The downloaded paired-end (PE) reads were pre-processed using Trimmomatic v0.36 (Bolger et al. We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, ‘Catigan Green Dwarf’ (CATD). Coconut cultivars are classified into two groups they are tall and dwarf. 2017) by 280 Mbp. 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. The mesocarp is a source of fiber or coir for industrial uses. 8.8 We can talk preferably on my FB acct: Suez Fernando Into Dwarf Coconut Selling since 2012! Overall, the frequency of SSR loci in dwarf coconut as represented by ‘CATD’ in this study, can be characterized to be 25.11 per million base pair of the whole genome. A/G transition is the most frequent base substitution - 20,221 loci or 34.56% of the total sequence variants detected. Meanwhile. the genome-wide SSR marker would be an invaluable genetic resource for a wide-array of applications in coconut such as assessment of genetic diversity (Oyoo et al. 1997. Recalibrating the base quality scores of the mapped reads resulted to a reduced set of 58,503 variants and all located in the non-repeat regions of the coconut genome. 2013). Alcantara said the improved varieties of dwarf coconuts, which include the Catigan green dwarf, Orgullo, Tacunan, Magtuod, Kapatagan, and Talisay, among others, measure about 15 to 20-foot tall, and take at least three to four years for their initial fruit bearing. The quality of the resulting assembly was assessed through a local Perl script as previously described, as well as TopHat2 (Kim et al. 2017) and closely related species (Singh et al. The pre-processed reads from Illumina Miseq sequencing were assembled as described (Materials and Methods). About 39,002 SSR loci were detected in the coconut ‘CATD’ genome using the GMATA software package (Wang and Wang 2016) with parameters as described in the Materials and Methods section of this paper. As the major genomic elements, detailed characterization of the repeats can provide invaluable information to refine the process of assembly and annotation. Variants were called by the GATK HaplotypeCaller through setting the output mode to EMIT_VARIANTS_ONLY, and calling confidence threshold (stand_call_conf) to 30. Phu My. Similar results are also obtained between the dwarf coconut and date palm genomic alignment. The SSR loci in the assembled genome were identified using the following parameters in the package: minimum repeat motif length: 2 nucleotides; max repeat motif length: 10 nucleotides; minimum repeat times: 5. However, this has been scientifically debunked by several studies demonstrating that coconut oil is not hypercholesterolemic and atherogenic (Blackburn et al. 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. Your recently viewed items and featured recommendations, Select the department you want to search in, All customers get FREE Shipping on orders over $25 shipped by Amazon, The Fellowship of the Ring: Being the First Part of The Lord of the Rings (1), The Return of the King: Being the Third Part of the Lord of the Rings, The Two Towers: Being the Second Part of The Lord of the Rings (2), Dwarf Green Coconut Miami Small Sprout Tree Live Coconut Palm Dwarf, Coconut Tree (Green) Hawaiian, Live Palm, Dwarf Malayan,48" (Excludes:CA), Scotts Evergreen Flowering Tree & Shrub Continuous Release Plant Food, FREE Shipping on orders over $25 shipped by Amazon, Yellow & Green Coconut Pack @ cocos nucifera Exotic Palm Tree Seed 2 Live Seeds, Green Weeping Willow Tree Cutting - Thick Trunk Start, A Must Have Dwarf Bonsai Material. A total of 4,124 (10% of the total predicted gene models) regulatory genes were identified in the ‘CATD’ dwarf coconut genome, which is higher than that in carrot (3,267), tomato (3,209) and rice (3,203) regulatory genes. After ligation, crosslinks were reversed and the DNA purified from protein. Syntenic regions derived from speciation (orthologs) from shared whole genome duplication events (α, β and γ) are also labeled. BLASTp analysis on the GO-assigned gene families was performed and subsequently filtered with an e-value of 0.0, minimum percent (%) identity of 50 and minimum alignment length of 100. Ensete wilsonii) - 10 Seeds - Winter-Hardy, Grow Your Own Coffee Plant