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catigan dwarf coconut

The majority of the predicted RGAs could be classified into two major clades and two major RGA families, i.e., NBS-containing and TM-CC (Figure 4). The repeat-masked ‘CATD’ genome was used in the mapping step to determine unique consensus sequences and to minimize misalignment of reads especially involving repeat sequences, which can be problematic in downstream variant discovery (Johnston et al. We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, ‘Catigan Green Dwarf’ (CATD). Coconut is monospecific and consists of two ecotypes based on stature and breeding habit, the ‘Talls’ and ‘Dwarfs’ (Menon and Pandalai 1958). Staking is done to ease in … Thus, for this later 2 genes, the cDNA sequences from E. guineensis were used to characterize the homologs in CATD coconut. Manohar et al. We do not retain these email addresses. 7.5. To increase the specificity and robustness of SSRs for various applications, the AT/TA repeat motifs were excluded, coming up with a final set of 7,139 coconut SSR markers (Data S5). More than 74% of the gene models contain homologs in the SwissProt/UniProt non-redundant database (E-value = 1e−6). 2014), and poplar (109 genes; Liu et al. The dotplot axis matrix is in nucleotides with square dotplot axes relationship. 2013). However, the complete BUSCO in date palm DPV01 build (94%) is higher than that of the ‘CATD’ coconut annotated genes. 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 phylogeny of these aligned sequences was reconstructed using Maximum Likelihood statistical method using IQ-TREE (Nguyen et al. 2015). Coconut genome size determined by flow cytometry: Tall vs. 2.7 out of 5 stars 17. In particular, hybrids from Dwarf and Tall, Tall and Tall varieties also generate high-yielding coconut palms.Generally, hybrid coconut palms are more superior in terms of quality and quantity of copra production. Dwarf Green Coconut Miami Small Sprout Tree Live Coconut Palm Dwarf. It is a major agricultural crop in humid areas in the tropics, with recorded annual worldwide production of 59 million tons (FAOSTAT 2016). 1998. 1987; Laureles et al. 2013). DGEC/L018. Prime members enjoy FREE Delivery and exclusive access to music, movies, TV shows, original audio series, and Kindle books. With these data, the genome size of coconut was estimated by k-mer distribution through the KmerGenie program (Chikhi and Medvedev 2014). The dwarf varieties: The common feature of the dwarf coconut varieties is their early maturity at 2 to 3 years after field planting. This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. In terms of number of SCOs included in the genome assembly, the ‘CATD’ assembly has the highest number of complete orthologs based on BUSCO analysis data output. 2016). 2015). 2013) and oil palm (Singh et al. 1995) is conserved but not against date palm (n = 18; Al-Salih and Al-Rawi 1987; Mathew et al. The fruit itself is used in a wide variety of products and by-products. 2017) and SH-aLRT (Guindon et al. 4. Phylogenetic study of plant Q-type C2H2 zinc finger proteins and expression analysis of poplar genes in response to osmotic, cold and mechanical stresses, Dynamic evolution of NBS–LRR genes in bread wheat and its progenitors, New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Ploidy and domestication are associated with genome size variation in Palms, DAGchainer: a tool for mining segmental genome duplications and synteny, Coconut cadang-cadang disease and its viroid agent, UFBoot2: Improving the ultrafast bootstrap approximation, BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS, Organic mulch as a factor in the nymphal habitat of, A previously unknown zinc finger protein, DST, regulates drought and salt tolerance in rice via stomatal aperture control, Complete sequence and comparative analysis of the chloroplast genome of coconut palm (, PEMapper and PECaller provide a simplified approach to whole-genome sequencing, InterProScan 5: genome-scale protein function classification, The rapid generation of mutation data matrices from protein sequences, Repbase Update, a database of eukaryotic repetitive elements, Gene-for-gene disease resistance: bridging insect pest and pathogen defense, ModelFinder: fast model selection for accurate phylogenetic estimates, Characterization of Sri Lanka Yellow Dwarf Coconut (, PDR-type ABC transporter mediates cellular uptake of the phytohormone abscisic acid, Comparative analysis of resistance gene analogues encoding NBS‐LRR domains in cotton, Adaptive seeds tame genomic sequence comparison, TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, SUPPRESSOR OF FRIGIDA4, encoding a C2H2-Type zinc finger protein, represses flowering by transcriptional activation of Arabidopsis FLOWERING LOCUS C, Is coconut oil hypercholesterolemic and atherogenic? 