GOVPH

Details

Sex: Male

Education:
Doctor of Philosophy in Veterinary Internal Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2003

Field of Specialization:
Phagocytosis
Gross Anatomy
Cattle Milk
Animal Production
Ruminant Medicine
Theriogenology

Read more: Dr. Rio John Ducusin

Details

Sex: Female
Education:
Doctor of Philosophy in Environmental Science, University of Los Baños, 2010

Fields of Specialization
Biodiversity
Conservation

Read more: Dr. Mary Joyce Flores

Details

Sex: Male

Education:
Master of Science in Molecular Biology and Biotechnology, University of the Philippines Los Baños, 2018
Bachelor of Science in Agricultural Biotechnology, Molecular Makers, University of the Philippines Los Baños, 2012

Field of Specialization:
Agricultural Biotechnology
Plant Biotechnology
Plant Breeding
Plant Molecular Biology
Plant Genetics
Molecular Plant Breeding
Molecular Markers
Molecular Marker Development
Bioinformatics
Genomics

Researches:

Article title: 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
Authors: Darlon V. Lantican, Susan R. Strickler, Alma O. Canama, Roanne R. Gardoce, Lukas A. Mueller, Hayde F. Galvez
Publication title: G3-Genes Genomes Genetics 9(8), 2019

Abstract:
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.
Full text available upon request to the author/s

Article title: Resistance Gene Analogs of Mango: Insights on Molecular Defenses and Evolutionary Dynamics
Authors: Darlon V. Lantican, Cris Q. Cortaga, Anand Noel C. Manohar,
Fe M. dela Cueva, and Maria Luz J. Sison
Publication title: Philippine Journal of Science 149(3-a):915-934, October 2020

Abstract:
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 (NBS- LRR), 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 well- annotated 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 mango- pest co-evolutionary arms race and offer a trove of markers for utilization in resistance breeding.
Full text available upon request to the author/s

Article title: Identification and characterization of genome-wide resistance gene analogs (RGAs) of durian (Durio zibethinus L.)
Authors: Cris Q. Cortaga, Romnick A. Latina, Rosteo R. Habunal & Darlon V. Lantican
Publication title: Journal of Genetic Engineering and Biotechnology 20(29):1-11, 2022

Abstract:
Background
Durian (Durio zibethinus L.) is a tropical fruit crop which is popular in Southeast Asia but recently gaining popularity in other parts of the world. In this study, we analyzed the resistance gene analogs (RGAs) of durian through mining of the currently available reference genome of its ‘Musang King’ cultivar (PRJNA400310).

Results
A total of 2586 RGAs were identified in the durian genome consisting of 47 nucleotide binding site proteins (NBS), 158 NBS-leucine rich repeat proteins (NL), 400 coiled-coil NBS-LRR (CNL), 72 toll/interleukin-1 receptor NBS-LRR (TNL), 54 coiled-coil NBS (CN), 10 toll/interleukin-1 receptor NBS (TN), 19 toll/interleukin-1 receptor with unknown domain (TX), 246 receptor-like proteins (RLP), 1,377 receptor-like kinases (RLK), 185 TM-CC, and 18 other NBS-containing proteins with other domains. These RGAs were functionally annotated and characterized via gene ontology (GO) analysis. Among the RGAs with the highest copies in durian genome include the putative disease resistance RPP13-like protein 1, disease resistance protein At4g27190, disease resistance protein RPS6, Probable disease resistance protein At4g27220, and putative disease resistance protein RGA3, while 35 RGAs were found to be novel. Phylogenetic analyses revealed that the genome-wide RGAs were broadly clustered into four major clades based on their domain classification.

