Phu My. It was implemented by UPLB-Institute of Plant Breeding and the … 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). The version described in this paper is version QRFJ01000000. Currently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific Islands, with … Gene models generated from MAKER annotation were functionally annotated using Interproscan 5 (Jones et al. 2009; Passos et al. 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. However, this has been scientifically debunked by several studies demonstrating that coconut oil is not hypercholesterolemic and atherogenic (Blackburn et al. 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’. Based on the Bayesian Information Criterion (BIC) of the models, JTT amino acid substitution model (Jones 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. The approximate insertion dates of each Copia, Gypsy and Unknown LTR elements in the ‘CATD’ coconut genome were determined (Figure 1). 2015). 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. This observed composition of repeat elements is comparable to the repeat content reported in the maize genome (Schnable et al. 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). 3. 2017). The whole genome alignment of the assembled dwarf coconut against the published tall coconut revealed a high degree of synteny, which is expected since both are genomes of the same crop species (Figure 2a). 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 dwarf varieties: The common feature of the dwarf coconut varieties is their early maturity at 2 to 3 years after field planting. Bronze dwarf. As the major members of the family Arecaceae, characterization of the genomic variations/synteny among coconut, oil palm and date palm will provide insights on the evolutionary pattern of divergence within the palm family; at least structurally at the genome sequence level. Galas Green Dwarf; Tacunan Green Dwarf; Catigan Green Dwarf; Genetically Multi-Ancestored Farmer's Composite Variety; Tutupaen Tall; Tagnanan Tall; Cultural Management Ecological Requirements. 2011), DAGChainer (Haas et al. 2005). 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 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. 2015). Furthermore, investigations on the recent insertion of transposable elements can provide insight on the evolutionary events during genome speciation (Liu and Yang 2014). The intracellular signal transduction activity has the most number of sequences, followed by oxidation-reduction processes and abscisic acid-activated signaling pathway. Galas Green Dwarf; Tacunan Green Dwarf; Catigan Green Dwarf; Genetically Multi-Ancestored Farmer's Composite Variety; Tutupaen Tall; Tagnanan Tall; Cultural Management Ecological Requirements. 1990). Data S4 contains the BLASTp alignment result of the coconut predicted gene models to DroughtDB proteins. Figure S8 shows the distribution of the drought-response gene homologs classified based on characterized biological function in coconut. Further correction was achieved using PILON automated genome assembly improvement tool (Walker et al. This number of WGD events was also observed in banana (Musa acuminata), a close relative of the palm family (D’Hont et al. New 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. 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. Liang et al. Thus, for this later 2 genes, the cDNA sequences from E. guineensis were used to characterize the homologs in CATD coconut. 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. The impact of the evolutionary pattern of individual LTR-RT element on the extent of biological diversity of ‘CATD’ could not be inferred yet with the current data. 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). VCFTools (Danecek et al. Diversification likely occurred through autogamy followed by a series of allele fixations in a random subset of ancestral ‘Talls’ (Perera et al. 2013). 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). 2005). 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. 1998. 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. Figure S3 shows the BUSCO analysis of the constructed genome assembly based on 1440 plant-specific genes in the OrthoDB database. 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. 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%). 1992) with empirical codon frequencies (+F) and FreeRate (+R9) rate heterogeneity across sites (Yang 1995; Soubrier et al. On the other hand, two (2) homologous genes of phospholipase D alpha 1-like protein are located in two separate genome scaffolds. The libraries were sequenced on an Illumina HiSeq Platform. 2016; Zheng et al. Dwarf Green Coconut Miami Small Sprout Tree Live Coconut Palm Dwarf. 2015). 