PARK, Jongsun
(InfoBoss Co., Ltd. and InfoBoss Research Center)
,
XI, Hong
(InfoBoss Co., Ltd. and InfoBoss Research Center)
,
OH, Sang-Hun
(Department of Biology, Daejeon University)
Complete chloroplast genome sequences provide detailed information about any structural changes of the genome, instances of phylogenetic reconstruction, and molecular markers for fine-scale analyses. Recent developments of next-generation sequencing (NGS) tools have led to the rapid accumulation of ...
Complete chloroplast genome sequences provide detailed information about any structural changes of the genome, instances of phylogenetic reconstruction, and molecular markers for fine-scale analyses. Recent developments of next-generation sequencing (NGS) tools have led to the rapid accumulation of genomic data, especially data pertaining to chloroplasts. Short reads deposited in public databases such as the Sequence Read Archive of the NCBI are open resources, and the corresponding chloroplast genomes are yet to be completed. The V. dilatatum complex in Korea consists of four morphologically similar species: V. dilatatum, V. erosum, V. japonicum, and V. wrightii. Previous molecular phylogenetic analyses based on several DNA regions did not resolve the relationship at the species level. In order to examine the level of variation of the chloroplast genome in the V. dilatatum complex, raw reads of V. dilatatum deposited in the NCBI database were used to reconstruct the whole chloroplast genome, with these results compared to the genomes of V. erosum, V. japonicum, and three other species in Viburnum. These comparative genomics results found no significant structural changes in Viburnum. The degree of interspecific variation among the species in the V. dilatatum complex is very low, suggesting that the species of the complex may have been differentiated recently. The species of the V. dilatatum complex share large unique deletions, providing evidence of close relationships among the species. A phylogenetic analysis of the entire genome of the Viburnum showed that V. dilatatum is a sister to one of two accessions of V. erosum, making V. erosum paraphyletic. Given that the overall degree of variation among the species in the V. dilatatum complex is low, the chloroplast genome may not provide a phylogenetic signal pertaining to relationships among the species.
Complete chloroplast genome sequences provide detailed information about any structural changes of the genome, instances of phylogenetic reconstruction, and molecular markers for fine-scale analyses. Recent developments of next-generation sequencing (NGS) tools have led to the rapid accumulation of genomic data, especially data pertaining to chloroplasts. Short reads deposited in public databases such as the Sequence Read Archive of the NCBI are open resources, and the corresponding chloroplast genomes are yet to be completed. The V. dilatatum complex in Korea consists of four morphologically similar species: V. dilatatum, V. erosum, V. japonicum, and V. wrightii. Previous molecular phylogenetic analyses based on several DNA regions did not resolve the relationship at the species level. In order to examine the level of variation of the chloroplast genome in the V. dilatatum complex, raw reads of V. dilatatum deposited in the NCBI database were used to reconstruct the whole chloroplast genome, with these results compared to the genomes of V. erosum, V. japonicum, and three other species in Viburnum. These comparative genomics results found no significant structural changes in Viburnum. The degree of interspecific variation among the species in the V. dilatatum complex is very low, suggesting that the species of the complex may have been differentiated recently. The species of the V. dilatatum complex share large unique deletions, providing evidence of close relationships among the species. A phylogenetic analysis of the entire genome of the Viburnum showed that V. dilatatum is a sister to one of two accessions of V. erosum, making V. erosum paraphyletic. Given that the overall degree of variation among the species in the V. dilatatum complex is low, the chloroplast genome may not provide a phylogenetic signal pertaining to relationships among the species.
* AI 자동 식별 결과로 적합하지 않은 문장이 있을 수 있으니, 이용에 유의하시기 바랍니다.
문제 정의
, 2014). Their focus was on phylogenetic relationships among the species of Viburnum based on sequences from the chloroplast genome, as opposed to assembling the chloroplast genome itself. These raw reads are important resources for those attempting to assemble the complete sequence of the chloroplast genome, generating new information about structural variations, additional nucleotide sequences for phylogenetic analyses, and comparative genomics for a better understanding of the evolution of Viburnum.
제안 방법
This study aims to establish a procedure to use when assembling a complete chloroplast genome from raw reads deposited in the NCBI database, to compare the chloroplast genomes of the V. dilatatum complex along with other species in Viburnum examining the level of variations among the species, and to reconstruct phylogenetic relationships of the species in the complex inferred from the entire genome of the chloroplast.
