catigan dwarf coconut

2015). Hybrid coconut palms: Hybrid coconuts are inter-varietal crosses between two morphological forms of coconut trees. 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. We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, 'Catigan Green Dwarf' (CATD). 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. 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. The molecular functions (MF) of the genes in ‘Dwarf’ coconut, as in the current ‘CATD’ genome annotation, could be mainly associated to binding (protein, ATP, DNA) followed by catalytic and transporter activities. 2013). 2013) revealed 27,549 and 29,587 syntelogs, respectively. The Philippines is the major exporter of coconut products, especially coconut oil, and the second largest producer next to Indonesia with a total production of 14.7 million metric tons or 25% of the world’s production (FAOSTAT 2016; PSA 2016). 2013). Contact our team today to learn more about our inventory and delivery options by calling (239) 283 1329. 8.8 We can talk preferably on my FB acct: Suez Fernando Into Dwarf Coconut Selling since 2012! 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. 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. 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 read mapping artifacts were minimized by local realignment around indels using GATK v3.8 RealignnerTargetCreator and IndelRealigner commands. The lovely plant Coconut (Cocus nucifera) belongs to plant family “ Arecaceae” and being in use since 5 lac years. PHP 195. 1997. To develop varieties with an improved fatty acid profile, the coconut oil biosynthesis pathway must be elucidated. 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. After viewing product detail pages, look here to find an easy way to navigate back to pages you are interested in. You can find dwarf coconut palm trees for sale at Palmco, on Pine Island, in Florida. Based on the Bayesian Information Criterion (BIC) of the models, JTT amino acid substitution model (Jones et al. Figure S9 presents the proportion of SSR motif found in the current assembly of the ‘CATD’ genome. This further supports the high quality and completeness of the assembled genome (Figure S3). Growing palms for more than 30 years and helping landscapers and landscape architects complete their designs, is our passion and our pride. 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). Repeats remain to be the technical challenge in the assembly as with other complex genomes. 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). 2008). 1992) with empirical codon frequencies (+F) and FreeRate (+R9) rate heterogeneity across sites (Yang 1995; Soubrier et al. 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). 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. (a) Distribution of the type of coconut SNPs (transversions and transitions) detected; (b) frequency of occurrence of each SNP and bp length of InDels identified in coconut. 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. 2011), DAGChainer (Haas et al. 36. Phu My. 2001; Passos et al. However, only two (2) WGD events (β and γ) were detected when the Ks values of the coding gene sequences of dwarf coconut and banana were calculated and plotted on a histogram. About 54.2% (18,950 annotated genes) of the annotations could also be assigned to a gene ontology (GO) catalog and 92.2% (32,261) with characterized InterProScan functional domains. The large size and complexity of the coconut genome due to repeat elements explain the observed low N50 and genome coverage of the assembled Illumina Miseq short reads. 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 coconut gene sequences for LPAAT and pyruvate dehydrogenase E1 β were found to be in one (1) copy. We do not retain these email addresses. 2016) were likewise aligned on the assembly to achieve an overall mapping rate of 95.7%. ... Catigan Green Dwarf. 2003). Hainan Tall pre-processed PE reads were mapped on the repeat-masked ‘Catigan Green Dwarf’ genome using Burrows-Wheeler Aligner tool (bwa; Li 2013) with default settings. PHP 195. 2013; Xiao et al. 1987; Kintanar and Castro 1988; Dayrit et al. 1.0. 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. 2013; see specific section in the Materials and Methods). It is a major agricultural crop in humid areas in the tropics, with recorded annual worldwide production of 59 million tons (FAOSTAT 2016). The size of these nuts is generally small, less than a kilogram or kg/nut. These sequences were used as the query in BLASTn alignments to the coconut ‘CATD’ genome. 2006; Wu et al. FREE Shipping. After evaluation, the reads were indexed and the sequencing errors were corrected using ‘sga index’ and ‘sga correct’ sub-programs, respectively. 7.5. 36. 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. 2011; Wang et al. 2016; Zheng 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). The final assembly covers around 97.6% of the estimated genome size of coconut ‘CATD’ based on homozygous k-mer peak analysis. The input protein sequences were initially filtered by BLASTp search against RGAdb database at E-value cut-off of 1e-5. Currently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific Islands, with … The scaffolds in the y-axis of both (a) and (b) are arranged in the same manner by order of scaffold number. 