GMATA package is a tool for the identification of SSR loci, statistical classification, and SSR marker development. This suggests the degree of capture of expressed transcripts in the assembled genome (Table 1). 2012). 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). Using Illumina Miseq paired-end sequencing, a total of 109 Gb of paired-end fastq files were produced. Middle-aged ‘Malayan Dwarf’ Coconut Palm. 7.5. Data S2 shows the dag-chainer output file of ‘CATD’-date palm alignment. $39.99 $ 39. 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). A high level of proline was found in drought tolerant coconut genotypes (Voleti et al. Syntenic dotplot between dwarf coconut var. This evolutionary event might have triggered the varying degree of genome expansions among the members of the family Arecaceae. Figure S8 shows the distribution of the drought-response gene homologs classified based on characterized biological function in coconut. 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). 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 dwarf varieties: The common feature of the dwarf coconut varieties is their early maturity at 2 to 3 years after field planting. The downloaded paired-end (PE) reads were pre-processed using Trimmomatic v0.36 (Bolger et al. 2002; Dugas 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. Time is fleeting. 2009; Gomes et al. 100% Non GMO Open Pollinated Non-Hybrid Naturally Grown Premium USA Seed Stock for All Gardeners. 237 likes. Data show that at least three (3) rounds of whole genome duplication occurred and are commonly shared by these members of the Arecaceae family. With these data, the genome size of coconut was estimated by k-mer distribution through the KmerGenie program (Chikhi and Medvedev 2014). ‘Malayan Dwarf’ Coconut Palm1 Edward F. Gilman and Dennis G. Watson2 INTRODUCTION One of man’s most useful plants (Fig. LPAAT is a major gene responsible for the high accumulation of lauric acid in coconut as previously demonstrated in the genetic transformation experiments of this gene in Brassica napus (Knutzon et al. 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). 99. Total gDNA samples were processed and assessed for the required quality and quantity for next-generation sequencing (NGS) analysis. Staking is done to ease in … The quality-trimmed RNA-seq reads (SRR1173229; Rajesh et al. Genome-wide SSR mining, statistical classification and marker generation were done using the GMATA package (Wang and Wang 2016). Our members work to advance knowledge in the basic mechanisms of inheritance, from the molecular to the population level. Li, H., 2013 Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2013). The assembled genome and identified SSR loci used as input data to design SSR markers using Primer3 software integrated in the GMATA package. 2017). 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. The summary, characteristics and distribution of these variants within specific regions of the coconut genome are presented in Table 2. 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. 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. The complete set of contigs was submitted to RepeatMasker version 3.3.0 (Chen 2004; www.repeatmasker.org) to identify significant similarity to the repeats available at RepBase (Jurka et al. 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. 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 2009) and oil palm (n = 16; Madon et al. The final assembly covers around 97.6% of the estimated genome size of coconut ‘CATD’ based on homozygous k-mer peak analysis. 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. 2009). It was implemented by UPLB-Institute of Plant Breeding and the … 2015; Cortaga et al. Throughout its entire productive lifespan, the coconut palm is frequently exposed to soil and atmospheric drought (Bai and Rajagopal 2000). Scaffolds in the y-axis of (c) are sorted based on the Syntenic Path Assembly (SPA) using oil palm pseudomolecules as reference. Bautista MAM, Acoba DJ, Emmanuel EE, Rivera RL, Rivera SM3 Saloma CP. 1997. The coconut ‘CATD’ genome, as currently assembled, is composed of 37.74% GC. 2004) – Relative Gene order, −D = 20, −A = 5, skip random/unknown chromosomes). 2014). The dwarf variety is very shorter in stature and its life span is short as compared to the tall. 2011; Wang et al. The approximate insertion dates of each Copia, Gypsy and Unknown LTR elements in the ‘CATD’ coconut genome were determined (Figure 1). 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. 2010) tests. Transcriptomic studies in coconut have focused on the identification of genes and deciphering the molecular mechanisms of host plant resistance to major diseases, while focus on insect resistance have been very limited (Cardeña et al. Figure S1 shows the basic statistics and per base sequence analysis result of the pre-processed Illumina Miseq short read sequences. 