Conclusion
To our knowledge, this is the most comprehensive analysis of durian RGAs which provides a valuable resource for genetic, agronomic, and other biological research of this important tropical fruit crop.
Full text available upon request to the author/s

Article title: Draft Genomes of Six Philippine Erwinia mallotivora Isolates: Comparative Genomics and Genome-Wide Analysis of Candidate Secreted Proteins
Authors: Aira F. Waje, Darlon V. Lantican, Nandita Pathania & Fe M. Dela Cueva
Publication title: Current Microbiology 79(6), June 2022

Abstract:
Erwinia mallotivora is one of the most important bacterial pathogens of papaya and causes bacterial crown rot disease in the Philippines. In this paper, we present the draft genome sequences of six Philippine E. mallotivora isolates to provide insights into the genes involved in host–pathogen interactions and compare their genomes to other Erwinia species. The genomes were sequenced using Illumina Miseq platform. The draft whole-genome assemblies of the E. mallotivora isolates are composed of 36–64 contigs with N50 value ranging from 285 to 332 kbp and cover 96.2–100% of the estimated genome size. Structural genome annotation of these assemblies has predicted 4489–4749 protein-coding genes. Comparative genomic analysis using orthologous gene sets led to the identification of conserved genes within the genus and species-specific gene orthologous groups, which collectively provide a baseline for functional genomic studies to determine genes affecting virulence and host specificity. Secreted proteins of E. mallotivora were also predicted and characterized to unravel putative genes involved in plant–pathogen interactions. This study provides the first draft whole-genome sequences of Philippine isolates of E. mallotivora, thus expanding the genomic knowledge for this species in comparison with other members of the genus Erwinia.
Full text available upon request to the author/s

Article title: Genome-wide SNP and InDel analysis of three Philippine mango species inferred from whole-genome sequencing
Authors: Cris Q. Cortaga, John Albert P. Lachica, Darlon V. Lantican & Eureka Teresa M. Ocampo
Publication title: Journal of Genetic Engineering and Biotechnology 20(46), 2022

Abstract:
Background
The Philippines is among the top 10 major exporters of mango worldwide. However, genomic studies of Philippine mangoes remain largely unexplored and lacking. Here, we sequenced the whole genome of the three Philippine mango species, namely, Mangifera odorata (Huani), Mangifera altissima (Paho), and Mangifera indica “Carabao” variety using Illumina HiSeq 2500, to identify and analyze their genome-wide variants (SNPs and InDels).

Results
The high confidence variants were identified by successfully mapping 93–95% of the quality-filtered reads to the Alphonso and Tommy Atkins mango reference genomes. Using these two currently available mango genomes, most variants were observed in M. odorata (4,353,063 and 4,277,287), followed by M. altissima (3,392,763 and 3,449,917), and lastly, M. indica Carabao (2,755,267 and 2,852,480). Approximately 50, 46, and 38% of the variants were unique in the three Philippine mango genomes. The analysis of variant effects and functional annotation across the three mango species revealed 56,982 variants with high-impact effects mapped onto 37,746 genes, of which 25% were found to be novel. The affected mango genes include those with potential economic importance such as 6945 genes for defense/resistance/immune response, 323 genes for fruit development, and 338 genes for anthocyanin production.

Conclusions
To date, this is the first sequencing effort to comprehensively analyze genome-wide variants essential for the development of genome-wide markers specific to these mango species native to the Philippines. This study provides an important genomic resource that can be used for the genetic improvement of mangoes.
Full text available upon request to the author/s

Article title: A novel SNP panel developed for targeted genotyping-by-sequencing (GBS) reveals genetic diversity and population structure of Musa spp. germplasm collection
Authors: Roanne R. Gardoce, Anand Noel C. Manohar, Jay-Vee S. Mendoza, Maila S. Tejano, Jen Daine L. Nocum, Grace C. Lachica, Lavernee S. Gueco, Fe M. Dela Cueva & Darlon V. Lantican
Publication title: Molecular Genetics and Genomics 2023

