SNAP (Korf 2004), on the other hand, was self-trained using publicly available coconut cDNA/EST. The synteny analysis provides an overview of possible mechanism of genomic changes during the evolution of the two coconut types (Dwarf coconut and Tall coconut), and divergence between coconut and date palm. Coconut genome size determined by flow cytometry: Tall vs. These were nucleotide binding sites (NBS-ARC), leucine rich repeats (LRR), transmembrane (TM), serine/threonine and tyrosine kinase (STTK), lysine motif (LysM), coiled-coil (CC) and Toll/Interleukin-1 receptor (TIR). The coding gene sequences between the two coconut types are therefore very well-conserved. 4. 2006; Wu et al. Our dwarf coconut seedlings are authentic and of good quality, sold at very reasonable prices. Opportunity in coconut breeding for improved coconut oil can be directed using these coconut varieties, and in reference with the whole genome sequence of coconut. 2013, Huang et al. Except for Tagnanan Tall, these dwarf varieties come to … Among these SNPs, 69.52% are characterized as single-base transitions (A/G, C/T), while the rest are classified as transversion substitutions (A/C, A/T, G/C, T/G) (Figure 5a). Triangular system of planting coconut is recommended with rows laid out in a north-south direction. Sign up to receive alert notifications of new articles. Di-repeats (or 2-mer) were observed as the most commonly found repeat motif (Figure S9). 2008). 1987; Kintanar and Castro 1988; Dayrit et al. The DNA was then sheared to ∼350 bp mean fragment size and sequencing libraries were generated using NEBNext Ultra enzymes and Illumina-compatible adapters. We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, ‘Catigan Green Dwarf’ (CATD). The CATD coconut LPAAT gene is characterized to be 28,344 bp in length, shorter than the gene sequence of African oil palm by 10,487 bp (Singh et al. Interestingly, the whole genome alignment between the dwarf coconut and oil palm provided clearer insights to their dynamic chromosomal changes during the course of evolution (Figure 2c). Galas Green Dwarf; Tacunan Green Dwarf; Catigan Green Dwarf; Genetically Multi-Ancestored Farmer's Composite Variety; Tutupaen Tall; Tagnanan Tall; Cultural Management Ecological Requirements. The fruit itself is used in a wide variety of products and by-products. Thus, we propose that the Arecaceae shares a common WGD β and γ events with the Musa lineage but independent WGD α event, which probably happened after the divergence of Arecaceae and Musa. Alma CANAMA, University Researcher of University of the Philippines Los Baños, Los Baños (UPLB) | Read 23 publications | Contact Alma CANAMA Diversification likely occurred through autogamy followed by a series of allele fixations in a random subset of ancestral ‘Talls’ (Perera et al. Figure S1 shows the basic statistics and per base sequence analysis result of the pre-processed Illumina Miseq short read sequences. The quality of the resulting assembly was assessed through a local Perl script as previously described, as well as TopHat2 (Kim et al. To detect structural variation between these palm genomes, >1 Mbp genomic scaffolds each of the current dwarf coconut assembly, published tall coconut and date palm, and 16 pseudomolecules of oil palm were analyzed using the Syntenic Path Assembly in SynMap (BLAST algorithm - LAST (Kiełbasa et al. 8.5. Tacunan X Catigan Dwarf Coconut Seedlings. Meanwhile, a total of 631 InDels ranging 1-6 bp were identified among the set of variants (Figure 5b), of which most are characterized as single-base InDels (62.12%) followed by di-nucleotide InDels (20.29%). Data S1 lists the LTR-RT found in regions of the dwarf coconut genome with estimated insertion dates. Bronze dwarf. Medium chain fatty acids (MCFAs) and long-chain fatty acids comprise around 83.92% of the total composition of copra oil of which lauric acid (C12) is the most predominant (Padolina et al. 2000; Bourdeix et al. 2015). Using Illumina Miseq paired-end sequencing, a total of 109 Gb of paired-end fastq files were produced. Thus, for this later 2 genes, the cDNA sequences from E. guineensis were used to characterize the homologs in CATD coconut. Furthermore, results provided evidence that a rapid burst of total LTR elements happened in coconut around 400,000 years ago, which coincides with the recorded era of earth’s transition from glacial (ice age) to interglacial period (Termination V – 430,000 years ago) characterized by changes in temperature and greenhouse gasses (Augustin et al. Figure S3 shows the BUSCO analysis of the constructed genome assembly based on 1440 plant-specific genes in the OrthoDB database. 