Abstract
BackgroundAll previously reported eukaryotic nuclear genome sequences have been incomplete, especially in highly repeated units and chromosomal ends. Because repetitive DNA is important for many aspects of biology, complete chromosomal structures are fundamental for understanding eukaryotic cells. Our earlier, nearly complete genome sequence of the hot-spring red alga Cyanidioschyzon merolae revealed several unique features, including just three ribosomal DNA copies, very few introns, and a small total number of genes. However, because the exact structures of certain functionally important repeated elements remained ambiguous, that sequence was not complete. Obviously, those ambiguities needed to be resolved before the unique features of the C. merolae genome could be summarized, and the ambiguities could only be resolved by completing the sequence. Therefore, we aimed to complete all previous gaps and sequence all remaining chromosomal ends, and now report the first nuclear-genome sequence for any eukaryote that is 100% complete.ResultsOur present complete sequence consists of 16546747 nucleotides covering 100% of the 20 linear chromosomes from telomere to telomere, representing the simple and unique chromosomal structures of the eukaryotic cell. We have unambiguously established that the C. merolae genome contains the smallest known histone-gene cluster, a unique telomeric repeat for all chromosomal ends, and an extremely low number of transposons.ConclusionBy virtue of these attributes and others that we had discovered previously, C. merolae appears to have the simplest nuclear genome of the non-symbiotic eukaryotes. These unusually simple genomic features in the 100% complete genome sequence of C. merolae are extremely useful for further studies of eukaryotic cells.
Highlights
All previously reported eukaryotic nuclear genome sequences have been incomplete, especially in highly repeated units and chromosomal ends
Because repetitive DNA is essential to genome function [14], and may contribute to the diversity of isoforms [15] and the evolution of life [16], complete chromosomal structures are fundamental for understanding eukaryotic cells
Using PCR with sequence-specific primers to amplify portions of the C. merolae bacterial artificial chromosomes (BACs) that contained gap regions of interest, and sequencing the resulting subclones, we have reduced the number of gaps between contigs from 46 to zero (Figure 1)
Summary
All previously reported eukaryotic nuclear genome sequences have been incomplete, especially in highly repeated units and chromosomal ends. Nearly complete genome sequence of the hot-spring red alga Cyanidioschyzon merolae revealed several unique features, including just three ribosomal DNA copies, very few introns, and a small total number of genes. Because the exact structures of certain functionally important repeated elements remained ambiguous, that sequence was not complete Those ambiguities needed to be resolved before the unique features of the C. merolae genome could be summarized, and the ambiguities could only be resolved by completing the sequence. Our recently published nuclear-genome sequence of the ultra-small, hot-spring red alga, Cyanidioschyzon merolae 10D, revealed some unique features, such as very few introns, only three copies of ribosomal (r)DNA, and a small total number of genes [9,10]. The results demonstrated that C. merolae possesses the simplest nuclear genome known among nonsymbiotic eukaryotes
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