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

Abstract

BackgroundForaminiferan 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.Results454 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.ConclusionsThese data provide the first window into genomic organization and genetic control in these organisms, and also complement and expands upon information about foraminiferal genes based on EST projects. The genomic data obtained are informative for environmental and cell-biological studies, and will also be useful for efforts to understand relationships between foraminiferans and other protists.

Biomineralization ofSchlumbergerella floresiana, a significant carbonate‐producing benthic foraminifer

“…Until now, only a few foraminiferal matrix components have been identified and characterized at the protein level (Weiner & Erez, 1984;Robbins & Donachy, 1991;Robbins & Healy-Williams, 1991). However, these characterizations will become more common as transcriptomes and other genomic resources are developed for foraminifera (Burki et al, 2006;Habura et al, 2011;Pawlowski et al, 2012).…”

“…For other foraminiferal taxa, data are also available on small and large subunits of rDNA genes and sequences for aand b-tubulin and actin genes (Bowser et al, 2006;Pawlowski et al, 2012). Recently, Habura et al (2011) provided the first consistent body of sequence information about the non-coding regions of the genome of a giant unilocular agglutinated foraminifer. However, genomic resources are not yet available for S. floresiana or other calcitic foraminifera.…”

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

“…The latter approach yielded four additional contigs matching our criteria. Three of these represented contigs from two different whole-genome shotgun (WGS) libraries of marine photosynthetic picoeukaryote populations dominated by the green alga Bathycoccus 37 , whereas the fourth one was from a WGS library of Astrammina rara, a foraminiferan protist 38 .…”

“…Reads from these two data sets were assembled with the same pipeline as the viromes, and three putative CHIV genomes were obtained. In addition, putative CHIV genome was retrieved from a WGS project of a foraminifera, Astrammina rara (NCBI Bioproject PRJNA47149; Contig ADNL01003178) 38 .…”

Gene discovery from a pilot study of the transcriptomes from three diverse microbial eukaryotes: Corallomyxa tenera, Chilodonella uncinata, and Subulatomonas tetraspora

“…This amoeboid organism consists of a net of fine pseudopods, with no distinct cell body ( Figure 1b). There is a paucity of genome scale data in the Rhizaria, although EST data from several lineages have been published recently [29,30]. There are currently only six protein-coding genes and SSU-rDNA from C. tenera available on GenBank.…”