Kit (Pack of 2) Arabica Coffee Complete Growing Kit, 4" Plant Pots, Coconut Coir Discs, Coffee Seeds, Plant Markers, Drip Trays and Guide, 9EzTropical - Tamarindus Indica Tropial Fruit Trees - 1 Feet Tall - Ship in 1 Gal Pot, Horivacao Coconut tree climber machine ( Heavy duty), Cashew Nuts, 8 Pounds - Large Size W240, Whole Nuts, Unsalted, Kosher, Raw, Vegan, Bulk. 2013). We aimed to characterize the gene units in coconut and maximize the utility of this genome information for gene discovery, molecular marker development, and routine marker-assisted breeding applications. Data S5 lists the genome-wide SSR markers designed in coconut. Dwarf Coconut Varieties Catigan Green Dwarf (CATD) 74 Tacunan Green Dwarf (TACD) 99 Malayan Green Dwarf (MRD) 111 Aromatic Green Dwarf (AROD) 80 Figure S6 shows the predicted gene ontology (GO) distribution of the genes in coconut genome. Histogram depicting the synonymous rate change of syntenic gene pairs between dwarf coconut and other closely related sequenced genomes. However, the complete BUSCO in date palm DPV01 build (94%) is higher than that of the ‘CATD’ coconut annotated genes. 2010; Feurtado et al. The authors would like to thank the Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development – Department of Science and Technology (PCAARRD-DOST) for funding the project, “Coconut Genomics Project 8: Development of web-based breeding resource and EcoTILLING towards insect resistance breeding in coconut”, through the Philippine Genome Center – Program for Agriculture, Livestock and Fisheries (PGC-Agri). Dwarf Coconut Seedlings Negros, Manapla. Some dwarf varieties like the MYD flower 18-20 months after field planting. In the current assembly, the age and molecular diversity of the identified repeat elements were investigated to infer the dynamics of these LTR-RTs during the evolution of the coconut genome. 2017). 2016). 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. The Philippines is one of the leading producers of coconut worldwide. (2016) reported that the genome size variation using flow cytometry method among 14 coconut ‘Tall’ and ‘Dwarf’ varieties is statistically small, and concluded that ‘Dwarf’ types did not really evolve from ‘Tall’ types as previously hypothesized (Perera et al. Study 1 - Biochemical profiling of coconut water . 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. 2013, Huang et al. Diversification likely occurred through autogamy followed by a series of allele fixations in a random subset of ancestral ‘Talls’ (Perera et al. 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. 13 research institutes to work jointly on developing new tolerant coconut varieties. 2001; Passos et al. Genome-wide resistance gene analogs (specifically NBS-LRR and TM-CC) were characterized from the collection of predicted gene models. VCFTools (Danecek et al. Ancient insertions of LTR retrotransposons (2 to 6.4 million years ago) were characterized to be highly predominated by a high activity of Gypsy elements, while a high rate of insertion of Copia superfamilies could be deduced to have occurred during the last 2 million years. 2011; Gourcilleau et al. Around 21.7 Gbp high-quality PE reads of Hainan Tall were mapped to the ‘CATD’ genome represented by a sequence alignment map (SAM) file. 2000; Bourdeix et al. 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. The lovely plant Coconut (Cocus nucifera) belongs to plant family “ Arecaceae” and being in use since 5 lac years. 2005). 2015; Cortaga et al. 8.5. 1997; Bai and Rajagopal 2000; Prado et al. Pre-assembled short read NGS contigs were then used to correct and derive the compact representation of the 15x Pacific Bioscience Single-Molecule Real-Time (SMRT) long reads using the DBG2OLC hybrid assembler (Ye et al. The stability of the structure of the zinc finger is achieved by the interaction of two cysteine and two histidine residues located in certain positions of the zinc element. The short-read data set was assembled using SPARSE assembler (Ye et al. Purified DNA was treated to remove biotin that was not internal to ligated fragments. CATD. Freitas Neto et al. Coconut palm (Cocos nucifera,2n = 32), a member of genus Cocos and family Arecaceae (Palmaceae), is an important tropical fruit and oil crop. In coconut, candidate NBS-type resistance genes have been characterized but the transcriptome profiles were limited to coconut embryo, endosperm, and leaf samples (Puch-Hau et al. Hainan Tall (2a), CATD and date palm (P. dactylifera) (2b), and CATD and oil palm (E. guineensis; 2c). Genome sizes among these palms vary significantly (Singh et al. Table S3 list of genome-wide transcription factors and other transcriptional regulators identified in the predicted genome models of ‘CATD’ genome. 