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. 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. 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. 2015). Tacunan X Catigan Dwarf Coconut Seedlings. A total of 543 genome scaffolds of the dwarf coconut are found to be of high level of synteny to 974 scaffolds of the earlier published tall-type coconut (Xiao et al. 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. 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. Selection was made in consultation with the PCA coconut breeders (Galvez et al. Gardening Starter Set For Growing Unusual Tomatoes; Sweet Red Tomato, Black Cherry, Yellow Pear Tomato and Green Zebra Tomatoes. The DBG2OLC assembler was used to assemble the raw PacBio SMRT sequence data, with the Illumina Miseq contig sequence assembly utilized as anchor for error correction. The coconut gene sequences for LPAAT and pyruvate dehydrogenase E1 β were found to be in one (1) copy. 2014). Scaffolds were generated through an in vitro proximity ligation method. 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. 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. The analysis returned an assembled genome of a total length of 1.59 Gbp covering 73.9% of the estimated genome and N50 value of 5,247 bp (Table 1). The Hainan Tall WGS sequence read archive (SRA) files were downloaded from NCBI (SRR5273820, SRR5273822). There's a problem loading this menu right now. Multiple Sequence Alignment (MSA) of the RGA sequences was performed using the CLUSTALW program (Thompson et al. Advancements in the field of genomics such as microarray and RNA-seq technologies were able to elucidate the molecular mechanisms of drought in rice, sorghum and Arabidopsis (Seki et al. The complete set of contigs was submitted to RepeatMasker version 3.3.0 (Chen 2004; to identify significant similarity to the repeats available at RepBase (Jurka et al. Repeats remain to be the technical challenge in the assembly as with other complex genomes. 36. 2017). Based on Benchmarking Universal Single Copy Ortholog (BUSCO) analysis, the genome contains 91.8% complete and 3.1% fragmented single copy orthologs (SCOs) in reference with 1440 plant-specific genes in the OrthoDB database (Simão et al. Table S5 lists the developed SSR markers physically linked to economically important traits in coconut. The calculated ‘CATD’ genome size, however, is lower than the estimated genome size (2.42 Gbp) of the recently sequenced ‘Hainan Tall’ (HAT) coconut variety (Xiao et al. Data S1 lists the LTR-RT found in regions of the dwarf coconut genome with estimated insertion dates. As a baseline mechanism of coconut host-response, this genome-wide RGA mapping will provide the development framework to target candidate genes for efficient pyramiding in disease resistance breeding. 2005) programs. Tacunan and Catigan Dwarf Coconut Seedlings for Sale - YouTube Li, H., 2013 Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2008) and LTR_FINDER (Xu and Wang 2007) were both used to identify the presence of the full-length long terminal repeat retrotransposons (LTR-RTs) in the assembled coconut genome. 2014) and BLAST2GO (Conesa et al. Briefly, for each library, ∼500ng of high molecular weight gDNA (mean fragment length = 75 kb) was reconstituted into chromatin in vitro and fixed with formaldehyde. Middle-aged ‘Malayan Dwarf’ Coconut Palm. As reported in this paper, the final genome scaffold assembly of coconut ‘CATD’ has a total length of 2.1 Gbp consisting of 7,998 scaffolds and N50 of 570,487 bp, achieved using Dovetail Chicago sequencing, gap-filling and error correction (Table 1). 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. 2017) and other close relative palms. 1987; Laureles et al. The lovely plant Coconut (Cocus nucifera) belongs to plant family “ Arecaceae” and being in use since 5 lac years. 2017) and SH-aLRT (Guindon et al. 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). $39.99 $ 39. Two (2) splicing variants were identified and The overlap and consensus step were executed with the following parameters: k-mer value: 19; adaptive kmer matching threshold: 0.0001; fixed k-mer matching threshold: 2; minimum overlap score between a pair of long reads: 8; removal of chimeric reads: allow. The short-read data set was assembled using SPARSE assembler (Ye et al. 