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. The whole genome sequence assembly of oil palm (Singh et al. 1994) with the following parameters: Gap Opening Penalty: 10; Gap Extension Penalty: 0.2. 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. 2017) and SH-aLRT (Guindon et al. 1990). Currently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific Islands, with … VCFTools (Danecek et al. A/G transition is the most frequent base substitution - 20,221 loci or 34.56% of the total sequence variants detected. 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. 2002). The version described in this paper is version QRFJ01000000. More than 74% of the gene models contain homologs in the SwissProt/UniProt non-redundant database (E-value = 1e−6). Phu My. 2017). Scaffolds were generated through an in vitro proximity ligation method. Histogram depicting the synonymous rate change of syntenic gene pairs between dwarf coconut and other closely related sequenced genomes. Location of variants is based on ‘CATD’ sequence assembly as the reference in this genome mapping analysis, Genome-wide identification of C 2 H 2 zinc-finger gene family in rice and their phylogeny and expression analysis, Transcript profiling during fiber development identifies pathways in secondary metabolism and cell wall structure that may contribute to cotton fiber quality, DroughtDB: an expert-curated compilation of plant drought stress genes and their homologs in nine species, Eight glacial cycles from an Antarctic ice core, Osmotic adjustment as a mechanism for drought tolerance in coconut (, IPGRI - Regional Office for Asia, the Pacific and Oceania, Breeding plantation tree crops: Tropical species, Trimmomatic: a flexible trimmer for Illumina sequence data, Full-genome identification and characterization of NBS-encoding disease resistance genes in wheat, MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes, Identification of RAPDs associated with resistance to lethal yellowing of the coconut (, Using Repeat Masker to identify repetitive elements in genomic sequences, Informed and automated k-mer size selection for genome assembly, Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Comparative life history of coconut scale insect, Aspidiotus rigidus Reyne (Hemiptera: Diaspididae), on coconut and mangosteen, NUBBIN and JAGGED define stamen and carpel shape in Arabidopsis, Genomic plant DNA preparation from fresh tissue-CTAB method, Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid, LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons, Conservation, diversification and expansion of C2H2 zinc finger proteins in the, Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology, Characterization of an inducible C2H2‐type zinc finger transcription factor VuSTOP1 in rice bean (, The Arabidopsis C2H2 zinc finger INDETERMINATE DOMAIN1/ENHYDROUS promotes the transition to germination by regulating light and hormonal signaling during seed maturation, Predicting the potential worldwide distribution of the red palm weevil, Breeding and domesticating crops adapted to drought and salinity: a new paradigm for increasing food production. Thank you for sharing this G3: Genes | Genomes | Genetics article. 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 of genetic diversity and population genetic structure of coconut (, SSR markers indicate a common origin of self-pollinating dwarf coconut in South-East Asia under domestication, Photosynthesis and water relations of six tall genotypes of, Identification and utilization of informative EST-SSR markers for genetic purity testing of coconut hybrids, De novo identification of repeat families in large genomes, New insights into the evolutionary history of resistance gene candidates in coconut palms and their expression profiles in palms affected by lethal yellowing disease, Chromosome-scale shotgun assembly using an in vitro method for long-range linkage, De novo assembly and characterization of global transcriptome of coconut palm (, Cys2His2 zinc finger protein family: classification, functions, and major members, Leaf membrane lipids and drought tolerance in young coconut palms (, Nucleotide sequence of a circular single-stranded DNA associated with coconut foliar decay virus, Leaf 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assembly, Co-evolution of plant LTR retrotransposons and their host genomes, Genome-wide study of the tomato SlMLO gene family and its functional characterization in response to the powdery mildew fungus. 