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Mango (Mangifera indica L.) is one of the most popular fruit crops grown and traded globally. Mango can withstand seasonal drought periods, especially during flowering. However, prolonged drought stress can cause the weakening of the plant and may encourage injuries and diseases caused by abiotic and biotic factors. With the availability of the mango genome, genomic studies related to drought adaptation of mango can now be extensively explored. In this study, genomewide drought-related genes (DRGs) of mango were analyzed using the whole genome sequences (WGS) of "Alphonso" and "Tommy Atkins" cultivars (PRJNA487154 and PRJNA450143, respectively). A total of 261 and 257 DRGs were identified in the genome of "Alphonso" and "Tommy Atkins," respectively, using BLASTP. Approximately 50% of these genes are involved in both molecular and physiological adaptations of mango to drought. Among the drought stress genes, the ABC transporter gene ABCG40 had the highest number of homologs in mango, followed by calcium-dependent protein kinase genes ZmCPK4, CPK21, and CDPK7, as well as the plasma membrane proton ATPase OST2. Gene ontology (GO) analysis of the DRGs revealed that protein binding, ATP binding, and mRNA binding are the most common molecular functions, whereas the predominant biological process of these DRGs is related to their response to water deprivation. Phylogenetic analysis showed that the drought-related proteins in "Alphonso" and "Tommy Atkins" are broadly clustered into seven and six major clades, respectively. This study, to date, offers the most comprehensive information on the genome-wide DRGs of the mango, which can strengthen marker-assisted breeding programs for drought tolerance in mango and other related fruit trees, as well as the future incorporation of favorable alleles toward improving the overall agronomic characteristics of this Philippine important fruit crop. [ABSTRACT FROM AUTHOR]

Mango is an economically important fruit crop largely cultivated in the tropics and, thus, is constantly challenged by a myriad of insect pests and diseases. However, no detailed analysis of its resistance gene analogs (RGAs) has been performed, which is a vital resource for plant breeding. Here, we analyzed the RGAs of mango via de novo assembly of transcriptomic sequences and mining of the recently published whole genome sequence (WGS). From the transcriptomic assembly, a core mango RGA database with 747 protein models was established. Meanwhile, 1,775 RGAs were identified in the mango WGS and classified based on conserved domains and motifs: 54 nucleotide binding site proteins (NBS), 107 NBS - leucine rich repeat proteins (NBSLRR), 242 coiled-coil NBS-LRR (CNL), 79 toll/interleukin-1 receptor NBS-LRR (TNL), 78 coiled-coil NBS (CN), 30 toll/interleukin-1 receptor NBS (TN), 45 toll/interleukin-1 receptor with unknown domain (TX), 133 receptor-like proteins (RLP), 917 receptor-like kinases (RLK), 83 transmembrane coiled-coil domain protein (TM-CC), and seven NBS-encoding proteins with other domains. The transcriptome- and genome-wide RGAs have been functionally wellannotated through gene ontology (GO) analysis, and their expression profiles across different mango varieties were also examined. Phylogenetic analyses of expressed and genome-wide RGAs suggest highly divergent functions of the RGAs, which were broadly clustered into 6 and 8 major clades, respectively, based on their domain classification. From the mango RGA transcripts, 134 unique EST-SSR (expressed sequence tags - simple sequence repeat) loci were identified and primers were designed targeting these potential markers. Moreover, comparative analysis of mango with other plant species revealed 65 species-specific RGA families (396 orthologous genes) and detected 1,005 RGA gene duplication events. To date, this is the most comprehensive analysis of mango RGAs, which also provide insights into the dynamic mangopest co-evolutionary arms race and offer a trove of markers for utilization in resistance breeding. [ABSTRACT FROM AUTHOR]

Coconut oil is a major source of medium chain fatty acids (MCFAs), which are health-promoting plant compounds. The MCFAs of coconut oil have been reported to exhibit various health properties such as antioxidant, antibacterial, antiviral, and cardiovascular benefits brought about by the multi-functionality of these complex MCFAs. Six (6) candidate genes involved in oil and MCFA synthesis were identified in the general seed oil biosynthetic pathway. The candidate gene sequences were mined using local BLAST in the coconut genome assembly constructed based on 15× PacBio® and 50× Illumina® MiSeq sequence reads of CATD coconut variety. Scaffolds harboring the candidate genes were mapped based on sequence homology alignment. Gene structures of all genes were elucidated using evidence-based and ab initio prediction algorithms. The coding DNA sequences of KasII and KasIII in coconut were characterized. These MCFA genes have not been characterized nor reported in coconut. Gene-specific PCR primers were designed targeting the coding regions of each gene. PCR conditions were optimized to mine natural allele variants across 48 established coconut varieties in the Philippines through EcoTILLING (Ecotype Targeting Induced Local Lesions IN Genomes).Asingle nucleotide polymorphism (SNP) on the lysophosphatidic acid acyltransferase genes (LPAAT) was detected in the 'West African Tall'(WAT) and 'Aguinaldo Tall' (AGDT) varieties. The partial LPAAT gene sequences of WAT and AGDT were cloned and sequenced in order to characterize the SNP. Based on the identified SNPs, robust DNA markers may be developed for high-throughput screening and selection of favorable alleles in genomics-assisted coconut breeding for outstanding high-quality oil producing varieties. [ABSTRACT FROM AUTHOR]

We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, 'Catigan Green Dwarf' (CATD). 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. The draft genome was improved through Chicago sequencing to generate a scaffold assembly that results in a total genome size of 2.1 Gbp consisting of 7,998 scaffolds with N50 of 570,487 bp. The final assembly covers around 97.6% of the estimated genome size of coconut 'CATD' based on homozygous k-mer peak analysis. 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. The assembled genome was used to infer the evolutionary relationship within the palm family based on genomic variations and synteny of coding gene sequences. Data show that at least three (3) rounds of whole genome duplication occurred and are commonly shared by these members of the Arecaceae family. A total of 7,139 unique SSR markers were designed to be used as a resource in marker-based breeding. In addition, we discovered 58,503 variants in coconut by aligning the Hainan Tall (HAT) WGS reads to the non-repetitive regions of the assembled CATD genome. The gene markers and genome-wide SSR markers established here will facilitate the development of varieties with resilience to climate change, resistance to pests and diseases, and improved oil yield and quality., (Copyright © 2019 Lantican et al.)