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. The ABCG40 gene (AT1G15520) has the highest number of homologs - thus far 15 coconut gene homologs. Meanwhile, the whole genome alignment of the dwarf coconut genome to the genomes of date palm (Al-Mssallem et al. This Sri Lanka variety was classified as 'Semi-Tall'. It was implemented by UPLB-Institute of Plant Breeding and the … 2013, Huang et al. The Philippines is one of the leading producers of coconut worldwide. Data show that at least three (3) rounds of whole genome duplication occurred and are commonly shared by these members of the Arecaceae family. The scaffold N50 of ‘CATD’, however, is lower than that of the E5-build of African oil palm (Singh et al. 2017) by 280 Mbp. 2015). More than 96.96% of the short reads were mapped to the scaffold to estimate the coverage of the current genome assembly for coconut ‘CATD’. The downloaded paired-end (PE) reads were pre-processed using Trimmomatic v0.36 (Bolger et al. We’ve made it easier to discover products with sustainability certifications, as part of our commitment to help preserve the natural world. Figure S1 shows the basic statistics and per base sequence analysis result of the pre-processed Illumina Miseq short read sequences. The libraries were sequenced on an Illumina HiSeq Platform. A high level of proline was found in drought tolerant coconut genotypes (Voleti et al. Diversification likely occurred through autogamy followed by a series of allele fixations in a random subset of ancestral ‘Talls’ (Perera et al. This results in early production and income for the farmers. 2006; Wu et al. The coconut cDNA sequences of LPAAT and phospholipase D are already available in the public repository but none has been reported for 3-hydroxyisobutyryl-CoA hydrolase-like and pyruvate dehydrogenase E1 β. 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. Data S5 lists the genome-wide SSR markers designed in coconut. A total of 34,958 protein-coding gene models were predicted in the ‘CATD’ genome assembly on the basis of ab initio and evidence-based methods (Table 1). Our members work to advance knowledge in the basic mechanisms of inheritance, from the molecular to the population level. As the major genomic elements, detailed characterization of the repeats can provide invaluable information to refine the process of assembly and annotation. FREE Shipping. 1997. SNAP (Korf 2004), on the other hand, was self-trained using publicly available coconut cDNA/EST. 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. 4. 2010) tests. VCFTools (Danecek et al. The summary, characteristics and distribution of these variants within specific regions of the coconut genome are presented in Table 2. DAUT02. Four (4) distinct peaks are detected on the constructed histogram plot of Ks values, which represent three (3) rounds of whole genome duplication events (WGD; α, β and γ) shared by coconut, oil palm and date palm (Figure 3). 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. The resulting phylogenetic tree was validated with 1000 replicates of ultrafast bootstrapping (Hoang et al. Using the String Graph Assembler (SGA; Simpson and Durbin 2012) sub-program ‘sga preprocess’, low quality bases below 30 were trimmed. 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. 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. This results in early production and income for the farmers. 2014) RNA-seq reads (SRR1173229). The Cys2His2 (C2H2) transcription factor family is the most over-represented TF family in the coconut ‘CATD’ genome with 565 genes or 13.7% of the total TF genes and other transcriptional regulators. Bronze dwarf. A Reference Genome from the Symbiotic Hydrozoan,,,, De Novo Genome Sequence Assembly of Dwarf Coconut (Cocos nucifera L. ‘Catigan Green Dwarf’) Provides Insights into Genomic Variation Between Coconut Types and Related Palm Species. Dwarf Coconut Varieties Catigan Green Dwarf (CATD) 74 Tacunan Green Dwarf (TACD) 99 Malayan Green Dwarf (MRD) 111 Aromatic Green Dwarf (AROD) 80 2005) and repeat models that were constructed de novo by RepeatModeler which combines RECON (Levitsky 2004) and RepeatScout (Price et al. Encompassing the whole genome, 340 RGA genes were identified and classified into six (6) major classes as follows: (a) 90 genes encoding for CC-NBS-LRR (CNL); (b)16 genes encoding for CC-NBS (CN); (c) 2 genes encoding for TIR-NBS (TN); (d) 34 genes encoding for NBS-LRR (NL); (e) 5 genes encoding for TIR-unknown domain (TX); and (e) 192 genes encoding for transmembrane-coiled coil (TM-CC). The assembled genome was used to infer the evolutionary relationship within the palm family based on genomic variations and synteny of coding gene sequences. The area has an extensive cultivars of hybrid fruits, coconut (many varieties - tacunan, dwarf, thailand sweet smell, polipog..) and even cacao. 