait loci (QTL) mapping using genotyping by sequencing (GBS) in a breeding population derived from a cross between Deli Dura and Ghana Pisifera, containing 153 F1 trees. RESULTS We constructed a high-density linkage map containing 1357 SNPs and 123 microsatellites. The 16 linkage groups (LGs) spanned 1527 cM, with an average marker space of 1.03 cM. One significant and three suggestive QTL for oil to bunch (O/B) and oil to dry mesocarp (O/DM) were mapped on LG1, LG8, and LG10 in a F1 breeding population, respectively. These QTL explained 7.6-13.3% of phenotypic variance. DNA markers associated with oil content in these QTL were identified. Trees with beneficial genotypes at two QTL for O/B showed an average O/B of 30.97%, significantly (P < 0.01) higher than that of trees without any beneficial QTL genotypes (average O/B of 28.24%). QTL combinations showed that the higher the number of QTL with beneficial genotypes, the higher the resulting average O/B in the breeding population. CONCLUSIONS A linkage map with 1480 DNA markers was constructed and used to identify QTL for oil content traits. Pyramiding the identified QTL with beneficial genotypes associated with oil content traits using DNA markers has the potential to accelerate genetic improvement for oil yield in the breeding population of oil palm.
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Affiliation(s)
- Bin Bai
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Le Wang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - May Lee
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Yingjun Zhang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Yuzer Alfiko
- Biotech Lab, Wilmar International, Jakarta, Indonesia
| | - Bao Qing Ye
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Zi Yi Wan
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Chin Huat Lim
- R & D Department, Wilmar International Plantation, Palembang, Indonesia
| | - Antonius Suwanto
- Biotech Lab, Wilmar International, Jakarta, Indonesia
- Bogor Agricultural University, Bogor, Indonesia
| | - Nam-Hai Chua
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
- Laboratory of Plant Molecular Biology, The Rockefeller University, New York, USA
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
- School of Biological Sciences, Nanyang Technological University, 6 Nanyang Drive, Singapore, 637551, Singapore.
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