Abstract:
The Philippines is situated in the geographic region regarded as the center of diversity of banana and its wild relatives (Musa spp.). It holds the most extensive collection of B-genome germplasm in the world along with A-genome groups and several natural hybrids with A- and B-genome combinations. Management of this germplasm resource has relied immensely on identification using local names and morphological characters, and the extent of genetic diversity of the collection has not been achieved with molecular markers. A high-throughput and reliable genotyping method for banana and its relatives will facilitate germplasm management and support breeding initiatives toward a marker-based approach. Here, we developed a 1 K SNP genotyping panel based on filtering of high-quality genome-wide SNPs from the Musa Germplasm Information System and used it to assess the genetic diversity and population structure of 183 accessions from a Musa spp. germplasm collection containing Philippine and foreign accessions. Targeted GBS using SeqSNP™ technology generated 70,376,284 next-generation sequencing (NGS) reads with an average effective target SNP coverage of 340 × . Bioinformatics pipeline revealed 971 polymorphic SNPs containing 76.9% homozygous calls, 23.1% heterozygous calls and 4% with missing data. A final set of 952 SNPs detected 2,092 alleles. Pairwise genetic distance varied from 0.0021 to 0.3325 with most pairs of accessions distinguished with 250 to 300 loci. The SNP panel was able to detect seven (k = 7) genetically differentiated groups and its composition through Principal Component Analysis (PCA) with k-means clustering algorithm and Discriminant Analysis of Principal Components (DAPC). Accession-specific SNPs were also identified. The 1 K SNP panel effectively distinguishes between genomic groups and provides relatively good resolution of genome-wide nucleotide diversity of Musa spp. This panel is recommended for low-density genotyping for application in marker-assisted breeding and germplasm management, and could be further enhanced to increase marker density for other applications like genetic association and genomic selection in bananas.
Full text available upon request to the author/s

Article title: Mining and validation of novel simple sequence repeat (SSR) markers derived from coconut (Cocos nucifera L.) genome assembly
Authors: Reina Esther S. Caro, Jesmar Cagayan, Roanne R. Gardoce, Anand Noel C. Manohar, Alma O. Canama-Salinas, Ramon L. Rivera, Darlon V. Lantican, Hayde F. Galvez & Consorcia E. Reaño
Publication title: Journal of Genetic Engineering and Biotechnology volume 20(71), 2022

Abstract:
Background
In the past, simple sequence repeat (SSR) marker development in coconut is achieved through microsatellite probing in bacterial artificial chromosome (BAC) clones or using previously developed SSR markers from closely related genomes. These coconut SSRs are publicly available in published literatures and online databases; however, the number is quite limited. Here, we used a locally established, coconut genome-wide SSR prediction bioinformatics pipeline to generate a vast amount of coconut SSR markers.

Results
A total of 7139 novel SSR markers were derived from the genome assembly of coconut ‘Catigan Green Dwarf’ (CATD). A subset of the markers, amounting to 131, were selected for synthesis based on motif filtering, contig distribution, product size exclusion, and success of in silico PCR in the CATD genome assembly. The OligoAnalyzer tool was also employed using the following desired parameters: %GC, 40–60%; minimum ΔG value for hairpin loop, −0.3 kcal/mol; minimum ΔG value for self-dimer, −0.9 kcal/mol; and minimum ΔG value for heterodimer, −0.9 kcal/mol. We have successfully synthesized, optimized, and amplified 131 novel SSR markers in coconut using ‘Catigan Green Dwarf’ (CATD), ‘Laguna Tall’ (LAGT), ‘West African Tall’ (WAT), and SYNVAR (LAGT × WAT) genotypes. Of the 131 SSR markers, 113 were polymorphic among the analyzed coconut genotypes.

Conclusion
The development of novel SSR markers for coconut will serve as a valuable resource for mapping of quantitative trait loci (QTLs), assessment of genetic diversity and population structure, hybridity testing, and other marker-assisted plant breeding applications.
Full text available upon request to the author/s

Article title: Comparative RNA-seq analysis of resistant and susceptible banana genotypes reveals molecular mechanisms in response to Banana bunchy top virus (BBTV)
Authors: Darlon V. Lantican, Jen Daine L. Nocum, and Noel C. Manohar, Jay-Vee S. Mendoza, Roanne R. Gardoce, Grace C. Lachica, Lavernee S. Gueco, Fe M. Dela Cueva
Publication title: Biorx IV, 2022

