Characteristics of SSRs in Zicaitai Mitochondrial Genome

XIAO Wanyu; ZHOU Xianyu; REN Hailong; HUANG Hongdi; ZHENG Yansong; ZHANG Jing; XU Donglin

doi:10.19303/j.issn.1008-0384.2024.01.007

Volume 39 Issue 1

Jan. 2024

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Article Navigation > Fujian Journal of Agricultural Sciences > 2024 > 39(1): 49-56

XIAO W Y, ZHOU X Y, REN H L, et al. Characteristics of SSRs in Zicaitai Mitochondrial Genome [J]. Fujian Journal of Agricultural Sciences，2024，39（1）：49−56 doi: 10.19303/j.issn.1008-0384.2024.01.007

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XIAO W Y, ZHOU X Y, REN H L, et al. Characteristics of SSRs in Zicaitai Mitochondrial Genome [J]. Fujian Journal of Agricultural Sciences，2024，39（1）：49−56 doi: 10.19303/j.issn.1008-0384.2024.01.007

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Characteristics of SSRs in Zicaitai Mitochondrial Genome

doi: 10.19303/j.issn.1008-0384.2024.01.007

1.
Guangzhou Institute of Agriculture Science, Guangzhou, Guangdong　510308, China
2.
Crop Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of Crops Genetics and Improvement, Guangzhou, Guangdong　510640, China
3.
Guangdong Provincial Improved Variety Introduce Service Corp., Guangzhou, Guangdong　510091, China

Received Date: 2023-05-10
Accepted Date: 2024-01-08
Rev Recd Date: 2024-01-04

Available Online: 2024-01-25

Publish Date: 2024-01-28

Abstract

Abstract

Objective The simple sequence repeats (SSRs) in the mitochondrial genome of zicaitai (Brassica rapa var. Purpuraria) were compared with those of other species in the genus. Method MISA software was used to search the mitochondrial genomes of zicaitai as well as 5 other major species and 3 mutants of Brassica rapa. The SSR sequence distributions of the specimens were compared and analyzed. Result In the mitochondrial genomes, 168, 170, 167, 168, 180, 280, 185, 165, and 179 complete SSRs were screened. The sequences showed relative densities of 764, 774, 760, 764, 775, 777, 721, 744, and 771 per Mb with total lengths of 1562, 1577, 1547, 1562, 1664, 2564, 1722, 1524, and 1646 bp that accounted for 0.71%, 0.72%, 0.70%, 0.71%, 0.72%, 0.71%, 0.67%, 0.69%, and 0.71% of the total sequence length of each specimen, respectively. Among the 1-6 different nucleotide repeat units in zicaitai and the other major Brassica species, most SSRs were mononucleotide, which was followed by dinucleotide, tetranucleotide, trinucleotide, and pentanucleotide, but no hexonucleotide. A/T, AG/CT, AT/AT, and C/G were the common repeat unit types in them. Conclusion The mitochondrial genome of zicaitai was 219779 bp with 168 SSRs at the relative density of 764 markers/Mb and 9 bp in length. Mono-, di-, and tetra-nucleotides were the most abundant repeat units, which could potentially be developed as highly polymorphic markers for species differentiation.
- Zicaitai,
- Brassica,
- mitochondrion,
- SSR

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References(35)

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