2011) was used to filter the high-quality SNP calls and to compute basic transversion/transition statistics. Data S2 shows the dag-chainer output file of ‘CATD’-date palm alignment. Two (2) splicing variants were identified and However, a recent molecular marker study has determined differences in the SSR allele frequency between ‘Dwarf’ and ‘Tall’ accessions. ‘Malayan Dwarf’ Coconut Palm1 Edward F. Gilman and Dennis G. Watson2 INTRODUCTION One of man’s most useful plants (Fig. The C2H2 TF is also higher in coconut compared to the identified C2H2 genes in Arabidopsis (176 genes; Englbrecht et al. 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. 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. 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. 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). Variants were called by the GATK HaplotypeCaller through setting the output mode to EMIT_VARIANTS_ONLY, and calling confidence threshold (stand_call_conf) to 30. 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. 1992) with empirical codon frequencies (+F) and FreeRate (+R9) rate heterogeneity across sites (Yang 1995; Soubrier et al. Prime members enjoy FREE Delivery and exclusive access to music, movies, TV shows, original audio series, and Kindle books. Figure S1 shows the basic statistics and per base sequence analysis result of the pre-processed Illumina Miseq short read sequences. Selection was made in consultation with the PCA coconut breeders (Galvez 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. 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. Overall Size. ABSTRACT. 1.7K likes. 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’. Coconut trees (Cocos nucifera), hardy to U.S. Department of Agriculture zones 10 through 11, are often categorized as either dwarf or tall. 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. A total of 7,139 unique SSR markers were designed to be used as a resource in marker-based breeding. Top subscription boxes – right to your door, © 1996-2020, Amazon.com, Inc. or its affiliates. Chowghat Dwarf Greens. Among these SNPs, 69.52% are characterized as single-base transitions (A/G, C/T), while the rest are classified as transversion substitutions (A/C, A/T, G/C, T/G) (Figure 5a). 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). Aside from neutral genome-wide SSR markers, 13 gene-linked SSRs were also designed from the whole genome assembly of ‘CATD’. The rate of synonymous substitution (Ks) values was also calculated (temporal calculation of synteny) for the detected syntelogous gene pairs using the Needleman-Wunch algorithm in the nwalign software (Needleman and Wunsch 1970) and CodeML of the PAML package (Yang 1997) both integrated in SynMap. Statistical summary of the ‘Catigan Green Dwarf’ (CATD) coconut assembly using various sequencing technologies and corresponding bioinformatics pipelines, Summary, characteristics and distribution of sequence variations between ‘Hainan Tall’ and ‘Catigan Green Dwarf’ (CATD) genomes. Total genomic DNA samples of ‘Catigan Green Dwarf’ (CATD) coconut variety (Palm number 1817) from Philippine Coconut Authority (PCA) - Zamboanga Research Center (ZRC), Philippines were extracted from healthy young leaflets of slightly opened leaf frond. 2002; Dugas et al. Gensan Fruit Trees and Hybrid Dwarf Coconut Seedlings, General Santos City. 2013). The endocarp is used as alternative fuel source in the form of charcoal. We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, 'Catigan Green Dwarf' (CATD). Syntenic dotplot between dwarf coconut var. 2018), gene flow characterization (Larekeng et al. The drought-related gene homologs in coconut were functionally annotated using BLAST2GO (Conesa et al. Several accounts of the negative impact of drought to coconut productivity as well as in its growth and physiology have been reported (Repellin et al. In total, there are 213 drought-related gene homologs in coconut (Data S4). Copra per nut seldom exceeds 100g. After viewing product detail pages, look here to find an easy way to navigate back to pages you are interested in. The branches colored as red are for TM-CC, blue for NBS-containing and green for TX and TN resistance gene analogs. 2013; Al-Mssallem et al. A total of 34,958 high-confidence gene models were predicted and functionally associated to various economically important traits, such as pest/disease resistance, drought tolerance, coconut oil biosynthesis, and putative transcription factors. 2015). The syntenic gene pairs were identified by DAGChainer, and colored based on their synonymous substitution rate as calculated by CodeML of the CoGe SynMap tool (Lyons et al. We aimed to characterize the gene units in coconut and maximize the utility of this genome information for gene discovery, molecular marker development, and routine marker-assisted breeding applications. In the Philippines, 26% of the total agricultural land is devoted to coconut production making coconut one of the most valuable industrial crop in the country. 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. arXiv preprint arXiv: 1303.3997. The lovely plant Coconut (Cocus nucifera) belongs to plant family “ Arecaceae” and being in use since 5 lac years. The SSR loci in the assembled genome were identified using the following parameters in the package: minimum repeat motif length: 2 nucleotides; max repeat motif length: 10 nucleotides; minimum repeat times: 5. 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. Manohar et al. A total of 199 drought-response genes were downloaded from DroughtDB (Alter et al. Segmental duplications of 602 scaffolds of date palm are found in synteny across 561 genomic scaffolds of coconut (Data S2). Fiaboe et al homozygous k-mer peak analysis which is 4 and 1.6 times higher than palm! Have never evolved in monocots ( Tarr and Alexander 2009 ) and Alexander 2009 ) located in two genome. The … Gensan fruit trees and Hybrid dwarf coconut genome duplicated genomic that. Trimmed ( Trimmomatic v0.36 ; SLIDINGWINDOW: 5:30 ; LEADING:5 ; TRAILING:5 ; MINLEN:50 available... 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