Complete chloroplast genome sequence and analysis of <i>Pinus ponderosa</i> P. Lawson & C. Lawson and <i>Picea pungens</i> Engelm.

Li Jia; Li Qing

doi:10.11913/PSJ.2095-0837.2022.60791

Plant Science Journal > 2022 > 40(6): 791-800. > DOI: 10.11913/PSJ.2095-0837.2022.60791 CSTR: 32231.14.PSJ.2095-0837.2022.60791

Li Jia, Li Qing. Complete chloroplast genome sequence and analysis of Pinus ponderosa P. Lawson & C. Lawson and Picea pungens Engelm.[J]. Plant Science Journal, 2022, 40(6): 791-800. DOI: 10.11913/PSJ.2095-0837.2022.60791

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Complete chloroplast genome sequence and analysis of Pinus ponderosa P. Lawson & C. Lawson and Picea pungens Engelm.

Li Jia^,,
Li Qing

College of Life Sciences and Food Engineering, Shaanxi Xueqian Normal University, Xi'an 710100, China

Funds:

This work was supported by grants from the Provincial Innovation and Entrepreneurship Training Program for College Students of Shaanxi Xueqian Normal University (S202014390065) and Science Foundation from the Education Department of Shaanxi Provincial Government (19JK0211).

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Received Date: July 22, 2022
Revised Date: August 27, 2022
Available Online: January 12, 2023

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Abstract

Abstract

In this study, the complete chloroplast genome sequences of Pinus ponderosa P. Lawson & C. Lawson and Picea pungens Engelm. were determined using next-generation sequencing technology. The genome sizes of Pinus ponderosa and Picea pungens were 120 274 bp and 124 237 bp, respectively. The chloroplast genome of P. ponderosa contained 107 genes, including 70 protein-coding genes, four ribosomal RNA (rRNA) genes, and 33 transfer RNA (tRNA) genes. The chloroplast genome of P. pungens contained 111 genes, including 71 protein-coding genes, four rRNA genes, and 36 tRNA genes. In total, 18 and 32 simple sequence repeats were identified in the Pinus ponderosa and Picea pungens chloroplast genomes, respectively. Phylogenetic analysis using 73 common chloroplast genes from 19 Pinaceae and two outgroups divided Pinaceae into two groups: the first clade included Cedrus, Pseudolarix, Tsuga, Keteleeria, and Abies; the second clade included Pinus, Cathaya,Picea,Larix, and Pseudotsuga. Analysis of chloroplast genome structure identified several rearrangements between different genera of Pinaceae, mediated by a trnS-GCU small inverted repeat sequence.
- Pinaceae,
- Pinus ponderosa,
- Picea pungens,
- Chloroplast genome,
- Phylogeny

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References (42)