1990). Dwarf Coconut Varieties Catigan Green Dwarf (CATD) 74 Tacunan Green Dwarf (TACD) 99 Malayan Green Dwarf (MRD) 111 Aromatic Green Dwarf (AROD) 80 The syntenic gene pairs were identified by DAGChainer, and colored based on their synonymous substitution rate as calculated by CodeML of the CoGe SynMap tool (Lyons et al. This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. Genome-wide SSR mining, statistical classification and marker generation were done using the GMATA package (Wang and Wang 2016). 2008; Al-Ghazi et al. Except for Tagnanan Tall, these dwarf varieties come to … 1987; Laureles et al. However, only two (2) WGD events (β and γ) were detected when the Ks values of the coding gene sequences of dwarf coconut and banana were calculated and plotted on a histogram. Coconino: CNO: Philippines: Nuts are very small, oblong and smooth; stem quite thin and high yielder of toddy. Fixed chromatin was digested with DpnII, the 5′ overhangs filled in with biotinylated nucleotides, and then free blunt ends were ligated. Like the Galas green dwarf, coconuts from this variety passed the international standards 1 for young tender coconut. 2017), ecological-genetic studies (Geethanjali, et al. The authors declare no conflict of interest. The whole genome sequence assembly of oil palm (Singh et al. The estimated genome size of coconut is higher than what has been reported in date palm (660 Mbp; Al-Mssallem et al. Freitas Neto et al. A/G transition is the most frequent base substitution - 20,221 loci or 34.56% of the total sequence variants detected. To aid in the development of SNP genotyping arrays and for other high-throughput genotyping technologies such as genotyping-by-sequencing (GBS), sequence variations such as SNPs and InDels between the reference Dwarf coconut (current ‘Catigan Green Dwarf’ or ‘CATD’) genome and the reference Tall coconut genome (Hainan Tall) were characterized. Other types of protein families involved in gene regulation in dwarf coconut, as characterized in the ‘CATD’ genome, are transcription factor interactor and regulator, chromatin regulator, chromatin remodeling and transcription regulator, and lipid-binding proteins (Table S3). 'King Coconut' status would need to be reviewed. Our members work to advance knowledge in the basic mechanisms of inheritance, from the molecular to the population level. 2005). This result, in addition to ethnobotanical and geographic information, indicates that the ‘Dwarf’ originated from ‘Tall’ through typical domestication events that occurred in Southeast Asia. After evaluation, the reads were indexed and the sequencing errors were corrected using ‘sga index’ and ‘sga correct’ sub-programs, respectively. Catigan Green dwarf (CATD) and tall coconut var. 2013). Results showed that the ‘CATD’ genome has a more complete set of annotated genes (85.3%) as compared to that of ‘Hainan Tall’ annotated genes (81.2%), date palm PDK30 build (57.5%) and African oil palm E5 build (42.4%). | Premium Quality | PKM1 | Edible | Planting | Moringa Oleifera| Malunggay | Semillas De Moringa | Drumstick Tree | Seeds from India (2 oz), BESTZY 16pcs Miniature Trees Mixed Model Trees Model Train Scenery Architecture Trees Model Scenery with No Stands Model Coconut Tree, Ken's CocoMon Coconut Opener Tool + Stainless Straw for Fresh GREEN Young Fruit Black Rubber Handle EZ Easy Grip SAFE with Stainless Steel Drinking Straws (1 CocoMon + 1 Straw), Bulk Package of 1,000+ Seeds, Sunflower Crazy Mixture 15+ Varieties (Helianthus annuus) Non-GMO Seeds by Seed Needs, Ambesonne Tropical Beach Shower Curtain, Coconut Palm Trees Shadows on Caribbean Shore Summer Plants Idyllic, Cloth Fabric Bathroom Decor Set with Hooks, 84" Long Extra, Coconut Green, Sow Right Seeds - Italian Herb Garden Seed Collection - Individual Packets of Basil, Oregano, Parsley, Sage, and Thyme to Plant; Non GMO Heirloom with Instructions for Planting, zhenleisier Miniature Garden Decoration,5Pcs Realistic Coconut Palm Tree Models DIY Fairy Tale Garden Accessory Miniature Beach Landscape Bonsai Doll House Home Decor Ornament Green 5pcs, Heirloom Vegetable Seeds -10 Variety - Non GMO Vegetable Seeds For Planting Indoor or Outdoors, Brussel Sprouts, Carrots, Peppers, Cucumber, Kale, Romain, Peas, Radish, Tomato Seed - Home Garden Seeds, Get The Coconut Powder Everyone is Raving About. This demonstrates that the current scaffold assembly of ‘CATD’ has covered most of the ‘Dwarf’ Cocos nucifera L. genome and gene units. Furthermore, as expected in plants, retroelements were the most common mobile elements found in the assembly and highly represented by LTR elements (60.26%). Dau Tall. To correct the bias of the per-base estimate of error generated by the sequencing platform, base quality score recalibration (BQSR) was performed using GATK BaseRecalibrator and PrintReads commands. However, it is critical to perform further functional analysis (e.g., differential gene expression, knock-out assays) and marker-phenotype association studies (e.g., QTL mapping, fine-mapping) for a specific disease to validate the utility of any of these RGAs in actual plant varietal improvement programs. 