National Committee on Marine Sciences (NCMS)
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- Occurrence of closely spaced genes in the nuclear genome of the agarophyte Gracilaria gracilisLluisma, Arturo O.; Ragan, Mark A. (Springer, 1999)Little is known about the structure and organisation of nuclear genomes in red algae. In particular, it is not known whether genes are densely or loosely packed, whether gene order is conserved, whether their genes tend to occur in one or multiple copies and whether their nuclear genes tend to be compact or interrupted by numerous introns. Sequencing of cloned genomic DNA from Gracilaria gracilis has begun to provide provisional answers to some of these questions. Four pairs of closely spaced genes have been found in G. gracilis upon sequencing genomic clones that contain genes for UDPglucose pyrophosphorylase, galactose-1-phosphate uridylyltransferase, the β subunit of tryptophan synthetase, and methionine sulphoxide reductase (a fifth pair of closely spaced genes, encoding polyubiquitin and aconitase, was reported earlier). An open reading frame with significant similarity to another known gene occurs close (< 1.7 kbp) to each of these genes. In two pairs the intergenic region is less than 400 bp in length, and for these the location of the putative polyadenylation signals indicates that the gene transcripts, encoded on opposite strands, have overlapping (hence complementary) 3′ regions. These somewhat unexpected findings begin to establish a basis for genome-level characterisation of red algae.
- Quantification and characterization of nuclear genomes in commercial red seaweeds (Gracilariales) from the PhilippinesKapraun, Donald F.; Lopez-Bautista, Juan; Trono, Gavino; Bird, Kimon T. (Springer, 1996-03)Eight species of Gracilariaceae from the Philippines, representing the genera Gracilaria, Gracilariopsis and Hydropuntia, were investigated to quantify and characterize their nuclear genomes. DNA reassociation kinetics were used to determine nuclear genome organization and complexity in six of these species. Results indicate the presence of three second order components corresponding to fast, intermediate and slow fractions. Repetitive sequences varied from 13–74% and unique DNA ranged from 26–84%. Microspectrophotometry with the DNA-localizing fluorochrome DAPI was used to quantify nuclear DNA contents. Comparisons of mean nuclear DNA (I f ) values to chicken erythrocytes (RBC) resulted in an estimate of 0.38–0.43 pg/2 C genomes for seven of the species investigated. Preliminary analyses of agar content and quality confirm the economic potential of Gracilaria firma, Gracilaria sp. 2 from Sorsogon and Gracilariopsis bailinae. Nuclear genome profiles developed from data for genome size, organization and complexity are compared with data for agar quantity and quality. Gel quality and quantity do not appear to be correlated with either large repetitive fraction DNA or a high degree of genome complexity.
- Detection of horizontal gene transfer in the genome of the choanoflagellate Salpingoeca rosettaMatriano, Danielle M.; Alegado, Rosanna A.; Conaco, Cecilia (Springer, 2021-03-16)Horizontal gene transfer (HGT), the movement of heritable materials between distantly related organisms, is crucial in eukaryotic evolution. However, the scale of HGT in choanoflagellates, the closest unicellular relatives of metazoans, and its possible roles in the evolution of animal multicellularity remains unexplored. We identified at least 175 candidate HGTs in the genome of the colonial choanoflagellate Salpingoeca rosetta using sequence-based tests. The majority of these were orthologous to genes in bacterial and microalgal lineages, yet displayed genomic features consistent with the rest of the S. rosetta genome—evidence of ancient acquisition events. Putative functions include enzymes involved in amino acid and carbohydrate metabolism, cell signaling, and the synthesis of extracellular matrix components. Functions of candidate HGTs may have contributed to the ability of choanoflagellates to assimilate novel metabolites, thereby supporting adaptation, survival in diverse ecological niches, and response to external cues that are possibly critical in the evolution of multicellularity in choanoflagellates.We thank Joshua Dizon and Francis Tablizo of the Philippine Genome Center Core Facility for Bioinformatics for assistance with scripts and database construction. We thank Becca Lensing (University of Hawai’i), Cheryl Andam (University of New Hampshire), Deo Onda and Ron Leonard Dy (University of the Philippines) for insightful comments and suggestions on the analysis and interpretation of the data. This work was supported by thesis grants from the Department of Science and Technology Accelerated Science and Technology Human Resource Development Program-National Science Consortium (DOST-ASTHRDP-NSC) and the University of the Philippines Marine Science Institute to DM.