References

[1]	Partelli-Feltrin R, Smith AMS, Adams HD, Kolden CA, Johnson DM. Short-and long-term effects of fire on stem hydraulics in Pinus ponderosa saplings[J]. Plant Cell Environ, 2021, 44(3):696-705.
[2]	Çetin M, Çobanoǧlu O. The possibilities of using blue spruce (Picea pungens Engelm.) as a biomonitor by measuring the recent accumulation of Mn in its leaves[J]. Kastamonu Univ J Eng Sci, 2019, 5(1):43-50.
[3]	Montagnoli A, Terzaghi M, Chiatante D, Scippa GS, Lasserre B, Dumroese RK. Ongoing modifications to root system architecture of Pinus ponderosa growing on a sloped site revealed by tree-ring analysis[J]. Dendrochronologia, 2019, 58:125650.
[4]	Remke MJ, Hoang T, Kolb T, Gehring C, Johnson NC, Bowker MA. Familiar soil conditions help Pinus ponderosa seedlings cope with warming and drying climate[J]. Restor Ecol, 2020, 28(S4):S344-S354.
[5]	Breygina M, Maksimov N, Polevova S, Evmenyeva A. Bipolar pollen germination in blue spruce (Picea pungens)[J]. Protoplasma, 2019, 256(4):941-949.
[6]	Tao J, Chen SG, Qin CY, Li QM, Cai JF, et al. Somatic embryogenesis in mature zygotic embryos of Picea pungens[J]. Sci Rep, 2021, 11(1):19072.
[7]	Daniell H, Jin SX, Zhu XG, Gitzendanner MA, Soltis DE,Soltis PS.Green giant-a tiny chloroplast genome with mighty power to produce high-value proteins:history and phylogeny[J]. Plant Biotechnol J, 2021, 19(3):430-447.
[8]	Mower JP, Vickrey TL. Structural diversity among plastid genomes of land plants[J]. Adv Bot Res, 2018, 85:263-292.
[9]	Daniell H, Lin CS, Yu M, Chang WJ. Chloroplast genomes:diversity, evolution, and applications in genetic engineering[J]. Genome Biol, 2016, 17(1):134.
[10]	Lubna, Asaf S, Khan AL, Jan R, Khan A, et al. The dynamic history of gymnosperm plastomes:insights from structural characterization, comparative analysis, phylo-genomics, and time divergence[J]. Plant Genome, 2021, 14(3):e20130.
[11]	Gitzendanner MA, Soltis PS, Wong GKS, Ruhfel BR, Soltis DE. Plastid phylogenomic analysis of green plants:a billion years of evolutionary history[J]. Am J Bot, 2018, 105(3):291-301.
[12]	Ruhfel BR, Gitzendanner MA, Soltis PS, Soltis DE, Burleigh JG. From algae to angiosperms-inferring the phylo-geny of green plants (Viridiplantae) from 360 plastid genomes[J]. BMC Evol Biol, 2014, 14:23.
[13]	Neale DB, Wheeler NC. The conifers[M]//Neale DB, Wheeler NC, eds. The Conifers:Genomes, Variation and Evolution. Cham:Springer, 2019:1-21.
[14]	Farjon A. The kew review:conifers of the world[J]. Kew Bull, 2018, 73(1):8.
[15]	Stull GW, Qu XJ, Parins-Fukuchi C, Yang YY, Yang JB, et al. Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms[J]. Nat Plants, 2021, 7(8):1015-1025.
[16]	García Esteban L, de Palacios P, García-Iruela A, García-Fernández F, García-Esteban L, de Vega DG. Comparative wood anatomy in Pinaceae with reference to its systematic position[J]. Forests, 2021, 12(12):1706.
[17]	Gernandt DS, Reséndiz Arias C, Terrazas T, Dugua XA, Willyard A. Incorporating fossils into the Pinaceae tree of life[J]. Am J Bot, 2018, 105(8):1329-1344.
[18]	Ran JH, Shen TT, Wang MM, Wang XQ. Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms[J]. Proc Roy Soc B Biol Sci, 2018, 285(1881):20181012.
[19]	Gernandt DS, Magallón S, Geada López G, Zerón Flores O, Willyard A,Liston A.Use of simultaneous analyses to guide fossil-based calibrations of pinaceae phylogeny[J]. Int J Plant Sci, 2008, 169(8):1086-1099.
[20]	Lin CP, Huang JP, Wu CS, Hsu CY, Chaw SM. Compa-rative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies[J]. Genome Biol Evol, 2010, 2:504-517.
[21]	Sudianto E, Wu CS, Lin CP, Chaw SM. Revisiting the plastid phylogenomics of Pinaceae with two complete plastomes of Pseudolarix and Tsuga[J]. Genome Biol Evol, 2016, 8(6):1804-1811.
[22]	Ran JH, Shen TT, Wu H, Gong X, Wang XQ. Phylogeny and evolutionary history of Pinaceae updated by transcriptomic analysis[J]. Mol Phylogenet Evol, 2018, 129:106-116.