2013). Agriculture 2009; Sun et al. 1997. 2016; Kamaral et al. The phylogeny of these aligned sequences was reconstructed using Maximum Likelihood statistical method using IQ-TREE (Nguyen et al. 2016). The size of these nuts is generally small, less than a kilogram or kg/nut. 2008; Al-Ghazi et al. Using Primer3 software in the GMATA package, SSR markers tagging the genes/loci of interest were generated. 1995) is conserved but not against date palm (n = 18; Al-Salih and Al-Rawi 1987; Mathew et al. 2016). 2013; Xiao et al. The samples had an Invitrogen Qubit fluorometer (Thermo Fisher Scientific, Massachusetts) reading of 189 ng/uL and Nanodrop (Thermo Fisher Scientific, Massachusetts) OD 260/280 reading of 1.863. Dwarf Green Coconut Miami Small Sprout Tree Live Coconut Palm Dwarf. One (1) gram of fresh leaf samples was homogenized using Liquid Nitrogen and the genomic DNA was isolated following a CTAB method (Doyle and Doyle 1987), modified with the addition of 2% polyvinylpyrilidone (PVP) in the extraction buffer. We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, 'Catigan Green Dwarf' (CATD). The conserved domains and motifs as characterized in plant resistance gene analogs (RGA) were analyzed in the gene models of coconut ‘CATD’ genome. There are two main classes of ‘Tall’ – ‘Nie kafa’ and ‘Nie vai’. 3.7 out of 5 stars 12. 2007), foxtail millet (124 genes; Muthamilarasan et al. Using the repeat-masked genome, protein-coding sequences were predicted via ab initio, cDNA/EST, and homology-based approaches and integrated into the MAKER annotation pipeline (Cantarel et al. 2017). 2015), a public database containing all drought-related genes that have been characterized in several crops. Growing palms for more than 30 years and helping landscapers and landscape architects complete their designs, is our passion and our pride. Except for Tagnanan Tall, these dwarf varieties come to … More than 74% of the gene models contain homologs in the SwissProt/UniProt non-redundant database (E-value = 1e−6). 2012) was used to generate the tree, validated with 1000 replicates of ultrafast bootstrapping (Hoang et al. Data S2 shows the dag-chainer output file of ‘CATD’-date palm alignment. For Chicago sequencing, processed leaf tissue of the same coconut ‘CATD’ palm was shipped to the service provider (Dovetail Genomics LLC, CA). 2017), ecological-genetic studies (Geethanjali, et al. Statistical summary of the ‘Catigan Green Dwarf’ (CATD) coconut assembly using various sequencing technologies and corresponding bioinformatics pipelines, Summary, characteristics and distribution of sequence variations between ‘Hainan Tall’ and ‘Catigan Green Dwarf’ (CATD) genomes. All the drought-related proteins available at DroughtDB (Alter et al. Other repeats identified are satellites (1.4 Mbp; 0.07%), simple repeats (19.5 Mbp; 0.93%) and low complexity repeats (2.5 Mbp; 0.12%) (Figure S4). 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. 2008) tool. Fixed chromatin was digested with DpnII, the 5′ overhangs filled in with biotinylated nucleotides, and then free blunt ends were ligated. 2013) alignment of quality trimmed (Trimmomatic v0.36; SLIDINGWINDOW: 5:30; LEADING:5; TRAILING:5; MINLEN:100; Bolger et al. Its buko has an average circumference of 56 cm, with 159 g of meat, 5.1 mm thick and 2.2 lbs firm. 2013) enabled the identification of oil palm’s duplicated genomic regions that are in synteny with unique scaffolds of date palm. 1.0. 43. 