Chloroplast genomes: diversity, evolution, and applications in genetic engineering
Abstract
Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication. Here, we also discuss the potential biotechnological applications of chloroplast genomes.
- Authors:
-
- Univ. of Pennsylvania, Philadelphia, PA (United States)
- Academia Sinica, Taipei (Taiwan)
- Publication Date:
- Research Org.:
- Univ. of Pennsylvania, Philadelphia, PA (United States)
- Sponsoring Org.:
- USDOE Advanced Research Projects Agency - Energy (ARPA-E)
- OSTI Identifier:
- 1375954
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Genome Biology (Online)
- Additional Journal Information:
- Journal Name: Genome Biology (Online); Journal Volume: 17; Journal Issue: 1; Journal ID: ISSN 1474-760X
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES
Citation Formats
Daniell, Henry, Lin, Choun -Sea, Yu, Ming, and Chang, Wan -Jung. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. United States: N. p., 2016.
Web. doi:10.1186/s13059-016-1004-2.
Daniell, Henry, Lin, Choun -Sea, Yu, Ming, & Chang, Wan -Jung. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. United States. https://doi.org/10.1186/s13059-016-1004-2
Daniell, Henry, Lin, Choun -Sea, Yu, Ming, and Chang, Wan -Jung. Thu .
"Chloroplast genomes: diversity, evolution, and applications in genetic engineering". United States. https://doi.org/10.1186/s13059-016-1004-2. https://www.osti.gov/servlets/purl/1375954.
@article{osti_1375954,
title = {Chloroplast genomes: diversity, evolution, and applications in genetic engineering},
author = {Daniell, Henry and Lin, Choun -Sea and Yu, Ming and Chang, Wan -Jung},
abstractNote = {Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication. Here, we also discuss the potential biotechnological applications of chloroplast genomes.},
doi = {10.1186/s13059-016-1004-2},
journal = {Genome Biology (Online)},
number = 1,
volume = 17,
place = {United States},
year = {Thu Jun 23 00:00:00 EDT 2016},
month = {Thu Jun 23 00:00:00 EDT 2016}
}
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- International Journal of Molecular Sciences, Vol. 19, Issue 3
The chloroplast genome of Cerasus humilis: Genomic characterization and phylogenetic analysis
journal, April 2018
- Mu, Xiaopeng; Wang, Pengfei; Du, Junjie
- PLOS ONE, Vol. 13, Issue 4
Sequencing, Characterization, and Comparative Analyses of the Plastome of Caragana rosea var. rosea
journal, May 2018
- Jiang, Mei; Chen, Haimei; He, Shuaibing
- International Journal of Molecular Sciences, Vol. 19, Issue 5
Completion of the Chloroplast Genomes of Five Chinese Juglans and Their Contribution to Chloroplast Phylogeny
journal, January 2017
- Hu, Yiheng; Woeste, Keith E.; Zhao, Peng
- Frontiers in Plant Science, Vol. 7
A Systematic View Exploring the Role of Chloroplasts in Plant Abiotic Stress Responses
journal, July 2019
- Yoo, Yo-Han; Hong, Woo-Jong; Jung, Ki-Hong
- BioMed Research International, Vol. 2019
Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species
journal, June 2019
- Guyeux, Christophe; Charr, Jean-Claude; Tran, Hue T. M.
- PLOS ONE, Vol. 14, Issue 6
Characterization and Comparative Analysis of the Complete Chloroplast Genome of the Critically Endangered Species Streptocarpus teitensis (Gesneriaceae)
journal, January 2018
- Kyalo, Cornelius M.; Gichira, Andrew W.; Li, Zhi-Zhong
- BioMed Research International, Vol. 2018
Characterization of the Complete Chloroplast Genome of Acer truncatum Bunge (Sapindales: Aceraceae): A New Woody Oil Tree Species Producing Nervonic Acid
journal, November 2019
- Ma, Qiuyue; Wang, Yanan; Zhu, Lu
- BioMed Research International, Vol. 2019
Draft genome of Santalum album L. provides genomic resources for accelerated trait improvement
journal, April 2019
- Dasgupta, Modhumita Ghosh; Ulaganathan, Kandasamy; Dev, Suma Arun
- Tree Genetics & Genomes, Vol. 15, Issue 3
Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known
journal, January 2019
- Schelkunov, Mikhail I.; Nuraliev, Maxim S.; Logacheva, Maria D.
