1
|
Liu Q, Wu Z, Tian C, Yang Y, Liu L, Feng Y, Li Z. Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1266797. [PMID: 38155854 PMCID: PMC10753190 DOI: 10.3389/fpls.2023.1266797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
Introduction Prunus pedunculata (Prunoideae: Rosaceae), a relic shrub with strong resistance and multiple application values, is endangered in China. Extensive research had been devoted to gene expression, molecular markers, plastid genome analysis, and genetic background investigations of P. pedunculata. However, the mitochondrial genome of this species has not been systematically described, owing to the complexity of the plant mitogenome. Methods In the present research, the complete mitochondrial genome of P. pedunculata was assembled, annotated, and characterized. The genomic features, gene content and repetitive sequences were analyzed. The genomic variation and phylogenetic analysis have been extensively enumerated. Results and discussion The P. pedunculata mitogenome is a circular molecule with a total length of 405,855 bp and a GC content of 45.63%, which are the smallest size and highest GC content among the known Prunus mitochondrial genomes. The mitogenome of P. pedunculata encodes 62 genes, including 34 unique protein-coding genes (PCGs, excluding three possible pseudogenes), three ribosomal RNA genes, and 19 transfer RNA genes. The mitogenome is rich in repetitive sequences, counting 112 simple sequence repeats, 15 tandem repeats, and 50 interspersed repetitive sequences, with a total repeat length of 11,793 bp, accounting for 2.91% of the complete genome. Leucine (Leu) was a predominant amino acid in PCGs, with a frequency of 10.67%, whereas cysteine (Cys) and tryptophan (Trp) were the least adopted. The most frequently used codon was UUU (Phe), with a relative synonymous codon usage (RSCU) value of 1.12. Selective pressure was calculated based on 20 shared PCGs in the mitogenomes of the 32 species, most of which were subjected to purifying selection (Ka/Ks < 1), whereas ccmC and ccmFn underwent positive selection. A total of 262 potential RNA editing sites in 26 PCGs were identified. Furthermore, 56 chloroplast-derived fragments were ascertained in the mitogenome, ranging from 30 to 858 bp, and were mainly located across IGS (intergenic spacer) regions or rRNA genes. These findings verify the occurrence of intracellular gene transfer events from the chloroplast to the mitochondria. Furthermore, the phylogenetic relationship of P. pedunculata was supported by the mitogenome data of 30 other taxa of the Rosaceae family. Understanding the mitochondrial genome characteristics of P. pedunculata is of great importance to promote comprehension of its genetic background and this study provides a basis for the genetic breeding of Prunus.
Collapse
Affiliation(s)
- Qian Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Zinian Wu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
| | - Chunyu Tian
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Yanting Yang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Lemeng Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Yumei Feng
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Zhiyong Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
| |
Collapse
|
2
|
Vu DD, Shah SNM, Pham MP, Bui VT, Nguyen MT, Nguyen TPT. De novo assembly and Transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics. BMC PLANT BIOLOGY 2020; 20:358. [PMID: 32727354 PMCID: PMC7391578 DOI: 10.1186/s12870-020-02571-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 07/23/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Understanding the genetic diversity in endangered species that occur inforest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers. RESULTS In this study, we employed Illumina HiSeq™ 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances. CONCLUSION Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.
Collapse
Affiliation(s)
- Dinh Duy Vu
- Vietnam - Russia Tropical Centre, 63 Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
- Department of Experimental Taxonomy & Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Syed Noor Muhammad Shah
- Department of Horticulture, Faculty of Agriculture, Gomal University Dera Ismail Khan, Dera Ismail Khan, Pakistan
| | - Mai Phuong Pham
- Vietnam - Russia Tropical Centre, 63 Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
| | - Van Thang Bui
- College of Forestry Biotechnology, Vietnam National University of Forestry, Xuan Mai, Hanoi, Vietnam
| | - Minh Tam Nguyen
- Department of Experimental Taxonomy & Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Thi Phuong Trang Nguyen
- Institute of Ecology and Biological Resource, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, , Cau Giay, Hanoi, Vietnam.