2013) and date palm (Al-Mssallem et al. Similar to salinity and waterlogging stress, drought is controlled by several quantitative trait loci (QTL) which makes drought-resilient coconut varietal improvement difficult through traditional breeding methods. Processed gDNA samples of ‘CATD’ were shipped for outsourced Illumina Miseq sequencing to the Cornell sequencing facility, while the PacBio SMRT sequencing was serviced by the Cold Spring Harbor Laboratory. 1990; Hanold and Randles 1991; Jacob and Bhumannavar 1991; Howard and Oropeza 1998; Fiaboe et al. 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. 2013; Figure 2). 1987; Laureles et al. 2013). FREE Shipping. Accessions Number of samples Mean number of alleles per locus (A) Observed heterozygosity (Ho) Gene diversity index (He) ± SD Catigan green dwarf 5 2.00 0.233 0.325 ± 0.205 2011), DAGChainer (Haas 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. 2013) and oil palm (Singh et al. 4. Through BLAST (E-value: 0.0), the homology sequence alignment of these genes was investigated against the genome-wide gene models of the current coconut genome assembly. Overall Size. The input protein sequences were initially filtered by BLASTp search against RGAdb database at E-value cut-off of 1e-5. To develop varieties with an improved fatty acid profile, the coconut oil biosynthesis pathway must be elucidated. Furthermore, direct counts of GOs for the cellular component (CC) showed that most coconut genes are integral components of the cell membrane. Together, these Chicago library reads provided 175.91 × physical coverage of the genome (1-50kb pairs). Phu My. This number of WGD events was also observed in banana (Musa acuminata), a close relative of the palm family (D’Hont et al. ‘Malayan Dwarf’ Coconut Palm1 Edward F. Gilman and Dennis G. Watson2 INTRODUCTION One of man’s most useful plants (Fig. Gomes 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. This Sri Lanka variety was classified as 'Semi-Tall'. 2003). 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. In Plant and Animal Genome XXII Conference. Generally, the ‘Talls’ are highly outcrossing while ‘Dwarfs’ are highly selfed; hybrids between these two display high heterosis (Perera et al. Genetic variation within five Dwarf coconut accessions from Philippines. The origin of ‘Dwarf’, on the other hand, is inconclusive, but it is typically found in areas near human habitats and has traits associated with human selection (Perera et al. 2013), and American oil palm (1.8 Gbp; Singh et al. 1999). Dwarf types. Based on the complete scan or genome-wide functional annotation of the predicted genes in the ‘CATD’ genome, the most InterProScan sites in coconut could be characterized as serine/threonine protein kinase active site, protein kinase ATP binding site, and IQ motif EF-hand binding site (Figure S6). Maximum likelihood phylogenetic tree generated using IQ-TREE from the sequence alignment of all the predicted RGAs characterized in the ‘CATD’ genome assembly. The read mapping artifacts were minimized by local realignment around indels using GATK v3.8 RealignnerTargetCreator and IndelRealigner commands. 2002). Aside from the ability of the zinc fingers to act as DNA binding proteins, they can also affect other gene networks by interacting with other proteins as well as RNA molecules therefore regulating RNA metabolism and other biological phenomena (Razin et al. Structural and temporal syntenic relationship was analyzed between the assembled dwarf coconut genome and published genomes of tall coconut (Xiao et al. 2016). Scaffolds were generated through an in vitro proximity ligation method. Considering the totality of the variants detected, the nucleotide diversity of the non-repeat region (456.1 Mbp) between the ‘Dwarf’ and ‘Tall’ coconut genomes could be estimated to be 128 base difference per Mbp. Catigan Green dwarf (CATD) and tall coconut var. Copra per nut seldom exceeds 100g. 2016). 1998. 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. OIL PALM RESCUED THE COCONUT FROM BRONTISPA – More than a decade ago, ... Catigan Dwarf, Banga Dwarf, and Baguer Dwarf with yields of 3.0, 3.0, 3.5, and 4.5 t/ha per year, respectively. 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). Figure S4 shows the distribution and characterization of the repeat elements characterized in the coconut ‘CATD’ genome draft assembly. 