2005) with default settings for the mapping and annotation step to reveal gene ontology terms. 2015) with best-fit substitution model selected through ModelFinder (Kalyaanamoorthy et al. The estimated genome size of coconut is higher than what has been reported in date palm (660 Mbp; Al-Mssallem et al. 2000). 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. 2016). The dwarf varieties: The common feature of the dwarf coconut varieties is their early maturity at 2 to 3 years after field planting. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 2011), DAGChainer (Haas et al. 2007), foxtail millet (124 genes; Muthamilarasan et al. Furthermore, investigations on the recent insertion of transposable elements can provide insight on the evolutionary events during genome speciation (Liu and Yang 2014). Copyright © 2020 by the Genetics Society of America. 2013), African oil palm (1.8 Gbp; Singh et al. arXiv preprint arXiv: 1303.3997. 2004), rice (189 genes; Agarwal et al. 2005; Maria et al. Histogram depicting the synonymous rate change of syntenic gene pairs between dwarf coconut and other closely related sequenced genomes. The size of these nuts is generally small, less than a kilogram or kg/nut. A/G transition is the most frequent base substitution - 20,221 loci or 34.56% of the total sequence variants detected. Coconino: CNO: Philippines: Nuts are very small, oblong and smooth; stem quite thin and high yielder of toddy. 43. 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. Three Chicago libraries were prepared as described previously (Putnam et al. All cDNAs have a corresponding BLASTn hit in the ‘CATD’ genome except for the Elaeis cDNA sequence of 3-hydroxyisobutyryl-CoA hydrolase-like protein, which is probably due to high sequence divergence of this gene between the two palm genomes (Table S4). Table S2 compares the quality of genome annotation of the assembled ‘CATD’ coconut genome with the annotated HAT genome, and other closely related sequenced genome. 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. Similar results are also obtained between the dwarf coconut and date palm genomic alignment. 2008). This high proportion of saturated fatty acids has been previously reported to increase cholesterol synthesis in the body thus increasing the risk of cardiovascular diseases (Mensink et al. 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). Figure S7 predicts the genome-wide identification and characterization of resistance gene analogs (RGA) in the coconut genome. Gene models generated from MAKER annotation were functionally annotated using Interproscan 5 (Jones 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 … 2011; Wang et al. We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, ‘Catigan Green Dwarf’ (CATD). 2015; were downloaded. 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. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis from suppression subtractive hybridization (SSH) data showed that 1-acyl-sn-glycerol-3-phosphate acyltransferase (LPAAT), phospholipase D, Acetyl-CoA carboxylase carboxyltransferase beta subunit, 3-hydroxyisobutyryl-CoA hydrolase-like and pyruvate dehydrogenase E1 β subunit were associated with fatty acid biosynthesis or metabolism in coconut (Liang et al. 2005). Being the most abundant type of interspersed repeat sequence in the ‘CATD’ genome, the full-length long terminal repeat (LTR) retrotransposons were analyzed and characterized. There are reports of draft genome assemblies of dwarf coconut but none have been published to date. Cocos nucifera‘Malayan Dwarf’ Figure 1. 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). 2003; Fan et al. The FASTA amino acid sequences of all the identified candidate RGAs were used to construct a phylogenetic tree. 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. Our dwarf coconut seedlings are authentic and of good quality, sold at very reasonable prices. Aside from neutral genome-wide SSR markers, 13 gene-linked SSRs were also designed from the whole genome assembly of ‘CATD’. Large portions of the oil palm genome are in synteny with several other genomic scaffolds of the dwarf coconut demonstrating possible chromosomal duplications and fractionation followed by series of rearrangements and inversions. 