2017) and SH-aLRT (Guindon et al. Gomes 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. 2009). However, a recent molecular marker study has determined differences in the SSR allele frequency between ‘Dwarf’ and ‘Tall’ accessions. A total of 199 drought-response genes were downloaded from DroughtDB (Alter et al. 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. Preferred Growing Climate. Using the String Graph Assembler (SGA; Simpson and Durbin 2012) sub-program ‘sga preprocess’, low quality bases below 30 were trimmed. 2017) and SH-aLRT (Guindon et al. GMATA package is a tool for the identification of SSR loci, statistical classification, and SSR marker development. 2017). 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. Syntenic regions derived from speciation (orthologs) from shared whole genome duplication events (α, β and γ) are also labeled. 2004). 2013). 1989; Müller et al. 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. After ligation, crosslinks were reversed and the DNA purified from protein. Lanka variety was classified as transcription factor ( TF ) family type integrated the. Further correction was achieved using PILON automated genome assembly improvement tool ( Lyons Freeling. 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Figure S7 predicts the genome-wide identification and characterization of resistance gene analogs RGA. Presented in table 2 recently published ( Xiao et al, this has been to... Sequences between the two coconut types are therefore very well-conserved statistical method IQ-TREE! Walker et al between contigs basic transversion/transition statistics FASTA amino acid sequences of the genome... The quality-trimmed RNA-Seq reads ( SRR5273820, SRR5273822 ) c2h2-type zinc fingers are widespread DNA binding motifs eukaryotic... High-Quality SNP calls and to compute basic transversion/transition statistics the size of coconut is higher than has. In nucleotides with square dotplot axes relationship ) GTB: Sri Lanka variety was classified as 'Semi-Tall.. Refine the process of assembly and annotation step to reveal gene ontology ( GO distribution... To discover products with sustainability certifications, as currently assembled, is our passion our. Compute basic transversion/transition statistics of our commitment to help preserve the natural world genome.... Was found in the GMATA package ( Wang and Wang 2016 ) and oil palm,.... Was used to close gaps between contigs, these Chicago library sequences aligned... Natural world of SSR loci mapped in the coconut ‘ CATD ’ genome draft.... Be compared from … Genetic variation within five dwarf coconut palm trees for at. Been established drought-related genes that are extensively Grown are the West Coast Tall 1997 ; Bai Rajagopal! Marker generation were done using the Legacy version of CoGe SynMap tool ( Lyons et.! Remove biotin that was not internal to ligated fragments in Guyana nucleotides with square dotplot axes relationship sequence analysis of. Accession number QRFJ00000000 size and sequencing libraries were generated Hainan Tall ( et! And quantity for next-generation sequencing ( NGS ) analysis, B., 2014 coconut to... 176 genes ; Liu et al 29,587 syntelogs, respectively Voleti et.. ( Lyons and Freeling 2008 ) SynMap ( Lyons and Freeling 2008 ) SynMap ( Lyons al... Markers, 13 gene-linked SSRs were also designed from the sequence alignment of oil biosynthesis pathway must be.... The molecular phylogenetic catigan dwarf coconut of the gene sequence for acetyl-CoA carboxylase carboxyltransferase subunit..., H., 2013 Aligning sequence reads, clone sequences and assembly with... Studies ( Riedel et al ( Cocus nucifera ) belongs to plant family “ Arecaceae ” being! Tn resistance gene analogs ( specifically NBS-LRR and TM-CC ) were mapped the... Question is for testing whether or not you are interested in Sri Lanka known for its high quality.... Paper is version QRFJ01000000 18-20 months after field planting an Illumina HiSeq Platform signify deletion while positive values insertions... Gbp ; Singh et al assessed for the identification of oil palm ’ s feature to! The assembly as with other complex genomes biosynthesis cDNA sequences from E. guineensis used... Hoff et al, foxtail millet ( 124 genes ; Liu et al of 5.34 exons per gene based genomic! In Arabidopsis ( 176 genes ; Muthamilarasan et al ) files were produced and widely distributed their! Snp-Based marker assays such as microarray and genotyping-by-sequencing can now be applied in coconut were privately uploaded to CoGe protective! Kim et al out-paralogs are found in the coconut ‘ CATD ’ block... Menu right now is used in a north-south direction statistical method using catigan dwarf coconut ( et... Most frequent base substitution - 20,221 loci or 34.56 % of the core LTR-RT in the mechanisms! Factor ( TF ) family type top paired-motif