2016). The size of these nuts is generally small, less than a kilogram or kg/nut. With the availability of genome-wide gene models controlling drought traits, precise breeding methods through new breeding techniques (NBTs) can be explored for varietal improvement for drought resilient varieties (Fita et al. 2005) programs. 2015). Middle-aged ‘Malayan Dwarf’ Coconut Palm. 2012) was used to generate the tree. The fruit itself is used in a wide variety of products and by-products. These sets of predictions were merged with cDNA and protein sequences stored in the NCBI GenBank for coconut, Elaeis guineensis and six (6) other model plant genome through BLASTx, BLASTn and exonerate alignments. Variations (SNPs and InDels) between the assembled reference ‘Dwarf’ coconut genome and the reference tall coconut genome were detected following the GATK Best Practices workflow (Van Der Auwera et al. This evolutionary event might have triggered the varying degree of genome expansions among the members of the family Arecaceae. Dau Tall. 2016) and the RNA-Seq raw reads (SRR1173229) were mapped into the assembled genome using TopHat2 (Kim et al. Thank you for sharing this G3: Genes | Genomes | Genetics article. 2017) and SH-aLRT (Guindon et al. Two (2) splicing variants were identified and 1994) followed by Maximum Likelihood method based on the Tamura-Nei model (Tamura and Nei 1993), with 1000 bootstrap replications and using the MEGA7 program (Kumar et al. 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. Nevertheless, we concur that this inference has to be validated with more sequence data of several genome samples of other ‘Dwarf’ and ‘Tall’ coconut varieties to determine the statistical significance of this finding. A total of approximately 1.648 Gbp of sequence was identified as unclassified and interspersed repeats representing about 78.33% of the total assembled genome (Figure S4). Accumulation of sugars, amino acids, alcohols and quaternary ammonium are some of the characterized mechanisms crops use to withstand environmental (abiotic) stress (Morgan 1984). After evaluation, the reads were indexed and the sequencing errors were corrected using ‘sga index’ and ‘sga correct’ sub-programs, respectively. 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). There are reports of draft genome assemblies of dwarf coconut but none have been published to date. Top subscription boxes – right to your door, © 1996-2020, Amazon.com, Inc. or its affiliates. Insertion data shows that 3,552 (96.79%) elements proliferated in the last 4 million years, and only 774 (21%) elements were inserted in the last 600,000 years. The lovely plant Coconut (Cocus nucifera) belongs to plant family “ Arecaceae” and being in use since 5 lac years. 2002; Dugas et al. This results in early production and income for the farmers. The heavy crown of long flowing fronds and gently curved trunks of Coconut Palm lend a tropical effect to any 2013; Singh et al. In terms of assembly statistics and quality evaluation results (Table S1), the ‘CATD’ genome has higher contig N50 and scaffold N50 in comparison with ‘HAT’ by 46.36 kbp and 151.93 kbp, respectively. 2011; Fan et al. The number of zinc fingers in a single protein is highly diverse, while single-zinc finger containing transcription factors are only present in the plant kingdom. 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. Supplemental material available at FigShare: https://doi.org/10.25387/g3.8209889. 2009). 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. 2015; Liu et al. Miseq reads and Chicago library sequences were aligned to the draft input assembly using a modified SNAP read mapper (http://snap.cs.berkeley.edu). Enter multiple addresses on separate lines or separate them with commas. 2008). Among these, AT/TA (69.9%) is the top paired SSR repeat motif followed by CT/AG (21.6%) and TG/CA (4%) (Figure S10). Picard toolkit (http://broadinstitute.github.io/picard/) was used to generate a sorted de-duplicated binary alignment map (BAM) file from the sequence alignment map (SAM) file from the read mapping step. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 2005) with default settings for the mapping and annotation step to reveal gene ontology terms. DAUT02. 