The Repeat Sequence Analysis Of The Genus Of Coix

Coix, an oriental genus of the tribe Maydea, is the closest group to the genus Zea after Tripsacum. This genus contains nine to eleven species at different ploidy levels, such as diploids (2n=10), tetraploids (2n=20) and hexaploids (2n=30). However, its genome composition and structure are largely unknown. In this study, low-coverage sequencing of Coix lacryma-jobi L.(2n=20) and Coix aquatica Roxb.(2n=30) were used for graph-based repeat sequence identification. Then the repeat sequences were used to analyze the genome structure, karyotype, the ploidy of C. lacryma-jobi and C. aquatica and the evolution of Zea, Sorghum and Coix. The major results were described as follows:1. We used the Zea mays inbred line B73as reference to estimate the genome size of C. lacryma-jobi and C. aquatica, the result of flow cytometry showed the genome size of C. lacryma-jobi is-1684Mb and the genome size of C. aquatica is～2335Mb.2. The graph-based methods for similarity-based clustering of reads were used to reveal the genome structure of these two species, and we found that approximately76%of the C. lacryma-jobi genome and73%of the C. aquatica genome is consist of repeat sequences. The proportion of LTR retrotransposon, a dominant repeat element, is69%in C. lacryma-jobi genome and64%in C. aquatica genome, respectively.3. Most of LTR retrotransposons are shared within these two genomes, but due to the sweep or the accumulation, the proportion of the LTR retrotransposon varied in the same families. Meanwhile, the variation of the tandem repeats level in these two species indicated the rapid evolution of the tandem repeats in Coix.4. Using tandem repeats as cytogenetic marker, we performed the karyotype analysis for C. lacryma-jobi and C. aquatica. The karyotype results showed C. lacryma-jobi should be a diploid, and C. aquatica should be a triploid. The fact that C. aquatica is almost completely sterile and the chromosome pairing during meiosis metaphase I of these two species support our prediction.5. The karyotype analysis also revealed that10chromosomes of C. aquatica with less homologue to C. lacryma-jobi only showed faint CentX (centromeric satellite for Coix) signal. Therefore, we conducted the ChIP-seq assay for C. aquatica to reveal if these is any new centromeric repeats on these10chromosomes. No any new centromeric repeat sequence but a distinct variant of CentX was found in C. aquatica, this variant only contained the102bp fragment of the153bp CentX. FISH data showed these10chromosomes probably contained two types of CentX, and CentX showed very faint signal on these10chromosomes is because they contained less CentX copies.6. In order to figure out the evolution relationship of Zea, Sorghum and Coix, we downloaded the Zea mays inbred lines B73, Zea luxurians and Sorghum bicolor inbred line Tx378pair-end sequences from DNAnexus. The evolution relationship of the genomic repeat sequences revealed that Coix is closer to Sorghum than Zea, and the relationship between Coix and Zea is closer than that of Zea and Sorghum. The RepeatMasker annotation and the classification of the LTR retrotransposon also support this conclusion.