Sung-Il Lee1, Kabwe Nkongolo2, Doori Park3, Ik-Young Choi4, Ah-Young Choi5, Nam-Soo Kim6,7. 1. Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266, Sinjeong, Jeongeup, 500-185, Republic of Korea. 2. Department of Biology, Laurentian University, Sudbury, ON, P3E 2C6, Canada. 3. Department of Molecular Bioscience, Kangwon National University, Chuncheon, 24341, Republic of Korea. 4. Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, 24341, Republic of Korea. 5. Genomics Institute, DNA Care Ltd., Seongnam, 13558, South Korea. 6. Department of Molecular Bioscience, Kangwon National University, Chuncheon, 24341, Republic of Korea. kimnamsu@kangwon.ac.kr. 7. Institute of Bioscience and Biomedical Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea. kimnamsu@kangwon.ac.kr.
Abstract
OBJECTIVE: Betulaceae is a relatively small birch family that comprises about 160 deciduous trees and shrubs. Chloroplast (cp) genome sequencing of Alnus rubra and Betula cordifolia was carried out to elucidate their molecular features and phylogenetic relationship among species in Betulaceae family. METHODS: Chloroplast genome sequencing was carried out using next generation sequencing method. Molecular and genomic features of the two cp genomes were characterized with other cp genomes in Betulaceae. Also, molecular phylogenetic analysis was performed using the whole cp genome sequences. RESULTS: The average cp genome length was 160,136 bp among the Betulaceae species. Base compositions of the cp genomes were skewed toward a high AT ratio, with an average of 63.4%. We identified 117 different genes 83 with protein coding, 4 with ribosomal RNA, and 30 with tRNA. Eighteen genes contained introns which were conserved among the cp genomes of all Betulaceae. We mined 82 SSRs from the cp genomes of A. rubra, A. cordifolia, and A. nana. The SSRs were variable in motif repeat numbers and presence/absence among the cp genomes. CONCLUSION: Chloroplast genome-wide sequence comparison from 11 Betulaceae species and one cp genome of evergreen oak revealed that the patterns of sequence variations were congruent with two subfamily classification Betuloideae (Alnus and Betula) and Corylaceae (Corylus, Ostrya, and Carpinus). Subsequent phylogenetic analysis also supports the sub-classifications of these species.
OBJECTIVE: Betulaceae is a relatively small birch family that comprises about 160 deciduous trees and shrubs. Chloroplast (cp) genome sequencing of Alnus rubra and Betula cordifolia was carried out to elucidate their molecular features and phylogenetic relationship among species in Betulaceae family. METHODS: Chloroplast genome sequencing was carried out using next generation sequencing method. Molecular and genomic features of the two cp genomes were characterized with other cp genomes in Betulaceae. Also, molecular phylogenetic analysis was performed using the whole cp genome sequences. RESULTS: The average cp genome length was 160,136 bp among the Betulaceae species. Base compositions of the cp genomes were skewed toward a high AT ratio, with an average of 63.4%. We identified 117 different genes 83 with protein coding, 4 with ribosomal RNA, and 30 with tRNA. Eighteen genes contained introns which were conserved among the cp genomes of all Betulaceae. We mined 82 SSRs from the cp genomes of A. rubra, A. cordifolia, and A. nana. The SSRs were variable in motif repeat numbers and presence/absence among the cp genomes. CONCLUSION: Chloroplast genome-wide sequence comparison from 11 Betulaceae species and one cp genome of evergreen oak revealed that the patterns of sequence variations were congruent with two subfamily classification Betuloideae (Alnus and Betula) and Corylaceae (Corylus, Ostrya, and Carpinus). Subsequent phylogenetic analysis also supports the sub-classifications of these species.
Authors: Pia Järvinen; Anna Palmé; Luis Orlando Morales; Mika Lännenpää; Markku Keinänen; Tuomas Sopanen; Martin Lascoux Journal: Am J Bot Date: 2004-11 Impact factor: 3.844
Authors: K Shinozaki; M Ohme; M Tanaka; T Wakasugi; N Hayashida; T Matsubayashi; N Zaita; J Chunwongse; J Obokata; K Yamaguchi-Shinozaki; C Ohto; K Torazawa; B Y Meng; M Sugita; H Deno; T Kamogashira; K Yamada; J Kusuda; F Takaiwa; A Kato; N Tohdoh; H Shimada; M Sugiura Journal: EMBO J Date: 1986-09 Impact factor: 11.598