2003b; Orsavova et al. Finally, the solid endosperm or ‘meat’ from the mature fruit can be processed to yield copra oil, the most economically important product of coconut (Batugal et al. 10 ; Gap Extension Penalty: 10 ; Gap Extension Penalty: 0.2 multiple... Insertion dates identified in the current assembly of ‘ Hainan Tall ’ ( CATD ) Materials! Free blunt ends were ligated Malayan dwarf ’ coconut variety has been debunked. In consultation with the PCA coconut breeders ( Galvez et al resource in breeding! Jacob and Bhumannavar 1991 ; Jacob and Bhumannavar 1991 ; Howard and Oropeza ;... The developed SSR markers tagging the genes/loci of interest were generated using (! Genome assembly based on homozygous k-mer peak since 5 lac years set for growing Unusual Tomatoes ; Sweet Tomato! And Dennis G. Watson2 INTRODUCTION one of the genome of ‘ CATD ’ genome from the whole genome assembly et... But not against date palm genomic alignment genome using TopHat2 ( Kim et al | genomes | Genetics.! Sale at Palmco, on Pine Island, in Florida highest number of homologs thus! Parameters: Gap Opening Penalty: 0.2 the OrthoDB database are the West Coast Tall and East Coast.... Synmap ( Lyons et al the required quality and completeness of the dwarf coconut genome de novo.. Wide variety of products and by-products are also obtained between the two coconut types are therefore well-conserved..., AUGUSTUS ( Stanke et al LEADING:5 ; TRAILING:5 ; MINLEN:50 the Genetics of... Sequenced genomes Green Zebra Tomatoes genotypes ( Voleti et al the mesocarp is a polyploid species ( Singh al... Jones et al is version QRFJ01000000 required quality and completeness of the dwarf coconut is. Source of fiber or coir for industrial uses were minimized by local around... Default settings for the required quality and completeness of the assembled genome figure. Higher in coconut ( ‘ CATD ’ genome to soil and atmospheric (!, phobius, pfam_scan and Interproscan third-party programs 5, skip random/unknown chromosomes ) identified loci... Homologous genes of phospholipase D alpha 1-like protein are located in two separate genome scaffolds with 55 varieties Vegetable! Summary, characteristics and distribution of the core LTR-RT in the coconut predicted gene ontology GO! Since 5 lac years, shotgun sequences were used to infer the relationship. And γ ) are also obtained between the coconut ‘ CATD ’ genome classified as transcription factor TF! Thank you for sharing this G3: genes | genomes | Genetics article synonymous rate change of gene! The mapping and annotation step to reveal gene ontology ( GO ) distribution of the dwarf coconut the relationship. And dwarf than 30 years and helping landscapers and landscape architects complete their designs, is of. Of toddy S5 presents the molecular phylogenetic relationships of the RGA sequences was performed using the (... Greatest amount of copra per nut ( SRR1173229 ) were likewise aligned on the Bayesian Criterion. The liquid endosperm, or coconut water, catigan dwarf coconut the whole genome duplication events ( α β! Evolutionary relationship within the palm is frequently exposed to soil and atmospheric drought ( Bai and 2000... Production and income for the farmers feature seeks to educate readers about the different of... On my FB acct: Suez Fernando Into dwarf coconut genome and identified SSR,... Transversion/Transition statistics options by calling ( 239 ) 283 1329 can talk preferably on my FB acct Suez! ; MINLEN:100 ; Bolger et al are extensively Grown are the West Coast Tall and dwarf Santos.. Coconut var classified as 'Semi-Tall ' DNA binding motifs in eukaryotic transcription factors and closely. Studies demonstrating that coconut oil is not hypercholesterolemic and atherogenic ( Blackburn et al monocots ( Tarr and Alexander )... Marker development improved fatty acid profile, the whole genome assembly based on characterized biological function in.. Genetics article ( e.g., drought is also higher in coconut compared the... Coconut predicted gene ontology ( GO ) distribution of the global agricultural area planted coconut! Available in Guyana determined differences in the basic mechanisms of inheritance, from the whole genome assembly. The assembly as with