대상 데이터
betulifolium with 130 genes consisting of 85 protein-coding genes (PCGs), 37 transfer RNAs, and eight ribosomal RNAs (Table 2). Seventeen genes consisting of seven tRNA genes (trnI-CAU, trnL-CAA, trnV-GAC, trnI-GAU, trnA-UGC, trnR-AGC, and trnN-GUU), four rRNA genes (rRNA5, rRNA4.5, rRNA23, and rRNA16), and six PCGs (ndhB, rps12, rpl23, ycf2, rps7, and rpl2) are duplicated in the IR regions. Eleven genes (trnK-UUU, rps16, atpF, rpoC1, petB, petD, rpl2, ndhB, trnI-GAU, trnA-UGC, and ndhA) contain one intron, and clpP, rps12, and ycf3 have two introns.
이론/모형
450 (Katoh and Standley, 2013). Based on these alignments, nucleotide diversity was calculated using the method proposed by Nei and Li (Nei and Li, 1979) implemented in the Plant Chloroplast Database (PCD; http://www.cp-genome.net) (Park et al., in preparation). The window size was set to 500 bp and the step size to 200 bp in the sliding-window analysis.
성능/효과
Nucleotide diversity of Viburnum chloroplast genomes. A. The X-axis denotes the positions of chloroplast genomes from multiple sequence aligned Viburnum chloroplast genomes and the Y-axis indicates the nucleotide diversity calculated with a windows size of 500 bp and a step size of 200 bp. Below the X-axis, the three block diagrams indicate the LSC, IR, and SSC regions, respectively.
Sampling may have resulted in seemingly biased nucleotide diversity. Based on four regions of chloroplast genomes (LSC, SSC, and two IRs), the two IR regions present the lowest nucleotide diversity, indicating that the IR regions are highly conservative. Except for the region (from 29,800 bp to 31,200 bp), which displays very high nucleotide diversity (Fig.
2). In this case, 7 SNPs and 19 INDELs and 9 SNPs and 42 INDELs were identified between V. dilatatum and each of the two accessions of V. erosum, respectively while 19 SNPs and 38 INDELs were found between V. dilatatum and V. japonicum. The numbers of SNP and INDEL within V.
japonicum, and it represented large deletions in the species. Presence of the gap region 1 in the species of V. dilatatum complex but not in V. betulifolium, all of which are members of the Succodontotinus clade, suggesting that the species of the V. dilatatum complex are more closely related to each other than they are to V. betulifolium. A previous phylogenetic study did not resolve the relationship (Clement et al.
amplificatum. Similarly, 944 SNPs and 3,080 INDELs were identified between V. amplificatum and V. utile, and 1,295 SNPs and 2,933 INDELs were found between V. amplificatum and V. betulifolium. Thus, the low level of interspecific variation within the V.
amplificatum is 159,009 bp with the four subregions: 87,545 bp of LSC and 18,518 bp of SSC regions, along with 26,473 bp of a pair of IRs (Table 1). The GC ratio of the complete chloroplast genome is 38.1% and those of the LSC, SSC, and IR regions are 36.3%, 32.1%, and 43.0%, respectively.
dilatatum is 158,586 bp in length and has four subregions: 87,064 bp of large single copy (LSC) and 18,492 bp of small single copy (SSC) regions, along with 26,515 bp of a pair of inverted repeats (IRs) (Table 1). The GC ratio of the complete chloroplast genome is 38.1% and those of the LSC, SSC, and IR regions are 36.4%, 32.0%, and 43.0%, respectively. The length of chloroplast genome of V.
The level of the interspecific variations of the chloroplast genome of the V. dilatatum complex in terms of the number of single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) was low (Fig. 2). In this case, 7 SNPs and 19 INDELs and 9 SNPs and 42 INDELs were identified between V.
japonicum. The numbers of SNP and INDEL within V. erosum are 16 and 49, suggesting that the intraspecific variation of chloroplast genomes of V. erosum is higher than interspecific variation between V. erosum and V. dilatatum (Fig. 2).