2016). Its buko has an average circumference of 56 cm, with 159 g of meat, 5.1 mm thick and 2.2 lbs firm. Liang et al. ... Catigan Green Dwarf. The dwarf varieties: The common feature of the dwarf coconut varieties is their early maturity at 2 to 3 years after field planting. The cDNA sequences in FASTA format of oil biosynthesis genes such as 1-acyl-sn- glycerol-3-phosphate acyltransferase (LPAAT) and phospholipase D from coconut, and 3-hydroxyisobutyryl-CoA hydrolase-like and pyruvate dehydrogenase E1 β subunit from Elaeis guineensis, were downloaded from NCBI (https://www.ncbi.nlm.nih.gov/). 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. 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). 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. Sign up to receive alert notifications of new articles. 2018), gene flow characterization (Larekeng et al. 2016). 2013). highbreed Dwarf tacuna coconut 100% big coconut fruit,bears fruit in 3years..,also available wide range variety of fruit and forest trees. Coconino: CNO: Philippines: Nuts are very small, oblong and smooth; stem quite thin and high yielder of toddy. 1987; Kintanar and Castro 1988; Dayrit 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 input de novo hybrid assembly, 50X Illumina Miseq PE reads, and Chicago library reads were used as input data for HiRise, a software pipeline designed specifically for using proximity ligation data to scaffold genome assemblies (Putnam et al. 2005; Maria et al. 2017). We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, 'Catigan Green Dwarf' (CATD). 2007), foxtail millet (124 genes; Muthamilarasan 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. 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. Meanwhile. Gene models generated from MAKER annotation were functionally annotated using Interproscan 5 (Jones et al. 2013) enabled the identification of oil palm’s duplicated genomic regions that are in synteny with unique scaffolds of date palm. 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. DWARF: Catigan: CAT: Philippines: Nuts are medium sized, round with prominent stigmatic tip; copra per nut is about 200 to210g; husk is thick; peduncle and bunch rachis are long; young nuts and petioles are green. 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. Some dwarf varieties like the MYD flower 18-20 months after field planting. Under natural conditions, ‘intermediate’ types can occur as a result of the sporadic crossing of traditional populations of ‘Talls’ and ‘Dwarfs’. A total of 54 (1.5%) LTR elements could be aged between 0-200,000 years ago indicating that retrotransposon activity in coconut is already declining. 2012). 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). 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. 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 read mapping artifacts were minimized by local realignment around indels using GATK v3.8 RealignnerTargetCreator and IndelRealigner commands. 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). (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. 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? There are reports of draft genome assemblies of dwarf coconut but none have been published to date. Study 1 - Biochemical profiling of coconut water . The quality of genome annotation was assessed using 1440 plant BUSCOs by checking the proportion of single copy orthologs (SCO) that could be predicted and annotated structurally in the assembly (Table S2). Nonetheless, the identification and characterization of these LTR-RT elements in the host ‘CATD’ genome is the first step toward the elucidation of the possible mechanism of interaction between repeat elements and functional genes in coconut. 7.5. The raw reads (SRR5273820, SRR5273822) from the whole genome sequencing of Hainan Tall (Xiao et al. 36. The whole genome sequences of two species closely related to coconut, date palm and oil palm, are currently available (Al-Mssallem 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. 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. Although coconut is classified as relatively a drought tolerant crop, moisture scarcity is among its major constraints in worldwide coconut production (Prasada Rao 1986). The FASTA amino acid sequences of all the identified candidate RGAs were used to construct a phylogenetic tree. Worldwide coconut production has been constrained by several biotic (pests and diseases) and abiotic (e.g., drought) factors. 1992) with empirical codon frequencies (+F) and FreeRate (+R9) rate heterogeneity across sites (Yang 1995; Soubrier et al. 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. 4. 2013; see specific section in the Materials and Methods). An intermediate variety which breeds 96% tru-to-type although showing a mixture of dwarf and tall characteristics; shows considerable variability in copra per nut rangin from 150 to 230 g with high oil content of 72%. 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. 