Abstract
Long terminal repeat retrotransposons (LTR-RTs) contribute a large fraction of many sequenced plant genomes and play important roles in genomic diversity and phenotypic variations. LTR-RTs are abundantly distributed in plant genomes, facilitating the development of markers based on LTR-RTs for a variety of genotyping purposes. Whole-genome analysis of LTR-RTs was performed in Cleistogenes songorica. A total of 299,079 LTR-RTs were identified and classified as Gypsy type, Copia type, or other type. LTR-RTs were widely distributed in the genome, enriched in the heterochromatic region of the chromosome, and negatively correlated with gene distribution. However, approximately one-fifth of genes were still interrupted by LTR-RTs, and these genes are annotated. Furthermore, four types of primer pairs (PPs) were designed, namely, retrotransposon-based insertion polymorphisms, inter-retrotransposon amplified polymorphisms, insertion site–based polymorphisms, and retrotransposon-microsatellite amplified polymorphisms. A total of 350 PPs were screened in 23 accessions of the genus Cleistogenes, of which 80 PPs showed polymorphism, and 72 PPs showed transferability among Gramineae and non-Gramineae species. In addition, a comparative analysis of homologous LTR-RTs was performed with other related grasses. Taken together, the study will serve as a valuable resource for genotyping applications for C. songorica and related grasses.
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Data availability
The datasets generated and analyzed during the current study project has been deposited at DDBJ/ENA/GenBank under the accession KDOP00000000. The version described in this paper is the first version, KDOP01000000.
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Funding
This research was supported by the program for grants from the National Natural Science Foundation of China (31572453, 31601984), The Gansu Provincial Science and Technology Major Projects (19ZD2NA002), The Gansu Provincial Intellectual Property Program (19ZSCQ044), and the Open Project Program of Arid Meteorology (IAM201703).
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Tiantian Ma and Jiyu Zhang conceived the study and designed the experiments; Xingyi Wei, Yufei Zhang, Jie Li, and Tiantian Ma performed the experiments; Tiantian Ma, Fan Wu, Qi Yan, Zhuanzhuan Yan, Yingbo Yang, and Zhengshe Zhang analyzed the data and interpreted the results; Tiantian Ma and Jiyu Zhang drafted the manuscript with contributions from Gisele Kanzana and Yufeng Zhao; all authors read and approved the final manuscript.
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Communicated by: Izabela Pawłowicz
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Supplementary Information
Table S1
Details of LTR retrotransposons identified in Cleistogenes songorica. (XLSX 13799 kb)
Table S2
Details of LTR retrotransposons identified in Cleistogenes songorica that can be successfully mapped to chromosomes. (XLSX 12667 kb)
Table S3
Details of the distribution of each type of LTR retrotransposons on 20 chromosomes of Cleistogenes songorica. (XLSX 14 kb)
Table S4
Details of the Cleistogenes songorica LTR retrotransposon-based markers developed in the study. (XLSX 36 kb)
Table S5
List of 80 LTR retrotransposon-based molecular marker primers with their sequence used to determine genetic diversity among 23 accessions of the genus Cleistogenes. (XLSX 16 kb)
Table S6
Nei’s genetic distance computed to evaluate genetic diversity among 23 accessions of the genus Cleistogenes using 80 LTR retrotransposon-based molecular marker primers. (XLSX 13 kb)
Fig. S1
Analysis of KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment pathway for Cleistogenes songorica genes which were interrupted with LTR-RTs. (PNG 8 kb)
Fig. S2
Distribution of LTR retrotransposon-based markers on the chromosomes of Cleistogenes songorica. (PNG 147336 kb)
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Ma, T., Wei, X., Zhang, Y. et al. Development of molecular markers based on LTR retrotransposon in the Cleistogenes songorica genome. J Appl Genetics 63, 61–72 (2022). https://doi.org/10.1007/s13353-021-00658-9
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DOI: https://doi.org/10.1007/s13353-021-00658-9