The Repeat Sequence Analysis Of The Genome Of Tripsacum

The genus Tripsacum belongs to Maydeae of the Poaceae family. Tripsacum is not only a horticultural crop but also widely used as pasture forage, with good resistance to insects and drought. In the subtribe Maydeae, Tripsacum is the genera closely related to Zea. Tripsacum was the important species in the process of maize evolution. The analysis of the genome is important to deeply undertand the species. Repetitive sequences are important to eukaryotes and occupied large porprotion of the genome. There are many types of repetitive DNA sequences with different characteristics. Satellite DNA evolves rapidly, and shows variation in sequences and copy numbers and distribution. Thus, satellite DNA is useful to identify chromosome and karyotyping analysis. Previous studies on Tripsacum focused mainly on using Tripsacum to improve maize and karyotype comparison with maize. However, genomic information of Tripsacum is extremely sparse.In our study, we sequenced the nucleic genome of two diploid MR (Tripsacum dactyloides var. meridonale,2n=36,) and diploid DD(Tripsacum dactyloides,2n=36), and one tetraploid DL (Tripsacum dactyloides,2n=72), obtained 7G,10G, and 8G datas. The main results showed as follows:1、We determine the genome size of MR, DD, and DL by flow cytometry. We used the genome size of Zea mays B73 reference. The estimated genome size of MR, DD, and DL was approximately 3103Mb,3814Mb, and 6892Mb, respectively.2、Low coverage sequenced on the genome of MR, DD and DL was performed by Hiseq2000. The sequencing data for MR, DD and DL were 7457.58Mb,10216.58Mb, and 8485.93Mb, respectively.3、Bioimformation analysis shows that repetitive sequences occupied 63.23%、59.20% and 61.57% of the genome of MR,DD,DL, respectively. The retrotransposons accounted for 46.53%,42.26%, and 51.86%, and satellite DNA occupied 14.66%,13.99% and 7.19% in MR, DD and DL, respectively.4、We performed karyotype analysis on diploid MR and DD mitosis metaphase chromosomes using satellites. And identify the different distribution of these satellites in DL. The distribution patterns presented similar in DD and DL.5、The analysis of ITS sequences showed that tetraploid DL is more close to DD than MR.6、To study whether Tripsacum centromere contained new centromere repetitive sequences, we preform ChIP-seq using OsCENH3 antibody and Realtime PCR. The results indicated that CentC and CRM are relatively enriched in the ChIP-DNA. And we didin’t find new type of centromere repetitive sequence. It indicated that the centromere repetitive sequences in Tripsacum are conserved.7、We performed comparative analysis on the repetitive sequences of DD, MR and DL. DL had more co-existing families with DD than with MR. We also performed comparative analysis on the repetitive sequences of Zea, Tripsacum, Coix, and Sorghum. The number of repetitive sequences families of Zea and Tripsacum shared is the largest. Zea and Sorghum only shared limited repetitive sequences families.All together, our results indicated that DL might relatively closer to DD than with MR. And we speculated that the tetraploid DL might be evolved from diploid DD.