Interspecific chloroplast genome sequence diversity and genomic resources in Diospyros
| Autor: | Li Wenqing, Zhili Suo, Xiaobai Jin, Yanlei Liu, Xiaoman Xie, Lu Yizeng, Wenpan Dong, Zhirong Yang, Yong Yang |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Genetic Markers Lotus Plant Science Genome Genetic diversity 03 medical and health sciences lcsh:Botany Chloroplast genome Hyper-variable region Genome Chloroplast Phylogeny NdhF Whole genome sequencing biology DNA Chloroplast food and beverages Genetic Variation Diospyros biology.organism_classification lcsh:QK1-989 030104 developmental biology Chloroplast DNA Evolutionary biology Genetic marker Research Article |
| Zdroj: | BMC Plant Biology BMC Plant Biology, Vol 18, Iss 1, Pp 1-11 (2018) |
| ISSN: | 1471-2229 |
| Popis: | Background Fruits of persimmon plants are traditional healthy food in China, Korea and Japan. However, due to the shortage of morphological and DNA markers, the development of persimmon industry has been heavily inhibited. Results Chloroplast genomes of Diospyros cathayensis, D. virginiana, D. rhombifolia and D. deyangensis were newly sequenced. Comparative analyses of ten chloroplast genomes including six previously published chloroplast genomes of Diospyros provided new insights into the genome sequence diversity and genomic resources of the genus. Eight hyper-variable regions, trnH-psbA, rps16-trnQ, rpoB-trnC, rps4-trnT-trnL, ndhF, ndhF-rpl32-trnL, ycf1a, and ycf1b, were discovered and can be used as chloroplast DNA markers at/above species levels. The complete chloroplast genome sequences provided the best resolution at inter-specific level in comparison with different chloroplast DNA sequence datasets. Conclusion Diospyros oleifera, D. deyangensis, D. virginiana, D. glaucifolia, D. lotus and D. jinzaoshi are important wild species closely related to the cultivated persimmon D. kaki. The hyper-variable regions can be used as DNA markers for global genetic diversity detection of Diospyros. Deeper study on these taxa would be helpful for elucidating the origin of D. kaki. Electronic supplementary material The online version of this article (10.1186/s12870-018-1421-3) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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