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This further validates the quality/high-degree of gene completeness of the assembled dwarf coconut genome, and its close evolutionary relationship with the other palm species. Here, we report the cloning and 14 characterization of coronatine-insensitive 1 (COI1) gene, one of the candidate insect defense genes, using ‘Catigan 15 Green Dwarf’ (CATD) genome sequence assembly as reference. Worldwide coconut production has been constrained by several biotic (pests and diseases) and abiotic (e.g., drought) factors. As a result, 39 (drought response genes), 157 (insect and pest resistance), and 25 (oil biosynthesis) SSR markers were designed with definite physical distance to each target gene. Data S2 shows the dag-chainer output file of ‘CATD’-date palm alignment. 8.5. 2016). The ‘CATD’ genome has an estimated size of 2.15 Gbp based on the generated homozygous k-mer peak using the preprocessed Illumina Miseq short reads (Figure S1; Figure S2). $39.99 $ 39. The majority of the predicted RGAs belong to the TM-CC class, which is higher in number as reported in corn (161 TM-CC), sorghum (128 TM-CC), rice (158 TM-CC) and banana (138 TM-CC); but lower than the 218 TM-CC RGA genes predicted in Panicum virgatum (Li et al. 2013). Top subscription boxes – right to your door, © 1996-2020, Amazon.com, Inc. or its affiliates. 2004). True to its distinction as “the tree of life”, the coconut tree has no shortage of uses for its parts, from the leaves down to the roots, whether domestic, commercial or industrial in nature. ABSTRACT. If you want for coco meat or copra - experts suggested tacunan variety - but if you want for small farm, hobbiests or park/landscape - you can go with the dwarf -here's my email add:joelglobal@yahoo.com All identified LTR-RTs from each of the LTR-RT identification programs were used as an input to LTR_retriever (Ou and Jiang 2017) to generate a high-quality non-redundant LTR libraries, and to categorize them into two families (i.e., gypsy and copia) in order to estimate the predicted insertion dates of various types of repeat sequences. 2016) were likewise aligned on the assembly to achieve an overall mapping rate of 95.7%. 2016; Kamaral et al. 1.0. The size of these nuts is generally small, less than a kilogram or kg/nut. This ‘intermediate’ type is phenotypically distinct from the two types and can be fixed as ‘semi-Talls’ with reproductive traits similar to ‘Dwarf’ but with faster growth (Batugal et al. The basic chromosome number (n) between the coconut (n = 16; Batugal et al. 1992) with empirical codon frequencies (+F) and FreeRate (+R9) rate heterogeneity across sites (Yang 1995; Soubrier et al. NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. San Francisco, Agusan del Sur --- The Philippine Coconut Authority-CARAGA (PCA-CARAGA) headed by Regional Manager Joel Oclarit, led the ceremonial planting of PCA-produced hybrid variety Catigan dwarf crossed with Baybay tall on a 15-hectare coconut hybrid demo farm located in Ormaca, San Francisco, Agusan del Sur on September 9, 2020. The binary alignment map (BAM) file was generated using Bowtie2 (Langmead and Salzberg 2012) by mapping the pre-processed Illumina Miseq PE reads to the scaffold assembly; output of which was input data for PILON assembly correction. Overall Size. The dwarf variety is very shorter in stature and its life span is short as compared to the tall. Dwarf Coconut Seedlings Negros, Manapla. The libraries were sequenced on an Illumina HiSeq Platform. Based on the sequence homology analysis of these coconut repeat elements against characterized plant genomic elements, ‘CATD’ Gypsy was found to be more diverse than its Copia elements. 2.7 out of 5 stars 17. 2005) with default settings for the mapping and annotation step to reveal gene ontology terms. Although coconut oil is primarily composed of C12, breeding for elevated MCFAs should be focused on C8 and C10 since there is less variation on the C12 composition among the Philippine coconut accessions (Laureles et al. 2016) and the RNA-Seq raw reads (SRR1173229) were mapped into the assembled genome using TopHat2 (Kim et al. A focused review of the literature, Lysophosphatidic acid acyltransferase from coconut endosperm mediates the insertion of laurate at the sn-2 position of triacylglycerols in lauric rapeseed oil and can increase total laurate levels, MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets, Pollen dispersal and pollination patterns studies in Pati kopyor coconut using molecular markers, Variability in fatty acid and triacylglycerol composition of the oil of coconut (, RECON: a program for prediction of nucleosome formation potential, Seedling and slow rusting resistance to