High-throughput sequencing of Astrammina rara : Sampling the giant genome of a giant foraminiferan protist

• Published in: BMC Genomics
• Main Authors: Reilly Andrew A, Hou Yubo, Habura Andrea, Bowser Samuel S
• Format: Article in Journal/Newspaper
• Language: English
• Published: BMC 2011
• Subjects: Biotechnology; TP248.13-248.65; Genetics; QH426-470; Antarctic; The Antarctic; Antarc*
• Online Access: https://doi.org/10.1186/1471-2164-12-169; https://doaj.org/article/58ee919eb1a7404793140fe1c2ca3441

Abstract Background Foraminiferan protists, which are significant players in most marine ecosystems, are also genetic innovators, harboring unique modifications to proteins that make up the basic eukaryotic cell machinery. Despite their ecological and evolutionary importance, foraminiferan genomes are poorly understood due to the extreme sequence divergence of many genes and the difficulty of obtaining pure samples: exogenous DNA from ingested food or ecto/endo symbionts often vastly exceed the amount of "native" DNA, and foraminiferans cannot be cultured axenically. Few foraminiferal genes have been sequenced from genomic material, although partial sequences of coding regions have been determined by EST studies and mass spectroscopy. The lack of genomic data has impeded evolutionary and cell-biology studies and has also hindered our ability to test ecological hypotheses using genetic tools. Results 454 sequence analysis was performed on a library derived from whole genome amplification of microdissected nuclei of the Antarctic foraminiferan Astrammina rara . Xenogenomic sequence, which was shown not to be of eukaryotic origin, represented only 12% of the sample. The first foraminiferal examples of important classes of genes, such as tRNA genes, are reported, and we present evidence that sequences of mitochondrial origin have been translocated to the nucleus. The recovery of a 3' UTR and downstream sequence from an actin gene suggests that foraminiferal mRNA processing may have some unusual features. Finally, the presence of a co-purified bacterial genome in the library also permitted the first calculation of the size of a foraminiferal genome by molecular methods, and statistical analysis of sequence from different genomic sources indicates that low-complexity tracts of the genome may be endoreplicated in some stages of the foraminiferal life cycle. Conclusions These data provide the first window into genomic organization and genetic control in these organisms, and also complement and expands upon information ...