[23]	Ni ZX, Ye YJ, Bai TD, Xu M, Xu LA. Complete chloroplast genome of Pinus massoniana (Pinaceae):Gene rearrangements, loss of ndh genes, and short inverted repeats contraction, expansion[J]. Molecules, 2017, 22(9):1528.
[24]	Chen L, Li LN, Yang GD, Qian HR, Li MZ. Characterization of the complete chloroplast genome sequence of Tsuga longibracteata W. C. Cheng (Pinaceae)[J]. Conserv Genet Resour, 2019, 11(2):117-120.
[25]	Li ZH, Zhu J, Yang YX, Yang J, He JW,Zhao GF.The complete plastid genome of Bunge's pine Pinus bungeana (Pinaceae)[J]. Mitochondrial DNA Part A, 2016, 27(4):2971-2972.
[26]	Li ZH, Qian ZQ, Liu ZL, Deng TT, Zu YM, et al. The complete chloroplast genome of Armand pine Pinus armandii, an endemic conifer tree species to China[J]. Mitochondrial DNA Part A, 2016, 27(4):2635-2636.
[27]	Li JF, Xu B, Yang Q, Liu ZL. The complete chloroplast genome sequence of Picea schrenkiana (Pinaceae)[J]. Mitochondrial DNA Part B, 2020, 5(3):2191-2192.
[28]	Wu CS, Lin CP, Hsu CY, Wang RJ, Chaw SM. Comparative chloroplast genomes of pinaceae:insights into the mechanism of diversified genomic organizations[J]. Genome Biol Evol, 2011, 3:309-319.
[29]	Sullivan AR, Schiffthaler B, Thompson SL, Street NR, Wang XR. Interspecific plastome recombination reflects ancient reticulate evolution in Picea (Pinaceae)[J]. Mol Biol Evol, 2017, 34(7):1689-1701.
[30]	Ranade SS, García-Gil MR, Rosselló JA. Non-functional plastid ndh gene fragments are present in the nuclear genome of Norway spruce (Picea abies L. Karsch):insights from in silico analysis of nuclear and organellar genomes[J]. Mol Genet Genomics, 2016, 291(2):935-941.
[31]	Dierckxsens N, Mardulyn P, Smits G. NOVOPlasty:de novo assembly of organelle genomes from whole genome data[J]. Nucleic Acids Res, 2017, 45(4):e18.
[32]	Qu XJ, Moore MJ, Li DZ, Yi TS. PGA:a software pac-kage for rapid, accurate, and flexible batch annotation of plastomes[J]. Plant Methods, 2019, 15(1):50.
[33]	Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, et al. IQ-TREE 2:new models and efficient methods for phylogenetic inference in the genomic era[J]. Mol Biol Evol, 2020, 37(5):1530-1534.
[34]	Darling AE, Mau B, Perna NT. progressiveMauve:multiple genome alignment with gene gain, loss and rearrangement[J]. PLoS One, 2010, 5(6):e11147.
[35]	Tsumura Y, Suyama Y, Yoshimura K. Chloroplast DNA inversion polymorphism in populations of Abies and Tsuga[J]. Mol Biol Evol, 2000, 17(9):1302-1212.
[36]	李佳, 姜斌, 苏应娟, 王艇. 白豆杉的叶绿体基因组结构与系统进化分析[J].植物科学学报, 2021, 39(1):5-13. Li J, Jiang B, Su YJ, Wang T. Structure and phylogenetic analysis of the Pseudotaxus chienii (W. C. Cheng) W. C. Cheng chloroplast genome[J]. Plant Science Journal, 2021, 39(1):5-13.
[37]	姚庆渭, 黄鹏成. 松科各属种子的研究[J].南京林业大学学报(自然科学版), 1980(1):28-42. Yao QW, Huang PC. A research of the seeds of genera in Pinaceae[J]. Journal of Nanjing Forestry University (Natural Sciences Edition), 1980(1):28-42.
[38]	Esteban LG, De Palacios P. Comparative wood anatomy in Abietoideae (Pinaceae)[J]. Bot J Linn Soc, 2009, 160(2):184-196.
[39]	Kim SC, Lee JW, Lee MW, Baek SH, Hong KN. The complete chloroplast genome sequences of Larix kaempferi and Larix olgensis var. koreana (Pinaceae)[J]. Mitochondrial DNA Part B, 2018, 3(1):36-37.
[40]	Hao ZD, Cheng TL, Zheng RH, Xu HB, Zhou YW, et al. The complete chloroplast genome sequence of a relict conifer Glyptostrobus pensilis:comparative analysis and insights into dynamics of chloroplast genome rearrangement in cupressophytes and Pinaceae[J]. PLoS One, 2016, 11(8):e0161809.
[41]	Gernandt DS, Holman G, Campbell C, Parks M, Mathews S, et al. Phylogenetics of extant and fossil Pinaceae:methods for increasing topological stability[J]. Botany, 2016, 94(9):863-884.
[42]	Ni ZX, Ye YJ, Xu M, Xu LA. Comparison among three methods for obtaining chloroplast genome sequences from the conifer Pinus massoniana[J]. Genomics, 2020, 112(3):2459-2466.

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Complete chloroplast genome sequence and analysis of Pinus ponderosa P. Lawson & C. Lawson and Picea pungens Engelm.

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