Abstract:
Banana is a major fruit crop in the Philippines and remains to be a large contributor to the country & prime dollar reserve. Among the main hindrances in global banana production, diseases such as Banana bunchy top disease (BBTD) caused by BBTV can bring catastrophic loss to any banana plantation. To elucidate the resistance mechanism and understand the interplay of host factors in the presence of the invading pathogen, we implemented RNA-seq-based comparative transcriptomics analyses of mock- and BBTV-inoculated resistant (wild M. balbisiana) and susceptible (M. acuminata & Lakatan & banana genotypes. Similar patterns of expression for 119 differentially expressed genes (DEGs) were observed on both genotypes, representing the typical defense response of banana to BBTV. A set of 173 DEGs specific to the susceptible ′Lakatan′ banana cultivar revealed potential host factors and susceptibility mechanisms involved in successful BBTV infection. Further, differential transcriptomic analysis revealed 268 DEGs exclusive to the resistant wild M. balbisiana, unraveling insights into the complex resistance mechanisms involved in BBTV defense such as pathogen perception, phytohormone action, reactive oxygen species (ROS), hypersensitive response (HR), production of secondary metabolites, and cell wall modification. The DEGs identified in this study will aid in the design of foreground markers for the precise integration of resistance genes during marker-assisted breeding programs. Furthermore, the application of these results will also enable the foreseen deployment of genome-edited banana cultivars targeting the resistance and host factor genes towards a future-proof banana industry.
Full text available upon request to the author/s

Article title: Identification of suitable internal control genes for gene expression analysis of banana in response to BBTV infection
Authors: Jen Daine L. Nocum, Anand Noel C. Manohar, Jay-Vee S. Mendoza, Fe M. Dela Cueva, Roanne R. Gardoce, Grace C. Lachica, Darlon V. Lantican
Publication title: Plant Gene 32(2):100383, September 2022

Abstract:
Banana is one of the most abundant crops produced annually in the Philippines. The presence of banana bunchy top virus (BBTV) leading to banana bunchy top disease is one of the factors hindering the continuous production of the fruit crop. The use of an appropriate and stable internal control gene as reference in validation of differentially-expressed genes in an organism is important. This study aims to identify appropriate internal control genes for differential gene expression analysis in Musa balbisiana and Musa acuminata specific for BBTV infection. RNA extraction, complementary DNA (cDNA) synthesis and RT-qPCR (quantitative real time polymerase chain reaction) of BBTV-resistant and BBTV-susceptible Musa genotypes were performed. The RT-qPCR quantification data were then subjected to analysis on RefFinder software and geomean ranking values were calculated along with the four statistical algorithms (delta Cq, Genorm, BestKeeper and NormFinder). Based on the comprehensive ranking values in the software, L2 gene was the most suitable internal control gene for the differential expression analysis of both BBTV-resistant and BBTV-susceptible banana accessions. The internal control gene is recommended for the validation of selected candidate resistance and host factor genes in response to BBTV infection.
Full text available upon request to the author/s

Article title: Reference-aided full-length transcript assembly, cDNA cloning, and molecular characterization of coronatine-insensitive 1b (COI1b) gene in coconut (Cocos nucifera L.)
Authors: Frenzee Kroeizha L. Pammit, Anand Noel C. Manohar, Darlon V. Lantican, Jen Daine L. Nocum, Roanne R. Gardoce & Hayde F. Galvez
Publication title: Molecular Biology Reports 49(3), June 2022

Abstract:
Background
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. However, the country’s multimillion-dollar coconut industry is threatened by the outbreak of coconut scale insect (CSI) and other re-emerging insect pests promoting national research institutes to work jointly on developing new tolerant coconut varieties. Here, we report the cloning and characterization of coronatine-insensitive 1 (COI1) gene, one of the candidate insect defense genes, using ‘Catigan Green Dwarf’ (CATD) genome sequence assembly as reference.

Methods and results
Two (2) splicing variants were identified and annotated—CnCOI1b-1 and CnCOI1b-2. The full-length cDNA of CnCOI1b-1 was 7919 bp with an ORF of 1176 bp encoding for a deduced protein of 391 amino acids while CnCOI1b-2 has 2360 bp full-length cDNA with an ORF of 1743 bp encoding a deduced protein of 580 amino acids. The 3D structural model for the two (2) isoforms were generated through homology modelling. Functional analysis revealed that both isoforms are involved in various physiological and developmental plant processes including defense response of plants to insects and pathogens. Phylogenetic analysis confirms high degree of COI1 protein conservation during evolution, especially among monocot species. Differential gene expression via qRT-PCR analysis revealed a seven-fold increase of COI1 gene expression in coconut post introduction of CSI relative to base levels.

