1. 基于生物信息学的睡莲SSR位点特征分析.
- Author
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苏群, 田敏, 刘俊, 王凌云, 李春牛, 李先民, 黄展文, and 王虹妍
- Subjects
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GENETIC variation , *WHOLE genome sequencing , *GENOME size , *PLANT-water relationships , *TRANSCRIPTOMES , *GENETIC markers in plants - Abstract
[Objective] The Unigene produced by leaf transcriptome of Nymphaea colorata and N.micrantha and the whole genome sequence of N.colorata were analyzed according to SSR loci characteristics. It provided basic data for the germplasm resource identification, genetic diversity analysis and genetic linkage map construction of water lily plants.[Method] Based on the leaf transcriptome data of N.colorata and N.micrantha which were acquired previously in the laboratory and the published genome of N.colorata,MISA software was used to search SSR loci and analyze the frequency, length and primitive types of SSR.[Result] 38 998 SSR loci were found among the 114 762 Unigenes sequences obtained from the transcriptome of N.colorata and N.micrantha.The SSR site frequency was 33.98%.Among them, 30 124 SSR loci belong to complete types. The total length of the SSR motif sequence was 465 550 bp, and had a total average of 21.65 bp.249 029 SSR sites were searched in the N.colorata genome, with an average distribution frequency of 609.0/Mb, including 163 265 intact SSR sites; the total length of SSR motif sequence was 2 775 181 bp, and 27.25 bp, accounted for 0.68% of N.colorata genome size. In the transcriptome and genome, the SSR loci were mainly dinucleotide and single nucleotide repeats, which respectively accounted for 48.87%,41.03% and 51.70%,43.37% of the total SSR. Among dinucleotide repeat motifs, AG/TC and AT/TA types were higher and both much higher than other types of repeat motifs. The number of repetitions of each type in the SSR primitive was mainly 5 to 11 times, of which 10 times were the most. Twelve pairs of SSR primers with good amplification and high polymorphism were selected based on fluorescence capillary electrophoresis from synthetic 144 pairs of SSR primers.[Conclusion] Low-level primitive types are abundant in the SSR of N.colorata and N.micrantha transcriptome and genome, which has great potential for developing and screening SSR primers with high polymorphism. The selected 12 pairs with good amplifications and high polymorphism of SSR primers can be used to study the identification of germplasm resources, genetic diversity analysis and genetic construction of plant chain map. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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