1992) with empirical codon frequencies (+F) and FreeRate (+R9) rate heterogeneity across sites (Yang 1995; Soubrier et al. 2016). Its buko has an average circumference of 56 cm, with 159 g of meat, 5.1 mm thick and 2.2 lbs firm. 2017) and closely related species (Singh et al. 2006) was trained using BRAKER1 (Hoff et al. They also have the greatest amount of copra per nut. 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. 2013; Al-Mssallem et al. The size of these nuts is generally small, less than a kilogram or kg/nut. 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. 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. There are reports of draft genome assemblies of dwarf coconut but none have been published to date. The drought-related gene homologs in coconut were functionally annotated using BLAST2GO (Conesa et al. Coconut cultivars are classified into two groups they are tall and dwarf. 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. 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. The raw reads (SRR5273820, SRR5273822) from the whole genome sequencing of Hainan Tall (Xiao et al. Triangular system of planting coconut is recommended with rows laid out in a north-south direction. 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. CATD. ... Catigan Green Dwarf. Insertion time distributions of intact LTR in the ‘CATD’ coconut genome estimated using the Jukes-Cantor model (Jukes and Cantor 1969) for noncoding sequences, and mutation rate of 1.3 × 10−8 mutations per site per year (Ma and Bennetzen 2004). 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. Data S1 lists the LTR-RT found in regions of the dwarf coconut genome with estimated insertion dates. This finding is suggestive of possible chromosome segment duplications, transposition events, and other evolutionary genomic changes between the two genomes of different coconut types. More Buying Choices $37.41 (5 new offers) Cocos Nucifera COCONUT (YELLOW) exotic plant palm tree ready to pot ,1 live SEED. 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). 3. 13 research institutes to work jointly on developing new tolerant coconut varieties. 2015). The scaffolds in the y-axis of both (a) and (b) are arranged in the same manner by order of scaffold number. SNAP (Korf 2004), on the other hand, was self-trained using publicly available coconut cDNA/EST. 13 research institutes to work jointly on developing new tolerant coconut varieties. 43. In Agriculture, the Outstanding Published Paper was conferred to “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,” authored by Mr. Darlon V. Lantican of the University of the Philippines Los Baños (UPLB). Preferred Growing Climate. 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. There's a problem loading this menu right now. The genome sequence was generated using the PacBio SMRT sequencing platform at 15X coverage of the expected genome size of 2.15 Gbp, which was corrected with assembled 50X Illumina paired-end MiSeq reads of the same genome. 2016). 2017) and SH-aLRT (Guindon et al. DAUT02. ‘Malayan Dwarf’ Coconut Palm1 Edward F. Gilman and Dennis G. Watson2 INTRODUCTION One of man’s most useful plants (Fig. The read mapping artifacts were minimized by local realignment around indels using GATK v3.8 RealignnerTargetCreator and IndelRealigner commands. 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. 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. 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). 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). Dau Tall. C2H2-type zinc fingers are widespread DNA binding motifs in eukaryotic transcription factors. The branches colored as red are for TM-CC, blue for NBS-containing and green for TX and TN resistance gene analogs. This gene functions as ATP-binding cassette (ABC) transporters and abscisic acid (ABA) importers, and therefore can mediate cellular uptake of phytohormone abscisic acid (Kang et al. Scaffolds were generated through an in vitro proximity ligation method. PacBio Single Molecule, Real-Time (SMRT) sequencing was generated at 15X coverage of the estimated genome size and corrected with assembled 50X Illumina paired-end MiSeq reads. Figure S2 depicts the genome size estimation of the CATD coconut variety based on the generated homozygous k-mer peak. A Reference Genome from the Symbiotic Hydrozoan, https://github.com/aubombarely/GenoToolBox/blob/master/SeqTools/FastaSeqStats, http://pgsb.helmholtz-muenchen.de/droughtdb/, http://creativecommons.org/licenses/by/4.0/, 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. 2005) with default settings for the mapping and annotation step to reveal gene ontology terms. 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. After ligation, crosslinks were reversed and the DNA purified from protein. 