Conclusion
This study provided the groundwork for further research on the actual role of COI1 in coconut in response to insect damage. The findings of this study are also vital to facilitate the development of improved insect-resistant coconut varieties for vibrant coconut industry.
Full text available upon request to the author/s

Article title: Species-specific PCR-based Marker for Rapid Detection of Aspidiotus rigidus Reyne (Hemiptera: Diaspididae)
Authors: Romnick A. Latina, Darlon V. Lantican, Michelle S. Guerrero, Edsel C. Rubico, Janice F. Laquinta, Barbara L. Caoili
Publication title: Journal of Asia-Pacific Entomology 25(3):101848, December 2021

Abstract:
The Philippine coconut production has been greatly affected by the recent devastating infestation of Aspidiotus spp. However, identification of the outbreak species, Aspidotus rigidus, has been a challenge using morphological approaches. Molecular identification via PCR sequencing of insect barcoding genes has been implemented, but the overall process is time-consuming and costly. Thus, we developed and optimized a species-specific PCR-based molecular marker for rapid, efficient and cost-effective molecular identification of A. rigidus. The molecular marker was designed based on the sequences of the partial 28S ribosomal RNA gene from species of Aspidiotus that feed on coconut in the Philippines, A. rigidus, A. destructor and A. excisus. Multiple alignment of nucleotide sequences revealed a conserved 16-bp insertion-deletion (InDel) site common to all A. rigidus specimens identified from which the A. rigidus-specific oligonucleotide (RIG1) primer targeting an approximately 570 bp fragment size was designed. Results showed that the species-specific DNA marker technology consistently delineated laboratory-reared and field-collected A. rigidus samples from A. destructor and A. excisus. The protocol offers a rapid and reliable method for the early detection of A. rigidus infestation in high-risk areas planted with coconut in the country.
Full text available upon request to the author/s

Article title: Development of Novel Coconut Ssr Markers Derived From Genome-Wide Bioinformatics Prediction
Authors: Reina Esther S. Caro, Jesmar Cagayan, Roanne R. Gardoce, Anand Noel C. Manohar, Alma O. Canama-Salinas, Ramon L. Rivera, Darlon V. Lantican, Hayde F. Galvez, Consorcia E. Reaño
Publication title: Preprint

Abstract:
In the past, simple sequence repeat (SSR) marker development in coconut is achieved through microsatellite probing in bacterial artificial chromosome (BAC) clones or using previously developed SSR markers from closely related genomes. These coconut SSR markers are publicly available in published literatures and online databases; however, the number is quite limited. Here, we used a locally established, coconut genome-wide SSR prediction bioinformatics pipeline to generate a vast amount of coconut SSR markers. A total of 7,139 novel SSR markers were derived from the genome assembly of coconut ‘Catigan Green Dwarf’ (CATD). A subset of the markers, amounting to 131, were selected for synthesis based on motif filtering, contig distribution, product size exclusion, and success of in silico PCR in the CATD genome assembly. OligoAnalyzer-tool was also employed using the following desired parameters: %GC: 40–60%; minimum ΔG value for hairpin loop: -0.3 kcal/mol; minimum ΔG value for self-dimer: -0.9 kcal/mol; and minimum ΔG value for hetero-dimer: -0.9 kcal/mol. We have successfully synthesized, optimized, and amplified 131 novel SSR markers in coconut using ‘Catigan Green Dwarf’ (CATD), ‘Laguna Tall’ (LAGT), ‘West African Tall’ (WAT), and SYNVAR (LAGT x WAT) genotypes. Of the 131 SSR markers, 113 were polymorphic among the analyzed coconut genotypes. The development of novel SSR markers for coconut will serve as a valuable resource for mapping of quantitative trait loci (QTLs), assessment of genetic diversity and population structure, hybridity testing, and other marker-assisted plant breeding applications.
Full text available upon request to the author/s

Article title: Genetic Structure and Diversity of Banana Bunchy Top Virus (BBTV) in the Philippines
Authors: Jay-Vee S. Mendoza, Fe M. dela Cueva, Cris Q. Cortaga, Anand Noel C. Manohar, Roanne R. Gardoce, Grace C. Lachica, Maricel C. Gonzales, John E. Thomas, Darlon V. Lantican
Publication title: Preprint