The structure and gene content of the two newly assembled chloroplast are identical to those of V. erosum and V. betulifolium with 130 genes consisting of 85 protein-coding genes (PCGs), 37 transfer RNAs, and eight ribosomal RNAs (Table 2). Seventeen genes consisting of seven tRNA genes (trnI-CAU, trnL-CAA, trnV-GAC, trnI-GAU, trnA-UGC, trnR-AGC, and trnN-GUU), four rRNA genes (rRNA5, rRNA4.
amplificatum was 13,064,398 and 23,639,938, respectively. These raw data provided 432-fold coverage for the chloroplast genome of V. dilatatum and 161-fold for V. amplificatum, which were sufficient amount to complete the whole genome. The chloroplast genome of V.
, 2018). Viburnum japonicum was supported as a monophyletic group in the ITS data but unresolved with V. dilatatum, V. erosum, and some accessions of V. wrightii. The cpDNA data showed one or two substitutions among the individuals of the complex included in the analysis.
참고문헌 (41)
Bleidorn, C. 2016. Third generation sequencing: technology and its potential impact on evolutionary biodiversity research. Systematics and Biodiversity 14: 1-8.
Cho, W.-B., E.-K. Han, H. J. Choi and J.-H. Lee. 2018. The complete chloroplast genome sequence of Viburnum japonicum (Adoxaceae), an evergreen broad-leaved shrub. Mitochondrial DNA Part B 3: 458-459.
Choi, Y. G., J. W. Youm, C. E. Lim and S.-H. Oh. 2018. Phylogenetic analysis of Viburnum (Adoxaceae) in Korea using DNA sequences. Korean Journal of Plant Taxonomy 48: 206-217.
Choi, Y. G., N. Yun, J. Park, H. Xi, J. Min, Y. Kim and S.-H. Oh. 2020. The second complete chloroplast genome sequence of the Viburnum erosum (Adoxaceae) showed a low level of intra-species variations. Mitochondrial DNA Part B 5: 271-272.
Choi, Y. G., N. Yun, J. Park, H. Xi, J. Min, Y. Kim, and S.-H. Oh. 2020. The second complete chloroplast genome sequence of the Viburnum erosum (Adoxaceae) showed a low level of intra-species variations. Mitochondrial DNA Part B 5: 271-272.
Clement, W. L., M. Arakaki, P. W. Sweeney, E. J. Edwards and M. J. Donoghue. 2014. A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution. American Journal of Botany 101: 1029-1049.
Donoghue, M. J. 1983. The phylogenetic relationships of Viburnum. Advances in Cladistics 2: 143-166.
Donoghue, M. J., B. G. Baldwin, J. Li and R. C. Winkworth. 2004. Viburnum phylogeny based on chloroplast trnK intron and nuclear ribosomal ITS DNA sequences. Systematic Botany 29: 188-198.
Goodwin, S., J. D. McPherson and W. R. McCombie. 2016. Coming of age: ten years of next-generation sequencing technologies. Nature Reviews Genetics 17: 333-351.
Greiner, S., P. Lehwark and R. Bock. 2019. OrganellarGenome-DRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research 47:W59-W64.
Hara, H. 1983. A Revision of Caprifoliaceae of Japan with Reference to Allied Plants in Other Districts and the Adoxaceae. Academia Scientific Books, Tokyo, 336 pp.
Hong, S.-Y., K.-S. Cheon, K.-O. Yoo, H.-O. Lee, K.-S. Cho, J.-T. Suh, S.-J. Kim, J.-H. Nam, H.-B. Sohn and Y.-H. Kim. 2017. Complete chloroplast genome sequences and comparative analysis of Chenopodium quinoa and C. album. Frontiers in Plant Science 8: 1696.
Hou, C., N. Wikstrom, J. S. Strijk and C. Rydin. 2016. Resolving phylogenetic relationships and species delimitations in closely related gymnosperms using high-throughput NGS, Sanger sequencing and morphology. Plant Systematics and Evolution 302: 1345-1365.
Jeon, J.-H. and S.-C. Kim. 2019. Comparative analysis of the complete chloroplast genome sequences of three closely related east-Asian wild roses (Rosa sect. Synstylae; Rosaceae). Genes (Basel) 10: 23.
Katoh, K. and D. M. Standley. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30: 772-780.
Kim, S.-H., J. Yang, J. Park, T. Yamada, M. Maki and S.-C. Kim. 2019a. Comparison of whole plastome sequences between thermogenic skunk cabbage Symplocarpus renifolius and nonthermogenic S. nipponicus (Orontioideae; Araceae) in East Asia. International Journal of Molecular Sciences 20: 4678.