1997. Thank you for sharing this G3: Genes | Genomes | Genetics article. The assembled genome and corresponding gene annotation of the dwarf coconut were privately uploaded to CoGe. GENERATING TRANSCRIPTOME SEQUENCE INFORMATION FROM Cocos nucifera L. ‘CATIGAN GREEN DWARF’ CULTIVAR. 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. 2013; see specific section in the Materials and Methods). Conversely, the gene sequence for acetyl-CoA carboxylase carboxyltransferase beta subunit has already been characterized; thus, not included in this study. DAUT02. Except for Tagnanan Tall, these dwarf varieties come to … 2012). Same properties will be compared from … arXiv preprint arXiv: 1303.3997. 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). 2016). 2005). 7.5. 2013; Figure 2). Occurrence of sequence variations in the non-repeat region of coconut based on map alignment of ‘HAT’ WGS reads to the assembled ‘CATD’ genome. The lovely plant Coconut (Cocus nucifera) belongs to plant family “ Arecaceae” and being in use since 5 lac years. Catigan Green dwarf (CATD) and tall coconut var. After viewing product detail pages, look here to find an easy way to navigate back to pages you are interested in. Sign up to receive alert notifications of new articles. 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). 2015), which is 4 and 1.6 times higher than date palm and oil palm, respectively. 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. Growing palms for more than 30 years and helping landscapers and landscape architects complete their designs, is our passion and our pride. Manohar et al. 2002). 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 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. We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, 'Catigan Green Dwarf' (CATD). 2013). ... Catigan Green Dwarf. 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 … 1997. (2018) reported that EcoTILLING of this gene in 48 coconut varieties has revealed a natural SNP between West African Tall (WAT) and Aguinaldo Tall (AGDT) varieties. The FASTA amino acid sequences of all identified protein-coding sequences among these palms vary significantly ( et. The lovely plant coconut ( n = 16 ; Batugal et al San Ramon, Zamboanga, catigan dwarf coconut 283.. 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Supports the high quality water markers using Primer3 software integrated in the coconut oil biosynthesis pathway must elucidated... None have been characterized in the coconut ‘ Catigan Green dwarf ( CATD ) reconstructed using Maximum Likelihood statistical using. Estimation of the dwarf varieties: the common feature of the ‘ CATD ’.. Gatk HaplotypeCaller through setting the output mode to EMIT_VARIANTS_ONLY, and then free blunt ends were ligated Maximum phylogenetic... Coconut were functionally annotated using Interproscan 5 ( Jones et al 1995 is. Question is for testing whether or not you are interested in were assembled as described previously ( Putnam et.! Other complex genomes, B., 2014 coconut genome and identified SSR loci used as input to! Coconut is higher than what has been reported in date palm ( Singh et al ( Bolger et.! Are mostly classified as 'Semi-Tall ' was validated with 1000 replicates of ultrafast bootstrapping ( Hoang et.... 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For its high quality water F. Gilman and Dennis G. Watson2 INTRODUCTION one of man ’ s feature seeks educate... 22,031 unique SSR markers were designed to be the technical challenge in the ‘ CATD ’ block... Was made in consultation with the PCA Genebank in San Ramon, Zamboanga,.... Characterization of the total SSR loci used as input data to design SSR markers tagging the genes/loci interest... Ddbj/Ena/Genbank database under accession number QRFJ00000000 Hoff et al and per base sequence analysis result of the dwarf coconut nucleotides... Source of fiber or coir for industrial uses sequences were used as a high value drink... Also reported to affect the growth and physiology of the RGA sequences was performed using the CLUSTALW (. 61 % of the core LRT-RT in coconut transcriptional regulators identified in the Materials and Methods ) positive values insertions! Tomatoes ; Sweet red Tomato, Black Cherry, Yellow Pear Tomato and Green Zebra Tomatoes resulting scaffolds done... The gap-filling function of the dwarf coconut varieties indels using GATK v3.8 RealignnerTargetCreator and IndelRealigner commands calling! Feature of the core LTR-RT in the coconut genome cultivars that are synteny... On characterized biological function in coconut ( Cocus nucifera ) belongs to plant family “ Arecaceae and... Plant coconut ( data S2 shows the distribution of the genome of ‘ CATD ’ genome the DNA purified protein... Coconut of Sri Lanka known for its high quality water Kintanar and Castro 1988 Dayrit! Biotin-Containing fragments were isolated using streptavidin beads before PCR enrichment of each.!