Abstract:
Banana bunchy top virus (BBTV) is an important disease of banana in the Philippines and in other banana-producing countries. This study was conducted to investigate the genetic structure and diversity of Philippine BBTV isolates which remain unexplored in the country. BBTV-infected plant tissues were sampled from banana-growing provinces (i.e., Cagayan, Isabela, Quirino, Batangas, Laguna, Rizal, Quezon, Palawan, Cebu, Leyte, and Davao del Sur) and the partial DNA-R gene of BBTV was sequenced. Analysis of all local BBTV isolates showed a nucleotide diversity (π) of 0.00721, average number of nucleotide differences (k) of 5.51984, and haplotype diversity (hd) of 0.971. Neutrality tests using Fu’s Fs and Tajima’s D showed significant and highly negative values which suggest an excess number of rare alleles due to recent population expansion or from genetic hitchhiking. Haplotype network and phylogenetic analyses revealed that the local BBTV isolates were closely related to Southeast Asian (SEA) group and exhibited a monophyletic clade with distinct haplotype grouping from other SEA sequences. However, some Indonesian and Indian reference sequences were also clustered within the Philippine BBTV group suggesting sequence homology. Results also showed that the local BBTV isolates may be categorized into three major haplotype groups (HA, HB, and HC) but only the HC group remained distinct upon comparison with other Philippine and SEA reference sequences. BBTV isolates from Quezon were the most diverse while isolates from Palawan displayed low genetic diversity indices and belonged only in the HC group. The assessment of the degree of variability among Philippine BBTV isolates will provide a reference towards the development of high-throughput BBTV detection systems as well as enable to devise plant breeding strategies to manage the current BBTV spread and variations.
Full text available upon request to the author/s

Article title: Reference-Aided Full-length Transcript Assembly, cDNA Cloning, and Molecular Characterization of Coronatine-insensitive 1b ( COI1b ) Gene in Coconut ( Cocos nucifera L.)
Authors: Frenzee Kroeizha L. Pammit, Anand Noel C. Manohar, Darlon V. Lantican, Roanne R. Gardoce, Hayde F. Galvez
Publication title: Preprint

Abstract:
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. However, the country’s multimillion-dollar coconut industry is threatened by the outbreak of coconut-scale insect (CSI) and other re-emerging insect pests promoting national research institutes to work jointly on developing new tolerant coconut varieties. Here, we report the cloning and characterization of coronatine-insensitive 1 (COI1) gene, one of the candidate insect defense genes, using ‘Catigan Green Dwarf’ (CATD) genome sequence assembly as reference. Two (2) splicing variants were identified and annotated – CnCOI1b-1 and CnCOI1b-2. The full-length cDNA of CnCOI1b-1 was 7,919 bp with an ORF of 1,176 bp encoding for a deduced protein of 391 amino acids while CnCOI1b-2 has 2,360 bp full-length cDNA with an ORF of 1,743 bp encoding a deduced protein of 580 amino acids. The 3D structural model for the two (2) isoforms were generated through homology modelling. Functional analysis revealed that both isoforms are involved in various physiological and developmental plant processes including defense response of plants to insects and pathogens. Phylogenetic analysis confirms high degree of COI1 protein conservation during evolution, especially among monocot species.
Full text available upon request to the author/s

Article title: Transcriptome-wide analysis of expressed resistance gene analogs (RGAs) in mango
Authors: Darlon Vasquez Lantican, Cris Q. Cortaga, Anand Noel C. Manohar, Fe M. dela Cueva, Maria Luz J. Sison
Publication title: Preprint