| |
Collapse
|
3
|
Jia B, Wang G, Zheng J, Yang W, Chang S, Zhang J, Liu Y, Li Q, Ge C, Chen G, Liu D, Yang F. Development of novel EST microsatellite markers for genetic diversity analysis and correlation analysis of velvet antler growth characteristics in Sika deer. Hereditas 2020; 157:24. [PMID: 32591015 PMCID: PMC7320565 DOI: 10.1186/s41065-020-00137-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/16/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Sika deer is one of the most popular and valued animals in China. However, few studies have been conducted on the microsatellite of Sika deer, which has hampered the progress of genetic selection breeding. To develop and characterize a set of microsatellites for Sika deer which provide helpful information for protection of Sika deer natural resources and effectively increase the yield and quantity of velvet antler. RESULTS We conducted a transcriptome survey of Sika deer using next-generation sequencing technology. One hundred eighty-two thousand two hundred ninety-five microsatellite markers were identified in the transcriptome, 170 of 200 loci were successfully amplified across panels of 140 individuals from Shuangyang Sika deer population. And 29 loci were found to be obvious polymorphic. Number of alleles is from 3 to 14. The expected heterozygosity ranged from 0.3087 to 0.7644. The observed heterozygosity ranged from 0 to 0.7698. The polymorphism information content values of those microsatellites varied ranged from 0.2602 to 0.7507. The marker-trait association was tested for 6 important and kernel characteristics of two-branched velvet antler in Shuangyang Sika deer through one-way analysis of variance. The results showed that marker-trait associations were identified with 8 different markers, especially M009 and M027. CONCLUSIONS This study not only provided a large scale of microsatellites which were valuable for future genetic mapping and trait association in Sika deer, but also offers available information for molecular breeding in Sika deer.
Collapse
Affiliation(s)
- Boyin Jia
- College of Animal Science and Technology, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Guiwu Wang
- Institute of Wild Economic Animals and Plants and State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Junjun Zheng
- Institute of Wild Economic Animals and Plants and State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Wanyun Yang
- Institute of Wild Economic Animals and Plants and State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Shuzhuo Chang
- Institute of Wild Economic Animals and Plants and State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Jiali Zhang
- College of Animal Science and Technology, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Yuan Liu
- College of Animal Science and Technology, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Qining Li
- College of Animal Science and Technology, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Chenxia Ge
- College of Vocational and Technical Education, Changchun Sci-Tech University, 1699 Donghua Street, Changchun, 130606, China
| | - Guang Chen
- Key laboratory of Straw Biology and Utilization, The Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Dongdong Liu
- Key laboratory of Straw Biology and Utilization, The Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China. .,College of Engineering and Technology, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China.
| | - Fuhe Yang
- Institute of Wild Economic Animals and Plants and State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China.
| |
Collapse
|
4
|
Liu Z, Shao W, Shen Y, Ji M, Chen W, Ye Y, Shen Y. Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana. Hereditas 2018; 155:23. [PMID: 29785177 PMCID: PMC5952850 DOI: 10.1186/s41065-018-0060-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/02/2018] [Indexed: 11/18/2022] Open
Abstract
Background Clematis is the biggest genus in the family Ranunculaceae with about 300 species. Clematis is also a globally important commercial group of flowers, especially in the United States and European countries. Their petals with different colors and shapes make the genus the “Queen of the Vines”. However, the genomic information and phylogeny of Clematis based on existing molecular studies are limited. In this paper, new microsatellites (SSR) markers were identified from the transcriptome data of C. finetiana obtained using the Illumina paired-end sequencing technology. Results Sequences on a total of 71,900 high-quality unigenes with the mean length of 865 bp were produced in this study. There were 6192unigenes annotated and classified into 49 functional sub-groups in three main ontology categories in GO (Gen Ontology) database,14,022 unigenes mapped to COGs (Clusters of Orthologous Groups) database and classified into 25 functional categories, and 21,494 unigenes obtained and divided into 128 pathways of KEGG (Kyoto Encyclopedia of Genes) Database. A total of 7532 SSRs were discovered from 6337 unigenes. We randomly tested 210 primer pairs, of which 52 primer pairs were able to generate specific products, and 19 possessed polymorphism in the 13 wild populations of six species from Clematis, which were used as a test material. Conclusions The dataset of C. finetiana transcriptome and the identified new SSR markers will promote genetic research and breeding effort in Clematis. Electronic supplementary material The online version of this article (10.1186/s41065-018-0060-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zhigao Liu
- 1College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037 Jiangsu People's Republic of China.,2College of Landscape Architecture, Zhejiang A & F University, Hangzhou 311300 Zhejiang, People's Republic of China
| | - Weili Shao
- 2College of Landscape Architecture, Zhejiang A & F University, Hangzhou 311300 Zhejiang, People's Republic of China
| | - Yamei Shen
- 2College of Landscape Architecture, Zhejiang A & F University, Hangzhou 311300 Zhejiang, People's Republic of China
| | - Mengcheng Ji
- 2College of Landscape Architecture, Zhejiang A & F University, Hangzhou 311300 Zhejiang, People's Republic of China
| | - Wenchao Chen
- 2College of Landscape Architecture, Zhejiang A & F University, Hangzhou 311300 Zhejiang, People's Republic of China
| | - Ying Ye
- 2College of Landscape Architecture, Zhejiang A & F University, Hangzhou 311300 Zhejiang, People's Republic of China
| | - Yongbao Shen
- 1College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037 Jiangsu People's Republic of China
| |
Collapse
|