Kim, Y., J. Park and Y. Chung. 2019b. Comparative analysis of chloroplast genome of Dysphania ambrosioides (L.) Mosyakin & Clemants understanding phylogenetic relationship in genus Dysphania R.Br. Korean Journal of Plant Resources 32: 644-668.
Kumar, S., G. Stecher, M. Li, C. Knyaz and K. Tamura. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution 35: 1547-1549.
Lexer, C., S. Mangili, E. Bossolini, F. Forest, K. N. Stolting, P. B. Pearman, N. E. Zimmermann and N. Salamin. 2013. 'Next generation' biogeography: towards understanding the drivers of species diversification and persistence. Journal of Biogeography 40: 1013-1022.
Li, H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997.
Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Furbin and 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079.
Lowe, T. M. and S. R. Eddy. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25: 955-964.
Nei, M. and W.-H. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences of the Unitd States of America 76: 5269-5273.
Nikiforova, S. V., D. Cavalieri, R. Velasco and V. Goremykin. 2013. Phylogenetic analysis of 47 chloroplast genomes clarifies the contribution of wild species to the domesticated apple maternal line. Molecular Biology and Evolution 30: 1751-1760.
Park, J., Y. G. Choi, N. Yun, H. Xi, J. Min, Y. Kim and S.-H. Oh. 2019a. The complete chloroplast genome sequence of Viburnum erosum (Adoxaceae). Mitochondrial DNA Part B 4: 3278-3279.
Park, J., Y. Kim and M. Kwon. 2019b. The complete mitochondrial genome of tulip tree, Liriodendron tulipifera L. (Magnoliaceae): intra-species variations on mitochondrial genome. Mitochondrial DNA Part B 4: 1308-1309.
Park, J., Y. Kim and K. Lee. 2019c. The complete chloroplast genome of Korean mock strawberry, Duchesnea chrysantha (Zoll. & Moritzi) Miq. (Rosoideae). Mitochondrial DNA Part B 4: 864-865.
Park, J., Y. Kim and H. Xi. 2019d. The complete chloroplast genome of aniseed tree, Illicium anisatum L. (Schisandraceae). Mitochondrial DNA Part B 4: 1023-1024.
Park, J., Y. Kim, H. Xi and K.-I. Heo. 2019e. The complete chloroplast genome of ornamental coffee tree, Coffea arabica L. (Rubiaceae). Mitochondrial DNA Part B 4: 1059-1060.
Park, J., Y. Kim, H. Xi, W. Kwon and M. Kwon. 2019f. The complete chloroplast and mitochondrial genomes of Hyunsasi tree, Populus alba x Populus glandulosa (Salicaceae). Mitochondrial DNA Part B 4: 2521-2522.
Rehder, A. 1908. The Viburnums of eastern Asia. In Trees and Shrubs, Vol. II, Part II. Sargent, C. S. (ed.), Houghton Mifflin, Boston, MA. Pp. 105-116.
Smith, S. A. and M. J. Donoghue. 2008. Rates of molecular evolution are linked to life history in flowering plants. Science 322: 86-89.
Wang, H.-X., H. Liu, M. J. Moore, S. Landrein, B. Liu, Z.-X. Zhu and H.-F. Wang. 2020. Plastid phylogenomic insights into the evolution of the Caprifoliaceae s.l. (Dipsacales). Molecular Phylogenetics and Evolution 142: 106641.
Xiang, C.-L., H.-J. Dong, S. Landrein, F. Zhao, W.-B. Yu, D. E. Soltis, P. S. Soltis, A. Backlund, H.-F. Wang, D.-Z. Li and H. Peng. 2019. Revisiting the phylogeny of Dipsacales: new insights from phylogenomic analyses of complete plastome sequences. Journal of Systematics and Evolution 58: 103-117.
Zerbino, D. R. and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18: 821-829.
Zhao, Q.-Y., Y. Wang, Y.-M. Kong, D. Luo, X. Li and P. Hao. 2011. Optimizing de novo transcriptome assembly from shortread RNA-Seq data: a comparative study. BMC Bioinformatics 12: S2.
Zimmer, E. A. and J. Wen. 2015. Using nuclear gene data for plant phylogenetics: progress and prospects II. Next-gen approaches. Journal of Systematics and Evolution 53: 371-379.
※ AI-Helper는 부적절한 답변을 할 수 있습니다.