Abstract:
Mango is an economically important fruit crop largely cultivated in the (sub)tropics and thus, is constantly challenged by a myriad of insect pests and diseases. Here, we identified and characterized the resistance gene analogs (RGAs) of mango from de novo assembly of transcriptomic sequences. A core RGA database of mango with 747 protein models was established and classified based on conserved domains and motifs: 53 nucleotide binding site proteins (NBS); 27 nucleotide binding site-leucine rich repeat proteins (NBS-LRR); 17 coiled-coil NBS-LRR (CNL); 2 toll/interleukin-1 receptor NBS-LRR (TNL); 29 coiled-coil NBS (CN); 4 toll/interleukin-1 receptor NBS (TN); 17 toll/interleukin-1 receptor with unknown domain (TX); 158 receptor-like proteins (RLP); 362 receptor-like kinases (RLK); 72 transmembrane coiled-coil domain protein (TM-CC), and 6 NBS-encoding proteins with other domains. The various molecular functions, biological processes, and cellular localizations of these RGAs were functionally well-annotated through gene ontology (GO) analysis, and their expression profiles across different mango varieties were also determined. Phylogenetic analysis broadly clustered the core RGAs into 6 major clades based on their domain classification, while TM-CC proteins formed subclades all across the tree. The phylogenetic results suggest highly divergent functions of the RGAs which also provide insights into the mango-pest co-evolutionary arms race. From the mango RGA transcripts, 134 unique EST-SSR loci were identified, and primers were designed targeting these potential markers. To date, this is the most comprehensive analysis of mango RGAs which offer a trove of markers for utilization in resistance breeding of mango.
Full text available upon request to the author/s

Article title: Glandular Trichome Gene-Linked SSR Marker Development for Genetic Diversity Analysis and Trait Association in ‘Tambulilid’ Coconut (Cocos nucifera L.)
Authors: Angelica Kate G. Gumpal, Darlon V. Lantican, Roanne R. Gardoce Melvin P. Dancel1, Jomari C. Domingo, Ronilo M. Bajaro, and Hayde F. Galvez
Publication title: Philippine Agricultural Scientist 102(Special Issue):64-76, December 2019

Abstract:
Massive infestation of coconut scale insect (Aspidiotus sp.) in major coconut growing regions in the country has caused serious damage to the coconut industry. Coconut ‘Tambulilid’, a Javanica variety grown in Bicol, was reported to exhibit antibiosis form of host-resistance against Aspidiotus sp. To further elucidate the mechanism of resistance of this variety, linked microsatellite (SSR) marker was designed, screened, and optimized to target each of the 10 candidate plant glandular trichome genes (PPO, ALS, GL3, SESQ, ETC3, CPC, GSD, TDA, COI1, TTG1) based on the coconut genome. Out of the ten SSR markers designed, eight SSRs were used to determine the extent of genetic differentiation among 30 ‘Tambulilid’, 7 ‘Coco Niño’, and 16 ‘Laguna Tall’ representative individual palms. Four sub-populations could be differentiated at 0.17 similarity coefficient, validated by pairwise F-test (FST) statistics involving the heterozygosity of the 8 SSR markers. Sub-clusters containing ‘Laguna Tall’ individuals exhibit considerable genetic differentiation when compared with sub-clusters generally consisting of ‘Tambulilid’ coconut palms. Single-factor ANOVA of SSR marker genotype segregation with existing trichome density data revealed that the SSR markers linked to germacrene synthase D could be associated to the trichome density trait.
Full text available upon request to the author/s

Article title: Isolation of a CEL 1 Homolog in Tomato (Solanum lycopersicum L.) Fruit as a Cost-effective Endonuclease Source for Targeting Induced Local Lesions IN the Genome (TILLING) Analysis
Authors: Rochelle E. Alcasid, Maria Elizabeth B. Naredo, Darlon V. Lantican, and Hayde F. Galvez
Publication title: Philippine Journal of Science 148(3):465-472, September 2019