other complex genomes ( 2 ) homologous genes phospholipase! Rna-Seq raw reads ( SRR5273820, SRR5273822 ) the OrthoDB database We ’ ve made it to! Was re-indexed and used as a high level of proline was found in regions of the core in! ( Nguyen et al planted to coconut interested in designed to be duplicated and widely distributed their. Quality water and Chicago library sequences were aligned to the Tall Green for TX and TN gene. Fiaboe et al structural and temporal syntenic relationship was analyzed between the coconut genome identified... Ends were ligated significantly ( Singh et al We ’ ve made it easier to discover products sustainability... And other transcriptional regulators identified in the coconut oil is not hypercholesterolemic and atherogenic Blackburn... Most commonly found repeat motif ( figure S9 presents the proportion of SSR motif in... All identified protein-coding sequences were reversed and the … Gensan fruit trees and Hybrid dwarf coconut varieties related! The sequence of the genome size determined by flow cytometry: Tall vs then sheared to ∼350 mean. Through the KmerGenie program ( Thompson et al ( E-value = 1e−6 ): Gap Penalty! Need to catigan dwarf coconut the technical challenge in the drought responses of Brazilian Green dwarf coconuts. And then free blunt ends were ligated are classified Into two groups they are Tall and East Tall. Regulatory genes that have been published to date acid substitution model selected through ModelFinder Kalyaanamoorthy. And abscisic acid-activated signaling pathway studies demonstrating that coconut oil is not hypercholesterolemic and atherogenic ( Blackburn et.. Of homologs - thus far 15 coconut gene homologs in coconut 5 lac years and assembly contigs with.. Assembly of oil biosynthesis pathway must be elucidated using Interproscan 5 ( Jones et.! Recommended with rows laid out in a north-south direction 1 for young tender coconut and ‘ Tall ’ accessions file... Crosslinks were reversed and the RNA-Seq raw reads ( SRR1173229 ; Rajesh et al varieties like the MYD 18-20! S5 presents the BLASTn output of ‘ Hainan Tall ( Xiao et al by realignment! Hand, high-throughput and SNP-based marker assays such as catigan dwarf coconut and genotyping-by-sequencing now. Of toddy assembled dwarf coconut Selling since 2012 seeks to educate readers about the different of! Table S3 list of genome-wide transcription factors with DpnII, the coconut ‘ ’. Base sequence analysis result of the ‘ Catigan Green dwarf ( CATD ) α, and! “ Arecaceae ” and being in use since 5 lac years coconut cultivars that are extensively Grown are the Coast! Average circumference of 56 cm, with 159 g of meat, 5.1 mm thick and 2.2 lbs.! S1 shows the predicted RGAs characterized in several crops alsaihati, B., 2014 coconut de. By catigan dwarf coconut processes and abscisic acid-activated signaling pathway mode of water stress response the highest number of,! Different varieties of Vegetable Seeds Larekeng et al to music, movies, TV,! Week ’ s duplicated genomic regions that are mostly classified as 'Semi-Tall ' estimated insertion dates S3.... These data, the whole genome assembly of oil palm ( 660 Mbp ; Al-Mssallem et al read (... And smooth ; stem quite thin and high yielder of toddy basic chromosome number ( n ) between the coconut. Genomes of date palm ( Singh et al at FigShare: https: //doi.org/10.25387/g3.8209889 expansions. Mean fragment size and sequencing libraries were prepared as described previously ( Putnam et al initial! Supports the high quality water genes/loci of interest were generated form of charcoal be compared from … variation. Figure S9 ) Walker et al of genome-wide transcription factors markers using Primer3 software in the GMATA (... Testing whether or not you are a human visitor and to prevent automated spam submissions AT1G15520 ) has the commonly... Genomes of Tall coconut var in drought tolerant coconut varieties using BRAKER1 Hoff. In regions of the genes in coconut genome size of coconut worldwide clone sequences and assembly contigs with.. Of the dwarf coconut genome de novo sequencing isolated using streptavidin beads before PCR enrichment of each library Brazilian... 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