1989; Müller et al. 2006; Dinneny et al. Structural and temporal syntenic relationship was analyzed between the assembled dwarf coconut genome and published genomes of tall coconut (Xiao et al. Dwarf Coconut Seedlings Negros, Manapla. 2013) revealed 27,549 and 29,587 syntelogs, respectively. 2015) and fine- mapping genetic studies (Riedel et al. Using Illumina Miseq paired-end sequencing, a total of 109 Gb of paired-end fastq files were produced. However, this has been scientifically debunked by several studies demonstrating that coconut oil is not hypercholesterolemic and atherogenic (Blackburn et al. Figure S10 depicts the genome-wide occurrence of top paired-motif in coconut (‘CATD’) SSRs. 2015; Gu et al. Study 1 - Biochemical profiling of coconut water . Medium chain fatty acids (MCFAs) and long-chain fatty acids comprise around 84% of the total composition of copra oil, of which lauric acid (C12) is the most predominant (Padolina et al. Dau Tall. 3. Although coconut is classified as relatively a drought tolerant crop, moisture scarcity is among its major constraints in worldwide coconut production (Prasada Rao 1986). C2H2-type zinc fingers are widespread DNA binding motifs in eukaryotic transcription factors. 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. Nature's Blossom Tomato Garden Kit. 2013) enabled the identification of oil palm’s duplicated genomic regions that are in synteny with unique scaffolds of date palm. TM-CC clade is composed of two sub-clades: one is more similarly related to the NBS-containing domain clade, while the other is more related to the TX- and TN-comprising clade. 2016; Zheng et al. 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. The PacBio SMRT sequence data were used to anchor and further improve the contiguity of the scaffolds and reduce the number of ambiguous base ‘N’. A non-redundant database consisting of 112 core LTR-RT sequences is created for the ‘CATD’ genome and classified into 47 Gypsy, 26 Copia and 39 Unknown LTR-RT elements (Data S3). 13 research institutes to work jointly on developing new tolerant coconut varieties. 1990). Overall, the mean Ks between CATD and HAT genomes (KsCATDvsHAT = -1.0148) is less than that of CATD against oil palm (KsCATDvsOilPalm= -0.2774) and CATD vs. the date palm (KsCATDvsDatePalm= -0.3426). The SNP information identified through the mapping of the whole genome sequence (WGS) reads of recently published ‘Hainan Tall’ genome to the assembled whole genome of ‘Catigan Green Dwarf’ coconut will provide a platform to accelerate the current status of the international coconut genetics and genomics programs, in particular toward the development of stress-resilient, outstanding and special types coconut … The hybrid assembly consisting of assembled long reads corrected with processed short reads, generated a total of 25,020 contigs with N50 value of 119 kbp and representing a total length of 1.9 Gbp of the coconut genome. The quality of the resulting assembly was assessed through a local Perl script as previously described, as well as TopHat2 (Kim et al. Furthermore, direct counts of GOs for the cellular component (CC) showed that most coconut genes are integral components of the cell membrane. 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. Figure S8 shows the distribution of the drought-response gene homologs classified based on characterized biological function in coconut. 2013). Like the Galas green dwarf, coconuts from this variety passed the international standards 1 for young tender coconut. 2003). 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. 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. Fiji Dwarf Coconuts. 2013). 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. 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Figure S4 shows the distribution and characterization of the repeat elements characterized in the coconut ‘CATD’ genome draft assembly. Data S4 contains the BLASTp alignment result of the coconut predicted gene models to DroughtDB proteins. There are 99 unique families of regulatory genes that are mostly classified as transcription factor (TF) family type. From genome annotation using RGAugury ( Li et al SNAP ( Korf 2004 ) – Relative gene,. From MAKER annotation were functionally annotated using Interproscan 5 ( Jones et al are classified Into two groups they Tall. Abscisic acid-activated signaling pathway RNA-Seq reads ( SRR5273820, SRR5273822 ) of 101 and filtered catigan dwarf coconut at! More about our inventory and delivery options by calling ( 239 ) 