Polymorphism of the rps16 gene intron in Malus Mill. and related Rosaceae Juss. species
The intron of the chloroplast rps16 gene encoding ribosomal protein 16S belongs to group II introns, which have the capacity to self-splice. The sequence of this intron may be quite polymorphic and is widely used for molecular-genetic studies of different plant families. But regions of the intron im...
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2017-11-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/944 |
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| author | M. A. Filyushin K. V. Boris |
| author_facet | M. A. Filyushin K. V. Boris |
| author_sort | M. A. Filyushin |
| collection | DOAJ |
| description | The intron of the chloroplast rps16 gene encoding ribosomal protein 16S belongs to group II introns, which have the capacity to self-splice. The sequence of this intron may be quite polymorphic and is widely used for molecular-genetic studies of different plant families. But regions of the intron important for splicing and organization of the pre-mRNA secondary structure in Rosaceae species including the genus Malus have not yet been described.The aim of the work was to characterize the nucleotide sequences of the rps16 gene intron, to study their polymorphism and to identify the individual structural elements of the intron determining the correct splicing of the rps16 gene in Malus species and related Rosaceae species. Nucleotide sequences of the rps16 chloroplast gene group II intron from 32 Malus species and 17 related Rosaceae species were amplified, sequenced and their polymorphism was analyzed. The rps16 intron sequence in the genus Malus appeared to be very conservative (1.5 %), as well as in Prunus species, the level of the rps16 intron polymorphism was slightly higher (2.25 %). In the studied sequences the boundaries of the six functional domains typical of group II introns and IBS/EBS binding sites were identified. Variability of all the domains and inter-domain regions was studied. Domains V and VI were the most conservative, which may be due to their role in the positioning of the pre-mRNA structures and formation of the catalytically active secondary structure. Thus, polymorphism of the rps16 gene intron was for the first time studied in Malus species and related Rosaceae species. The boundaries of all six functional domains typical of group II introns and IBS/EBS binding sites were identified. The most conservative were domains V and VI. |
| format | Article |
| id | doaj-art-8b1ca9d18baf458abfe5b29733e4b201 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2017-11-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-8b1ca9d18baf458abfe5b29733e4b2012025-02-01T09:58:04ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592017-11-0121559660010.18699/VJ17.20-o656Polymorphism of the rps16 gene intron in Malus Mill. and related Rosaceae Juss. speciesM. A. Filyushin0K. V. Boris1Institute of Bioengineering, Research Center of Biotechnology RAS;Institute of Bioengineering, Research Center of Biotechnology RAS; Vavilov Institute of General Genetics RASThe intron of the chloroplast rps16 gene encoding ribosomal protein 16S belongs to group II introns, which have the capacity to self-splice. The sequence of this intron may be quite polymorphic and is widely used for molecular-genetic studies of different plant families. But regions of the intron important for splicing and organization of the pre-mRNA secondary structure in Rosaceae species including the genus Malus have not yet been described.The aim of the work was to characterize the nucleotide sequences of the rps16 gene intron, to study their polymorphism and to identify the individual structural elements of the intron determining the correct splicing of the rps16 gene in Malus species and related Rosaceae species. Nucleotide sequences of the rps16 chloroplast gene group II intron from 32 Malus species and 17 related Rosaceae species were amplified, sequenced and their polymorphism was analyzed. The rps16 intron sequence in the genus Malus appeared to be very conservative (1.5 %), as well as in Prunus species, the level of the rps16 intron polymorphism was slightly higher (2.25 %). In the studied sequences the boundaries of the six functional domains typical of group II introns and IBS/EBS binding sites were identified. Variability of all the domains and inter-domain regions was studied. Domains V and VI were the most conservative, which may be due to their role in the positioning of the pre-mRNA structures and formation of the catalytically active secondary structure. Thus, polymorphism of the rps16 gene intron was for the first time studied in Malus species and related Rosaceae species. The boundaries of all six functional domains typical of group II introns and IBS/EBS binding sites were identified. The most conservative were domains V and VI.https://vavilov.elpub.ru/jour/article/view/944group ii intronsmalusrosaceaepre-mrna secondary structuregenetic polymorphism |
| spellingShingle | M. A. Filyushin K. V. Boris Polymorphism of the rps16 gene intron in Malus Mill. and related Rosaceae Juss. species Вавиловский журнал генетики и селекции group ii introns malus rosaceae pre-mrna secondary structure genetic polymorphism |
| title | Polymorphism of the rps16 gene intron in Malus Mill. and related Rosaceae Juss. species |
| title_full | Polymorphism of the rps16 gene intron in Malus Mill. and related Rosaceae Juss. species |
| title_fullStr | Polymorphism of the rps16 gene intron in Malus Mill. and related Rosaceae Juss. species |
| title_full_unstemmed | Polymorphism of the rps16 gene intron in Malus Mill. and related Rosaceae Juss. species |
| title_short | Polymorphism of the rps16 gene intron in Malus Mill. and related Rosaceae Juss. species |
| title_sort | polymorphism of the rps16 gene intron in malus mill and related rosaceae juss species |
| topic | group ii introns malus rosaceae pre-mrna secondary structure genetic polymorphism |
| url | https://vavilov.elpub.ru/jour/article/view/944 |
| work_keys_str_mv | AT mafilyushin polymorphismoftherps16geneintroninmalusmillandrelatedrosaceaejussspecies AT kvboris polymorphismoftherps16geneintroninmalusmillandrelatedrosaceaejussspecies |