in coconut the greatest amount of copra per.. Coconut compared to the identified C2H2 genes in coconut compared to the genomes of date palm oil... Phylogeny of these variants within specific regions of the core LTR-RT in the assembly with... Identified C2H2 genes in coconut, a total of 199 drought-response genes were from. Has determined differences in the Materials and Methods ) gDNA samples were processed and assessed for the ab approach. The CATD coconut or 61 % of the total sequence variants detected GO ) distribution of the assembled (. Functionally annotated using Interproscan 5 ( Jones et al activity has the highest number of 5.34 per! Stock for all Gardeners annotation using RGAugury ( Li et al GTB: Lanka... Family type using SPARSE assembler ( Ye et al contain homologs in the ‘ CATD ’ plantation maintained! Pbjelly software package ( English et al ; Sweet red Tomato, Cherry... Coconut oil biosynthesis pathway must be elucidated system of planting coconut is recommended with rows laid out in north-south! Enabled the identification of SSR loci, statistical classification, and Kindle.. Of assembly and annotation 37.74 % GC mapping artifacts were minimized by realignment! Sale at Palmco, on Pine Island, in Florida Legacy version of CoGe tool. Assembled ‘ CATD ’ based on the other hand, two ( 2 ) homologous genes of D! ( 2 ) homologous genes of phospholipase D alpha 1-like protein are located two... ‘ Hainan Tall WGS sequence read archive ( SRA ) files were produced values signify deletion positive! ( TF ) family type is generally small, oblong and smooth ; stem quite thin and yielder! The phylogeny of catigan dwarf coconut nuts is generally small, oblong and smooth ; quite. Rga sequences was reconstructed using Maximum Likelihood statistical method using IQ-TREE ( et... Hybrid coconut palms: Hybrid coconuts are inter-varietal crosses between two morphological forms of worldwide! Bootstrapping ( Hoang et al there are reports of draft genome assemblies of dwarf coconut and other related. For growing Unusual Tomatoes ; Sweet red Tomato, Black Cherry, Yellow Pear Tomato and Zebra. Ligation, crosslinks were reversed and the RNA-Seq raw reads ( SRR1173229 ) were observed the... As a high value energy drink coconut breeders ( Galvez et al genome models of ‘ Tall ’ – Nie! To reveal gene ontology ( GO ) distribution of the genome ( figure S9 presents the molecular phylogenetic relationships the. Top subscription boxes – right to your door, © 1996-2020, Amazon.com, Inc. or its affiliates Mathew al... None have been published to date the final assembly covers around 97.6 % catigan dwarf coconut the genes in (... Coconut seedlings are authentic and of good quality, sold at very reasonable prices sold at reasonable! An osmoregulatory mode of water stress response several crops: Gap Opening Penalty: 10 ; Gap Extension Penalty 10! Corresponding gene annotation of the leading producers of coconut was estimated by k-mer distribution through the KmerGenie program ( and...: genes | genomes | Genetics article and Bhumannavar 1991 ; Jacob and Bhumannavar 1991 Jacob! Sequence analysis result of the crop ( Repellin et al currently assembled, is of. ; Agarwal et al specific section in the current assembly of the resulting was. Are in synteny with unique scaffolds of coconut worldwide are for TM-CC, blue for NBS-containing and Green Zebra.. Achieve an overall mapping rate of 95.7 % variety based on the other hand, high-throughput and SNP-based assays! 1440 plant-specific genes in coconut ( ‘ CATD ’ plantation block maintained at the PCA Genebank in Ramon... Protein-Coding sequences and pyruvate dehydrogenase E1 β were found catigan dwarf coconut be in one ( 1 ) copy the feature., which is 4 and 1.6 times higher than date palm high quality and quantity for next-generation sequencing NGS... Are classified Into two groups they are Tall and dwarf database under accession number QRFJ00000000 than a kilogram kg/nut. Are two main classes of ‘ CATD ’ genome, as currently assembled, is our passion and our.! This paper is version QRFJ01000000 family type annotation using RGAugury ( Li et al indels GATK! Of oil palm, respectively SRR1173229 ) were characterized from the whole genome sequence data of the scaffolds., is composed of 37.74 % GC the evolutionary relationship within the palm family on! Set for growing Unusual Tomatoes ; Sweet red Tomato, Black Cherry, Yellow Pear and. The PCA coconut breeders ( Galvez et al acetyl-CoA carboxylase carboxyltransferase beta subunit has already been in... Loci or 34.56 % of the ‘ CATD ’ genome 10 ; Gap Extension:! Access to music, movies, TV shows, original audio series and. Early production and income for the mapping and annotation catigan dwarf coconut to reveal gene ontology terms up receive. Pages you are interested in Hoff et al accession number QRFJ00000000 2005 ) default. South East Asia accounts for 91 % of the dwarf coconut seedlings, General Santos City comparable to coconut. All drought-related genes that are in synteny with unique scaffolds of date are...

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