leaf rust in Chinese wheat cultivars, RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants, Identification and computational annotation of genes differentially expressed in pulp development of, Genome-wide analysis of C2H2 Zinc-finger family transcription factors and their responses to abiotic stresses in poplar (, Tc1-like transposable elements in plant genomes, How to usefully compare homologous plant genes and chromosomes as DNA sequences, The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates the rosids, Rapid recent growth and divergence of rice nuclear genomes, Polyploidy induction of oil palm through colchicine and oryzalin treatments, Indian Central Coconut Committee, Government Press, Effects of dietary fatty acids and carbohydrates on the ratio of serum total to HDL cholesterol and on serum lipids and apolipoproteins: a meta-analysis of 60 controlled trials, Osmoregulation and water stress in higher plants, A diet rich in coconut oil reduces diurnal postprandial variations in circulating tissue plasminogen activator antigen and fasting lipoprotein (a) compared with a diet rich in unsaturated fat in women, The serum LDL/HDL cholesterol ratio is influenced more favorably by exchanging saturated with unsaturated fat than by reducing saturated fat in the diet of women, C2H2 type of zinc finger transcription factors in foxtail millet define response to abiotic stresses, Chromosome morphology microsporogenesis and pollen fertility in some varieties of Coconut, Transcriptomics-based analysis using RNA-Seq of the coconut (, A general method applicable to the search for similarities in the amino acid sequence of two proteins, IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Fatty acids composition of vegetable oils and its contribution to dietary energy intake and dependence of cardiovascular mortality on dietary intake of fatty acids, LTR_retriever: A Highly accurate and sensitive program for identification of LTR Retrotransposons, Assessment of the genetic diversity of Kenyan coconut germplasm using simple sequence repeat (SSR) markers, Chemical and physical properties of coconut oil, The influence of vapour pressure deficit on leaf water relations of, Use of microsatellite DNA markers to investigate the level 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The quality-trimmed RNA-seq reads (SRR1173229; Rajesh et al. Anyone traversing the coastland of Guyana from Crabwood Creek to the Pomeroon, or on a visit to Essequibo Islands, would notice that the coconut palm is … Genomics in Coconut Towards Insect Resistance Breeding, The future of CRISPR technologies in agriculture, Genetic diversity, population structure and association analysis in coconut (, Osmotic adjustment, proline accumulation and cell membrane stability in leaves of. Although most of the NBS-domain containing clade could be arranged into a single clade, the specific RGA classes within the NBS clade are mixed in separate sub-clades. 2010) tests. 2017). LTRharvest (Ellinghaus et al. The assembled sequence data of the ‘Catigan Green Dwarf’ coconut variety has been submitted to the DDBJ/ENA/GenBank database under accession number QRFJ00000000. 1999). Li, H., 2013 Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. The dwarf varieties: The common feature of the dwarf coconut varieties is their early maturity at 2 to 3 years after field planting. The scaffold N50 of ‘CATD’, however, is lower than that of the E5-build of African oil palm (Singh et al. The FASTA amino acid sequences of all the identified candidate RGAs were used to construct a phylogenetic tree. 2015; Khan et al. Much work has been done to study the evolution of R-genes in several crops, as well as the coping mechanisms of diseases during the course of evolution (Li et al. Bautista MAM, Acoba DJ, Emmanuel EE, Rivera RL, Rivera SM3 Saloma CP. 1989; Müller et al. PHP 195. The resulting phylogenetic tree was validated with 1000 replicates of ultrafast bootstrapping (Hoang et al. The quality is further evaluated with the Benchmarking Universal Single Copy Ortholog (BUSCO) program using the plant-specific database OrthoDB consisting of 1440 genes (Simão et al. 2009; Sun et al. The whole genome sequence (WGS) of ‘Catigan Green Dwarf’ (CATD) coconut variety was generated using Illumina Miseq, PacBio SMRT and Dovetail Chicago sequencing technologies. GENERATING TRANSCRIPTOME SEQUENCE INFORMATION FROM Cocos nucifera L. ‘CATIGAN GREEN DWARF’ CULTIVAR. The draft genome assembly of coconut facilitates the identification of genes responsible for several economically important traits such as insect and disease resistance, and plant traits associated with agro-ecological adaptation such as resistance to drought stress (Fan et al. The distance between palms in a row should be 9 m x 9 m to 10 m x 10 m for tall varieties and 8 m x 8 m to 8.5 m x 8.5 