Genome-Wide SNP and Indel Discovery in Abaca (Musa textilis Née) and among Other Musa spp. for Abaca Genetic Resources Management.

Abaca (Musa textilis Née) is an economically important fiber crop in the Philippines. Its economic potential, however, is hampered by biotic and abiotic stresses, which are exacerbated by insufficient genomic resources for varietal identification vital for crop improvement. To address these gaps, this study aimed to discover genome-wide polymorphisms among abaca cultivars and other Musa species and analyze their potential as genetic marker resources. This was achieved through whole-genome Illumina resequencing of abaca cultivars and variant calling using BCFtools, followed by genetic diversity and phylogenetic analyses. A total of 20,590,381 high-quality single-nucleotide polymorphisms (SNP) and DNA insertions/deletions (InDels) were mined across 16 abaca cultivars. Filtering based on linkage disequilibrium (LD) yielded 130,768 SNPs and 13,620 InDels, accounting for 0.396 ± 0.106 and 0.431 ± 0.111 of gene diversity across these cultivars. LD-pruned polymorphisms across abaca, M. troglodytarum, M. acuminata and M. balbisiana enabled genetic differentiation within abaca and across the four Musa spp. Phylogenetic analysis revealed the registered varieties Abuab and Inosa to accumulate a significant number of mutations, eliciting further studies linking mutations to their advantageous phenotypes. Overall, this study pioneered in producing marker resources in abaca based on genome-wide polymorphisms vital for varietal authentication and comparative genotyping with the more studied Musa spp.

Draft Genome Sequence of the Cadmium-Resistant Strain JJU2, Belonging to the Family Hapalosiphonaceae of the Cyanobacteria.

Here, we report the genome of strain JJU2, a cyanobacterium of the family Hapalosiphonaceae known to be resistant to high cadmium levels, assembled from a nonaxenic, unialgal culture from Marinduque, Philippines. The draft genome is 7.1 Mb long with a GC content of 40.05% and contains 5,625 protein-coding genes.

Preliminary screening for microsatellite instability and loss of heterozygosity in the deleted in colorectal cancer (DCC) gene among Filipino patients with colorectal adenocarcinoma

OBJECTIVE: This study aimed to detect the presence of microsatellite (MSI) and loss of heterozygosity (LOH) of the Deleted in Colorectal Cancer (DCC) gene in normal and tumor tissues of Filipino colorectal cancer patients and examine its correlation with age, gender, tumor grade, tumor stage and site of lesion.METHODS: Paired frozen normal and tumor tissues from thirtynine (39) patients with colorectal adenocarcinoma were used by polymerase chain reaction (PCR). Single strand conformation polymorphism - polyacrylamide gel electrophoresis (SSCP - PAGE) was used to determine MSI and restriction fragment length polymorphism (RFLP) was used to study LOH.RESULTS: Based on our data, out of the 39 patients, 10 showed LOH of the DCC gene using the LOH markers VNTR, M2 and M3, while no MSI was detected in the samples using the MSI markers BAT25 and BAT26. Correlation with clinicopathological characteristics showed that there is significance for the site of lesion. The LOH has correclation with tumor samples from the colon but not with those from the rectum.CONCLUSION: Preliminary screening for MSI and LOH of the DCC gene shows that occurrences of colorectal cancer among Filipino patients can be correlated with LOH of the DCC gene with colorectal cancer in a Filipino sample population.