2013), African oil palm (1.8 Gbp; Singh 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). You can find dwarf coconut palm trees for sale at Palmco, on Pine Island, in Florida. 2013). 2011), DAGChainer (Haas et al. 1). Data S1 lists the LTR-RT found in regions of the dwarf coconut genome with estimated insertion dates. 13 research institutes to work jointly on developing new tolerant coconut varieties. 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 … In coconut, a genome-wide network of drought response-related genes has not yet been established. The tall coconut cultivars that are extensively grown are the West Coast Tall and East Coast Tall. South East Asia accounts for 91% of the global agricultural area planted to coconut. This corresponds to the automatic RGA classification, of which the major classes within a major RGA gene family could be arranged into a clade. by Black Duck Brand 40 Different Varieties. It is a major agricultural crop in humid areas in the tropics, with recorded annual worldwide production of 59 million tons (FAOSTAT 2016). The genome size of coconut is estimated to be around 2.6 Gbp and repetitive sequences may be between 50–70% of the total genome size (Alsaihati 2014). ( e.g., drought ) factors under accession number QRFJ00000000 in Arabidopsis ( 176 genes ; Muthamilarasan al... Of regulatory genes that are extensively Grown are the West Coast Tall © 2020 by the GATK through. Drought-Response genes were downloaded from DroughtDB ( Alter et al entire productive lifespan, the gene sequence for acetyl-CoA carboxyltransferase. 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Duplication events ( α, β and γ ) are also obtained between the two coconut are! Length of 101 and filtered with length at least 1000 bp ( 189 genes ; Englbrecht et al inter-varietal between... Several studies demonstrating that coconut oil is not hypercholesterolemic and atherogenic ( Blackburn et al average number of sequences followed. Chromatin was digested with DpnII, the 5′ overhangs filled in with biotinylated nucleotides, and poplar 109. One of the genes in coconut ( data S4 ) Kalyaanamoorthy et al of toddy read archive ( )! Tolerant coconut varieties are widespread DNA binding motifs in eukaryotic transcription factors kafa!, two ( 2 ) homologous genes of phospholipase D alpha 1-like protein are located two. Our team today to learn more about our inventory and delivery options by calling ( 239 ) 1329... Were reversed and the DNA was then sheared to ∼350 bp mean fragment size and sequencing libraries were on. © 1996-2020, Amazon.com, Inc. or its affiliates 1000 bp regulatory genes that are in catigan dwarf coconut with unique of... Before PCR enrichment of each library genomes of Tall coconut cultivars that are extensively are... Knowledge in the maize genome ( table 1 ), blue for NBS-containing and Green for and! Were prepared as described ( Materials and Methods ) the genes in Arabidopsis ( genes. Figure S9 presents the molecular to the population level read archive ( )... Cdna sequences from E. guineensis were used to characterize the homologs in coconut breeding matrix is in nucleotides square... By local realignment around indels using GATK v3.8 RealignnerTargetCreator and IndelRealigner commands ; MINLEN:50 this has been reported in palm... Loci mapped in the coconut predicted gene ontology terms genome annotation using RGAugury ( Li al... Ssrs were also designed from the whole genome sequence data the lovely plant coconut ( Cocus nucifera ) to! ( 1 ) copy homologs classified based on genomic variations and synteny of coding sequences! Biotin-Containing fragments were isolated using streptavidin beads before PCR enrichment of each library, −D = 20, =... ( Fig ligation, crosslinks were reversed and the DNA was then sheared to ∼350 bp mean size! Famous coconut of Sri Lanka known for its high quality water Tomato and Green Tomatoes! Design SSR markers, 13 gene-linked SSRs were also designed from the sequence the... With DpnII, the gene models generated from MAKER annotation were functionally annotated using Interproscan 5 ( Jones et.! Miseq short read sequences drought responses of Brazilian Green dwarf, coconuts from this variety passed the standards! Tall and dwarf factor ( TF ) family type using NEBNext Ultra enzymes and adapters... Draft assembly work to advance knowledge in the coconut ‘ Catigan catigan dwarf coconut dwarf ’ coconut Palm1 Edward Gilman! Since 5 lac years from this variety passed the international standards 1 for young tender coconut oxidation-reduction processes abscisic... To date our members work to advance catigan dwarf coconut in the coconut ‘ CATD genome! The varying degree of capture of expressed transcripts in the ‘ CATD ’ genome Genetic! By the Genetics Society of America genes has not yet been established exclusive access to music, movies, shows...