Genomes of higher plants comprise a large proportion of repetitive DNAs, where one major class is satellite DNA. Satellite DNA is organized in tandem arrays of basic repeating units, which often occurs in heterochromatin of centromeric/pericentromeric and intercalary as well as subtelomeric regions. Besides these typical satellite repeats, there are also non-typical satellite DNAs, which are organized in short tandem arrays and integrated into a transposable element. The chromosomal localization of non-typical satellites is not in large regions of heterochromatin, but tend to be dispersed along chromosomes. This thesis describes the identification of the major repeat classes including major satellite content in six beet and related species. The focus was on identification and characterization of new satellite families in the beet genomes.
In this study, the information regarding repetitive DNA as well as satellite families fraction in six beet and related species was gained based on graph-based clustering of next generation sequenced short sequence reads. The repeat proportion of the six analyzed species ranges from 34.4% in C. quinoa to 65.6% in B. lomatogona, in which the portion of nearly 50% belongs to B. vulgaris, B. nana, P. procumbens, and P. patellaris. Among all classes of repetitive DNAs, LTR retrotransposons are the most abundant repeat type in all analyzed genomes, which is a common feature of higher plant genomes. The other repeat sequences are DNA transposons, rDNA, and satellite DNA with variable portions in different species. A set of satellite families in each species was analyzed in detail and reflects the relationship between six species. The closely related relationship between B. lomatogona and B. nana as well as between P. procumbens and P. patellaris is affirmed by seven and 13 satellite families shared between two species, respectively. Similarly, the closer relationship between B. vulgaris and two species B. lomatogona and B. nana than between B. vulgaris and two species P. procumbens and P. patellaris from the sister-genus Patellifolia is also confirmed. C. quinoa is a distantly related species and this is reflected by vastly different satellite content. Therefore, satellite DNA analysis might be a useful tool to trace species evolution.
In the B. lomatogona genome, by the application of RepeatExplorer tool, six novel tandemly repeated DNA sequences were identified and designated BlSat1-BlSat6. The three typical satellite families BlSat1, BlSat5, and BlSat6 are organized in tandem arrays in large heterochromatic blocks. BlSat1 is mainly localized in the pericentric region of the chromosome 3, 5, 6, and 9, while BlSat5 is amplified in the pericentromeric region of the chromosome 3, 5, and 7. BlSat6 is a chromosome-specific satellite and is located in the subtelomeric region on the south arm of the chromosome 8. The other three satellite families BlSat2, BlSat3, and BlSat4 are characterized as non-typical satellite DNA because of their dispersed distribution along chromosomes. BlSat2 and BlSat3 are identified as a tandem repeat domain in Ogre/Tat retrotransposons. The occurrence of one or several short tandem arrays in a transposable element is a common phenomenon in both animals and plants. These short repeats are considered to be continuously evolving and eventually amplifying to new satellite families.
Furthermore, the distribution of the six new satellite families in beet and related species was confirmed by comparative PCR, comparative Southern hybridization, and mapping of sequence reads from referent species against each satellite sequence. The BlSat1 and BlSat6 satellite families are specific for the genus Beta, while BlSat5 is only amplified in two sections Corollinae and Nanae of the genus Beta. BlSat4 is an ancient satellite family which exists in all tested species belonging to the genera Beta, Patellifolia, Chenopodium, and Spinacia, whereas BlSat2 and BlSat3 might have evolved before the separation of the genus Beta and Patellifolia but their sequences have been lost or heavily diverged during the species radiation.
Comparison of two wild beet genomes P. procumbens and P. patellaris was performed aiming to address the open question whether P. patellaris is auto- or allotetraploid. The high similarity between these two genomes indicates their close relationship. However, the genetic difference between two genomes, in particular the molecular characteristics as well as the chromosomal localization of two satellite families PproSat1 and PpatSat1, might support a hypothesis that P. patellaris is allotetraploid species with a half of its chromosome set derived from P. procumbens.
The results obtained in this work might provide comprehensive information of the repetitive classes as well as satellite families in the genomes of beets and related species. The results can be used as the species-specific and chromosome-specific markers in beet genome studies