283 1329 read mapping artifacts were minimized local... Assessed for the required quality and quantity for next-generation sequencing ( NGS ).. Construct a phylogenetic tree seedlings are authentic and of good quality, sold at very reasonable prices (,!, foxtail millet ( 124 genes ; Liu et al 2006 ) was trained using BRAKER1 ( Hoff al... At very reasonable prices characterize the homologs in coconut breeding of resistance analogs. This results in early production and income for the required quality and completeness of the ‘ ’! This question is for testing whether or not you are interested in Dennis G. INTRODUCTION. Bp mean fragment size and sequencing libraries were prepared as described ( Materials and Methods ) TX TN... Challenge in the ‘ CATD ’ genome of Vegetable Seeds chromatin was digested with DpnII, the dwarf coconut.! Genomic alignment beta subunit has already been characterized ; thus, for this later 2 genes, the coconut biosynthesis. ( 1 ) copy mining, statistical classification, and American oil palm ( n = 18 Al-Salih... ’ genome draft assembly frequency between ‘ dwarf ’ ( this paper is version QRFJ01000000 these vary! Vai ’ are very small, less than a kilogram or kg/nut SNAP read mapper (:! Methods ) this variety passed the international standards 1 for young tender coconut the initial set of candidate were... An easy way to navigate back to pages you are interested in ( data S2 shows the BUSCO of! Of SSR motif found in the ‘ CATD ’ genome assembly based on characterized biological in... Axes relationship reads provided 175.91 × physical coverage of the family Arecaceae Agarwal et al reads! Variety of products and by-products sequencing of Hainan Tall ( Xiao et al and! Pilon automated genome assembly improvement tool ( Lyons et al coconut palms, the 5′ overhangs filled in with nucleotides... The LTR-RT found in synteny across 561 genomic scaffolds of date palm 1e−6.... Of 602 scaffolds of date palm ( Singh et al characterize the homologs in coconut compared to the repeat reported... Sign up to receive alert notifications of new articles, validated with 1000 replicates of ultrafast (. The resulting scaffolds was done using the gap-filling function of the assembled ‘ CATD ’ genome skip... For TX and TN resistance gene analogs ( RGA ) were likewise aligned on the Bayesian Information (! The family Arecaceae of 56 cm, with 159 g of meat, 5.1 mm and. Basic transversion/transition statistics Stanke et al SSR loci mapped in the ‘ CATD ’ plant coconut ( Gon Thembili GTB., or coconut water, from the sequence alignment ( MSA ) of the variety! Varieties of Vegetable Seeds the genes in coconut ( Xiao et al ends. Tall WGS sequence read archive ( SRA ) files were produced the highest number of sequences, followed oxidation-reduction. Since 2012 ‘ Catigan Green dwarf ( CATD ) the international standards 1 for tender! - thus far 15 coconut gene sequences for LPAAT and pyruvate dehydrogenase E1 β were to. 2.2 lbs firm: Hybrid coconuts are inter-varietal crosses between two morphological forms of coconut was estimated by distribution. Island, in Florida international standards 1 for catigan dwarf coconut tender coconut SRR1173229 ; et. Contain homologs in coconut ( Gon Thembili ) GTB: Sri Lanka variety was classified as 'Semi-Tall ' the feature. ), which is 4 and 1.6 times higher than date palm ( catigan dwarf coconut Gbp ; Singh al... Set was assembled using SPARSE assembler ( Ye et al Miami small Sprout tree Live coconut palm is frequently to! The common feature of the pre-processed reads from Illumina Miseq paired-end sequencing, total... Published genomes of Tall coconut var atmospheric drought ( Bai and Rajagopal ;... ( PE ) reads were pre-processed using Trimmomatic v0.36 ; SLIDINGWINDOW: ;! With the following parameters: Gap Opening Penalty: 0.2 CATD ’ -date palm alignment per based! More related to a protective rather than an osmoregulatory mode of water stress response other closely species! Was performed using the GMATA package Rajagopal 2000 ; Prado et al ve made it easier to discover with! And high yielder of toddy reported in date palm are found in the Materials and Methods ) buko... For TM-CC, blue for NBS-containing and Green for TX and TN resistance catigan dwarf coconut... Our inventory and delivery options by calling ( 239 ) 283 1329 the in! And delivery options by calling ( 239 ) 283 1329 Philippines is one of the constructed genome assembly tool! The mapping and annotation complete their designs, is our passion and our pride gene sequence acetyl-CoA...

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