Abstract:
CEL 1, an endonuclease originally purified from celery, has been used in TILLING (Targeting Induced Local Lesions IN the Genome) analysis to cut the hairpin loop and single-strand DNA generated from heteroduplex of mutant and wild DNA molecules. However, one major limitation as with most mutation screening technologies and especially in a large-scale application is the availability of affordable sources of endonuclease. This study searched for CEL 1 gene homologs in tomato through Basic Local Alignment Search Tool for nucleotides (BLASTn) and relevant bioinformatics analysis in public genomic databases. Results showed that the SlENDO 1 gene (SGN Accession Number Solyc02g078910.1.1) of tomato (Solanum lycopersicum) has the highest homology of 78% to CEL 1 among all the Solanum species. As annotated, the SlENDO 1 gene has a genome sequence length of 2.182 Kb and consisting of eight and nine intron-exon sequences, respectively. For molecular confirmation, polymerase chain reaction (PCR) primers were designed to target the conserved gene region of SlENDO 1. The amplification and specificity of these primers were further verified first by in silico PCR prior to synthesis. The designed SlENDO 1-specific DNA marker has successfully amplified the target gene in five tomato varieties in actual wet-laboratory PCR experiments. Interestingly, the designed marker was able to cross-amplify orthologous regions (candidate regions of nuclease PA3, TIGR LOC_Os04g54390) in Nipponbare and IR64 rice varieties. Once validated using a wide-range of crop species, the developed SlENDO 1-specific DNA marker can be potentially used in rapid detection of gene homologs in other plants. The isolation of the SlENDO 1 enzyme was also done using a modified protocol for CEL 1 isolation in celery. Through preliminary EcoTILLING with rice positive control samples, the purified SlENDO 1 from unripe fruits of non-transgenic tomato was confirmed to have the same mutation cleavage specificity as that of the CEL 1 endonuclease. Unlike celery, tomato fruits are readily available in any vegetable market, shop, or store in the Philippines. Likewise, they can easily be grown in greenhouse and field production.
Full text available upon request to the author/s

Article title: Genome-guided Molecular Characterization of Oil Genes in Coconut (Cocos nucifera L.)
Authors: Anand Noel C. Manohar, Darlon V. Lantican, Melvin P. Dancel, Don Emanuel M. Cardona, Alissa Carol M. Ibarra, Cynthia R. Gulay, Alma O. Canama, Roanne R. Gardoce, and Hayde F. Galvez
Publication title: Philippine Journal of Science 148(S1):183-191, March 2019

Abstract:
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). A single 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.
Full text available upon request to the author/s

Paper Presentation:

Article title: Genomics in Coconut Towards Insect Resistance Breeding
Authors: Hayde Galvez, Darlon Vasquez Lantican, Maria Luz Josue Sison, Roanne Gardoce
Conference title: 14th Quadrennial Congress of the International Association for Plant Biotechnology (IAPB)At: Dublin, Ireland, 2018

Article title: Genome-guided characterization of medium-chain fatty acid (MCFA) genes in coconut (Cocos nucifera L.) towards marker-assisted breeding
Authors: Anand Noel C. Manohar, Darlon Vasquez Lantican, Darlon Vasquez Lantican, Don Emanuel Mendoza Cardona
Conference title: 48th CSSP Scientific ConferenceAt: La Piazza Hotel, Legazpi City, Philippines, 2018

Article title: Coconut Genetics and Genomics for Host Insect Resistance
Authors: Hayde Galvez, Darlon Vasquez Lantican, Maria Luz Josue Sison, Roanne Gardoce
Conference title: Plant and Animal Genome Conference XXVIAt: Town and Country Hotel, San Diego, California, 2018

Article title: The Coconut Genome: Providing a Reference Sequence Towards Coconut Varietal Improvement
Authors: Darlon Vasquez Lantican, Susan R Strickler, Alma O. Canama-Salinas, Roanne Gardoce
Conference title: Plant and Animal Genome Conference XXVI At: Town and Country Hotel, San Diego, California, 2018

Article title: Host resistance screening in coconut against the invasive coconut scale insect, Aspidiotus rigidus Reyne (Hemiptera: Diaspididae)
Authors: Maria Luz Josue Sison, Don Serville Del Rosario Reynoso, Joseph P. Lagman, Cris Q. Cortaga
Conference title: 49th Pest Management Council of the Philippines, Inc. (PMCP) Scientific ConferenceAt: Crown Regency Resort and Convention Center, Boracay Island, Malay, Aklan, Philippines, 2017

Article title: Development of Tomato Non-Host to Tomato Virus through Targeted Mutagenomics and Bioinformatics Approaches
Authors: Hayde Galvez, Roland Schafleitner, Alma O. Canama-Salinas, Reynaldo B. Quilloy, et al
Conference title: 44th Tomato Breeders Round Table (TBRT) MeetingAt: Chiang Mai, Thailand, 2013