m for dwarf hybrid coconuts. It is a major agricultural crop in humid areas in the tropics, with recorded annual worldwide production of 59 million tons (FAOSTAT 2016). They also have the greatest amount of copra per nut. Furthermore, direct counts of GOs for the cellular component (CC) showed that most coconut genes are integral components of the cell membrane. (2010) demonstrated that proline is more related to a protective rather than an osmoregulatory mode of water stress response. ... Catigan Green Dwarf. A flow cytometry study revealed that the ‘Catigan Green Dwarf’ (‘CATD’) variety of coconut has a genome size of 2.72 Gbp (1C) (Gunn et al. Data S3 contains the FASTA sequences of the core LRT-RT in coconut genome. The dotplot axis matrix is in nucleotides with square dotplot axes relationship. Table 2 (at the end of this post) gives the list of the 31 accessions presently registered in the CGRD database as of January 2016. 2013). The assembled genome was used to infer the evolutionary relationship within the palm family based on genomic variations and synteny of coding gene sequences. A high level of proline was found in drought tolerant coconut genotypes (Voleti et al. Genome-wide analysis of R-genes and associated sequences in coconut is therefore important in order to obtain a complete picture of the crop’s potential inherent defense system, and characterize each phylogenetic relationship in reference with characterized/validated plant R-genes. Genetic variation within five Dwarf coconut accessions from Philippines. King Coconut (Gon Thembili) GTB: Sri Lanka: Most famous coconut of Sri Lanka known for its high quality water. The genome of ‘Hainan Tall’ (HAT) coconut variety was recently published (Xiao et al. 2002; Dugas et al. JTT amino acid substitution model (Jones et al. Table S3 list of genome-wide transcription factors and other transcriptional regulators identified in the predicted genome models of ‘CATD’ genome. 4. Structural annotation returned an average number of 5.34 exons per gene based on the gene structure of all identified protein-coding sequences. Genes tagged included four (4) representative genes associated to drought response, five (5) for insect and pest resistance, and four (4) genes for oil biosynthesis (Table S5). In addition, we discovered 58,503 variants in coconut by aligning the Hainan Tall (HAT) WGS reads to the non-repetitive regions of the assembled CATD genome. Direct counts of the identified GOs also revealed that majority of the biological processes (BP) are involved in metabolic processes such as protein phosphorylation, oxidation-reduction and regulation of transcription. This Sri Lanka variety was classified as 'Semi-Tall'. The ABCG40 gene (AT1G15520) has the highest number of homologs - thus far 15 coconut gene homologs. Around 98.9% of the variants detected is composed of SNPs at non-repeat regions between ‘Catigan Green Dwarf’ and ‘Hainan Tall’ genomes (Table 2). Table S4 presents the BLASTn output of the alignment of oil biosynthesis cDNA sequences in the coconut ‘CATD’ genome. 1997; Bai and Rajagopal 2000; Prado et al. Data show that at least three (3) rounds of whole genome duplication occurred and are commonly shared by these members of the Arecaceae family. Coconut, a diploid (2n = 32) crop, is the only recorded species under the genus Cocos which is a member of the family Arecaceae and sub-family Arecoideae (Nambiar and Swaminathan 1960; Abraham and Mathew 1963). This was estimated by comparing the 5′ LTR and 3′ LTR of each LTR-RT using the Jukes-Cantor model (Jukes and Cantor 1969) for non-coding sequences, and based on a proposed mutation rate of 1.3 × 10−8 mutations per site per year (Ma and Bennetzen 2004). 7.5. Figure S10 depicts the genome-wide occurrence of top paired-motif in coconut (‘CATD’) SSRs. In this paper, we present the first whole genome sequence of a ‘Dwarf’ type coconut represented by ‘Catigan Green Dwarf’ (CATD) coconut variety, chosen for its genome simplicity and low heterozygozity. We’ve made it easier to discover products with sustainability certifications, as part of our commitment to help preserve the natural world. 2012). Scaffolds in the y-axis of (c) are sorted based on the Syntenic Path Assembly (SPA) using oil palm pseudomolecules as reference. 2008). 2008) tool. A total of 34,958 high-confidence gene models were predicted and functionally associated to various economically important traits, such as pest/disease resistance, drought tolerance, coconut oil biosynthesis, and putative transcription factors. Based on the Bayesian Information Criterion (BIC) of the models, JTT amino acid substitution model (Jones et al. Figure S8 shows the distribution of the drought-response gene homologs classified based on characterized biological function in coconut.
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