Basic Characteristics of Flower Transcriptome Data and Derived Novel EST-SSR Markers of <i>Luculia yunnanensis</i>, an Endangered Species Endemic to Yunnan, Southwestern China
<i>Luculia yunnanensis</i> (Rubiaceae), an evergreen shrub or small tree, is endemic to China and confined to Nujiang Prefecture, Yunnan Province. This plant is of high ornamental value owing to its attractive pink flowers, sweet fragrance, and long flowering period. Due to the influence...
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MDPI AG
2022-04-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/11/9/1204 |
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| author | Yao Zhang Xi Liu Yuying Li Xiongfang Liu Hong Ma Suping Qu Zhenghong Li |
| author_facet | Yao Zhang Xi Liu Yuying Li Xiongfang Liu Hong Ma Suping Qu Zhenghong Li |
| author_sort | Yao Zhang |
| collection | DOAJ |
| description | <i>Luculia yunnanensis</i> (Rubiaceae), an evergreen shrub or small tree, is endemic to China and confined to Nujiang Prefecture, Yunnan Province. This plant is of high ornamental value owing to its attractive pink flowers, sweet fragrance, and long flowering period. Due to the influence of climate change and human factors, the distribution range of <i>L. yunnanensis</i> has exhibited a significant shrinking trend, and it has become a vulnerable species that is in urgent need of conservation and rational utilization research. In this study, the flower transcriptome sequencing of <i>L. yunnanensis</i> was conducted using an Illumina HiSeq platform. We designed and developed a series of EST-SSR primers based on the flower transcriptome data of <i>L. yunnanensis</i>. The results showed that 98,389 unigenes were obtained from the <i>L. yunnanensis</i> flower transcriptome, all of which were aligned with sequences in public databases. Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG, and GO annotated 31,859, 13,853, 22,684, 10,947, 21,416, 9722, and 23,390 unigenes, respectively. The MISA (Microsatellite) tool was used to identify SSR loci from all unigenes, and a total of 15,384 SSRs were identified. Repeat motifs were given priority with mononucleotides, dinucleotides, and trinucleotides. The 81 primer pairs were synthesized randomly, of which 44 pairs showed effective amplification. A total of 17 primers showed stable amplification, and rich polymorphism was observed in 6 populations. We concluded via genetic diversity analysis that the average effective number of alleles (Ne), Shannon’s information index (I), and polymorphism information content (PIC) were 1.925, 0.837, and 0.403, respectively. In conclusion, 17 EST-SSR primers can be used for subsequent population genetic diversity analysis and molecular-marker-assisted breeding, which is of great significance for formulating resource conservation and utilization strategies for <i>L. yunnanensis</i>. |
| first_indexed | 2024-03-10T03:47:27Z |
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| spelling | doaj.art-030e089190964308b4979b3dfe51d82d2023-11-23T09:02:59ZengMDPI AGPlants2223-77472022-04-01119120410.3390/plants11091204Basic Characteristics of Flower Transcriptome Data and Derived Novel EST-SSR Markers of <i>Luculia yunnanensis</i>, an Endangered Species Endemic to Yunnan, Southwestern ChinaYao Zhang0Xi Liu1Yuying Li2Xiongfang Liu3Hong Ma4Suping Qu5Zhenghong Li6Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, ChinaSchool of Geography and Ecotourism, Southwest Forestry University, Kunming 650224, ChinaCollege of Grassland Science, Shanxi Agricultural University, Jinzhong 030801, ChinaInstitute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, ChinaInstitute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, ChinaFlower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, ChinaInstitute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China<i>Luculia yunnanensis</i> (Rubiaceae), an evergreen shrub or small tree, is endemic to China and confined to Nujiang Prefecture, Yunnan Province. This plant is of high ornamental value owing to its attractive pink flowers, sweet fragrance, and long flowering period. Due to the influence of climate change and human factors, the distribution range of <i>L. yunnanensis</i> has exhibited a significant shrinking trend, and it has become a vulnerable species that is in urgent need of conservation and rational utilization research. In this study, the flower transcriptome sequencing of <i>L. yunnanensis</i> was conducted using an Illumina HiSeq platform. We designed and developed a series of EST-SSR primers based on the flower transcriptome data of <i>L. yunnanensis</i>. The results showed that 98,389 unigenes were obtained from the <i>L. yunnanensis</i> flower transcriptome, all of which were aligned with sequences in public databases. Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG, and GO annotated 31,859, 13,853, 22,684, 10,947, 21,416, 9722, and 23,390 unigenes, respectively. The MISA (Microsatellite) tool was used to identify SSR loci from all unigenes, and a total of 15,384 SSRs were identified. Repeat motifs were given priority with mononucleotides, dinucleotides, and trinucleotides. The 81 primer pairs were synthesized randomly, of which 44 pairs showed effective amplification. A total of 17 primers showed stable amplification, and rich polymorphism was observed in 6 populations. We concluded via genetic diversity analysis that the average effective number of alleles (Ne), Shannon’s information index (I), and polymorphism information content (PIC) were 1.925, 0.837, and 0.403, respectively. In conclusion, 17 EST-SSR primers can be used for subsequent population genetic diversity analysis and molecular-marker-assisted breeding, which is of great significance for formulating resource conservation and utilization strategies for <i>L. yunnanensis</i>.https://www.mdpi.com/2223-7747/11/9/1204<i>Luculia yunnanensis</i>transcriptomeEST-SSR markerspolymorphismconservation genetics |
| spellingShingle | Yao Zhang Xi Liu Yuying Li Xiongfang Liu Hong Ma Suping Qu Zhenghong Li Basic Characteristics of Flower Transcriptome Data and Derived Novel EST-SSR Markers of <i>Luculia yunnanensis</i>, an Endangered Species Endemic to Yunnan, Southwestern China Plants <i>Luculia yunnanensis</i> transcriptome EST-SSR markers polymorphism conservation genetics |
| title | Basic Characteristics of Flower Transcriptome Data and Derived Novel EST-SSR Markers of <i>Luculia yunnanensis</i>, an Endangered Species Endemic to Yunnan, Southwestern China |
| title_full | Basic Characteristics of Flower Transcriptome Data and Derived Novel EST-SSR Markers of <i>Luculia yunnanensis</i>, an Endangered Species Endemic to Yunnan, Southwestern China |
| title_fullStr | Basic Characteristics of Flower Transcriptome Data and Derived Novel EST-SSR Markers of <i>Luculia yunnanensis</i>, an Endangered Species Endemic to Yunnan, Southwestern China |
| title_full_unstemmed | Basic Characteristics of Flower Transcriptome Data and Derived Novel EST-SSR Markers of <i>Luculia yunnanensis</i>, an Endangered Species Endemic to Yunnan, Southwestern China |
| title_short | Basic Characteristics of Flower Transcriptome Data and Derived Novel EST-SSR Markers of <i>Luculia yunnanensis</i>, an Endangered Species Endemic to Yunnan, Southwestern China |
| title_sort | basic characteristics of flower transcriptome data and derived novel est ssr markers of i luculia yunnanensis i an endangered species endemic to yunnan southwestern china |
| topic | <i>Luculia yunnanensis</i> transcriptome EST-SSR markers polymorphism conservation genetics |
| url | https://www.mdpi.com/2223-7747/11/9/1204 |
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