Plant Gene and Trait 2025, Vol.16, No.1, 23-31 http://genbreedpublisher.com/index.php/pgt 24 of the entire genome was 38.4%. From the perspective of base composition, adenine (A) and thymine (T) each account for 30.8%, while cytosine (C) and guanine (G) each account for 19.2%. This structure is similar to that of most other angiosperms, indicating that the chloroplast genome of Eucommia ulmoides has strong conservation. 2.2 Gene content and organization The chloroplast genome of Eucommia ulmoides contains 135 genes, among which 89 are protein-coding genes, 38 are transfer RNA (tRNA) genes, and 8 are ribosomal RNA (rRNA) genes. The quantity and arrangement of these genes are relatively stable, and most of them are related to photosynthesis, transcription and translation. Some SSRs and SNPs were also found in the chloroplast genome of Eucommia ulmoides. These variant regions are very helpful for studying genetic diversity and developing molecular markers (Zhang et al., 2016). Zhong et al. demonstrated in their 2022 study that their presence also indicates that there are some mutation hotspots and potential genetic variations in Eucommia ulmoides. 2.3 Comparison with other plant species The phylogenetic study by Jin et al. (2022) indicates that Eucommia ulmoides is closely related to Aucuba japonica, both belonging to the Oleocales order. This is also supported by the similarity of their chloroplast genomes. Li et al. (2014a) found that the genome of Eucommia ulmoides also exhibited some interesting difference patterns. Most SNPs occurred in gene regions, while insertions and deletions (Indels) were mainly concentrated in the blank areas between genes. This pattern also shows a similar phenomenon in other angiosperms, indicating that the chloroplast genomes of different plants have been relatively conserved during the evolutionary process. The chloroplast genome of Eucommia ulmoides has a typical quad structure, rich genes and obvious genetic variations. 3 Molecular Markers from Chloroplast Genomes 3.1 Types of molecular markers 3.1.1 Simple sequence repeats (SSRs) Simple sequence repeats (also known as microsatellites) are short and repetitive DNA sequences that usually have a high degree of diversity. Researchers have identified and developed some SSR markers in the chloroplast genome of Eucommia ulmoides that can be used as molecular markers. Jin et al. (2020) developed eight polymorphic chloroplast SSR (cpSSR) loci, which can be used to study the population genetics of Eucommia ulmoides. 3.1.2 Single nucleotide polymorphisms (SNPs) Single nucleotide polymorphism (SNPs) refers to the change of a certain base in a DNA sequence. Many such SNPs have been discovered in the chloroplast genome of Eucommia ulmoides. Meng et al. identified 75 SNPs in their 2023 study, among which 59 were located in genetic regions. Among the 40 SNPs presumed to belong to the coding region, all are synonymous mutations, indicating that they do not change the structure of the protein. 3.1.3 Insertions and deletions (Indels) Sometimes, DNA sequences may undergo some changes due to the addition or deletion of certain bases, which are known as insertions and deletions (Indels). Zhong et al. (2022) identified 80 such Indels in the chloroplast genome of Eucommia ulmoides, with the majority occurring in the regions between genes. These Indels can be used as “molecular markers”, which are helpful for phylogenetic research and analyzing the relationships among different populations. 3.2 Development and identification of markers Researchers conducted a comprehensive genomic analysis to develop and identify molecular markers in the chloroplast genome of Eucommia ulmoides. They obtained the complete chloroplast genome by screening methods and then compared different samples to identify the regions with differences. In their 2020 study, Li et al. discovered 71 mutated chloroplast DNA fragments and selected 20 loci from them for population genetic analysis. High-throughput sequencing technologies such as PacBio and Hi-C make genome assembly more accurate and make it easier to find reliable markers (Figure 1).
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