- PeerJ, Vol. 7
Complete Chloroplast Genome Sequences of Kaempferia Galanga and Kaempferia Elegans: Molecular Structures and Comparative Analysis
journal, January 2019
- Li, Dong-Mei; Zhao, Chao-Yi; Liu, Xiao-Fei
- Molecules, Vol. 24, Issue 3
Comparative Chloroplast Genomics of Dipsacales Species: Insights Into Sequence Variation, Adaptive Evolution, and Phylogenetic Relationships
journal, May 2018
- Fan, Wei-Bing; Wu, Ying; Yang, Jiao
- Frontiers in Plant Science, Vol. 9
Phenotypic and Genetic Variation of an Interspecific Centaurium Hybrid (Gentianaceae) and Its Parental Species
journal, July 2019
- Banjanac, Tijana; Đurović, Sanja; Jelić, Mihailo
- Plants, Vol. 8, Issue 7
Complete chloroplast genome sequence and phylogenetic analysis of Spathiphyllum 'Parrish'
journal, October 2019
- Liu, Xiao-Fei; Zhu, Gen-Fa; Li, Dong-Mei
- PLOS ONE, Vol. 14, Issue 10
Intergeneric Relationships within the Early-Diverging Angiosperm Family Nymphaeaceae Based on Chloroplast Phylogenomics
journal, November 2018
- He, Dingxuan; Gichira, Andrew; Li, Zhizhong
- International Journal of Molecular Sciences, Vol. 19, Issue 12
Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul
journal, November 2019
- Kahraman, Kadriye; Lucas, Stuart James
- BMC Genomics, Vol. 20, Issue 1
Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case
journal, December 2018
- Wang, Weiwen; Schalamun, Miriam; Morales-Suarez, Alejandro
- BMC Genomics, Vol. 19, Issue 1
Complete Chloroplast Genome Sequences and Comparative Analysis of Chenopodium quinoa and C. album
journal, October 2017
- Hong, Su-Young; Cheon, Kyeong-Sik; Yoo, Ki-Oug
- Frontiers in Plant Science, Vol. 8
The Plastid Genome of Deschampsia cespitosa (Poaceae)
journal, January 2019
- Chiapella, Jorge; Barfuss, Michael; Xue, Zhi-Qing
- Molecules, Vol. 24, Issue 2
Validation of leaf enzymes in the detergent and textile industries: launching of a new platform technology
journal, February 2019
- Kumari, Uma; Singh, Rahul; Ray, Tui
- Plant Biotechnology Journal, Vol. 17, Issue 6
Characterization of the complete plastome of Dendrophthoe pentandra (Loranthaceae), a stem hemiparasite
journal, July 2019
- Guo, Xiaorong; Ruan, Zhijie
- Mitochondrial DNA Part B, Vol. 4, Issue 2
The Complete Chloroplast Genomes of Two Lespedeza Species: Insights into Codon Usage Bias, RNA Editing Sites, and Phylogenetic Relationships in Desmodieae (Fabaceae: Papilionoideae)
journal, December 2019
- Somaratne, Yamuna; Guan, De-Long; Wang, Wen-Qiang
- Plants, Vol. 9, Issue 1
Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny
journal, November 2019
- Wang, Juan; Li, Yuan; Li, Chunjuan
- BMC Plant Biology, Vol. 19, Issue 1
Comparative Chloroplast Genomics of Endangered Euphorbia Species: Insights into Hotspot Divergence, Repetitive Sequence Variation, and Phylogeny
journal, February 2020
- Khan, Arif; Asaf, Sajjad; Khan, Abdul Latif
- Plants, Vol. 9, Issue 2
What can we do with 1000 plastid genomes?
journal, March 2017
- Tonti‐Filippini, Julian; Nevill, Paul G.; Dixon, Kingsley
- The Plant Journal, Vol. 90, Issue 4
Complete chloroplast genome sequence of Betula platyphylla: gene organization, RNA editing, and comparative and phylogenetic analyses
journal, December 2018
- Wang, Sui; Yang, Chuanping; Zhao, Xiyang
- BMC Genomics, Vol. 19, Issue 1
Development of the chloroplast genome-based InDel markers in Niitaka (Pyrus pyrifolia) and its application
journal, January 2019
- Chung, Ho Yong; Won, So Youn; Kim, Yoon-Kyung
- Plant Biotechnology Reports, Vol. 13, Issue 1
The complete plastome of real yellow wood (Podocarpus latifolius): gene organization and comparison with related species
journal, June 2019
- Saina, Josphat K.; Li, Zhi-Zhong; Gichira, Andrew W.
- Holzforschung, Vol. 73, Issue 6
Sequencing and Analysis of Chrysanthemum carinatum Schousb and Kalimeris indica. The Complete Chloroplast Genomes Reveal Two Inversions and rbcL as Barcoding of the Vegetable
journal, June 2018
- Liu, Xia; Zhou, Boyang; Yang, Hongyuan
- Molecules, Vol. 23, Issue 6
Characterization of sequence variability hotspots in Cranichideae plastomes (Orchidaceae, Orchidoideae)
journal, January 2020
- Smidt, Eric de Camargo; Páez, Michelle Zavala; Vieira, Leila do Nascimento
- PLOS ONE, Vol. 15, Issue 1
Isolation of Intact Chloroplast for Sequencing Plastid Genomes of Five Festuca Species
journal, December 2019
- Islam, Md. Shofiqul; Buttelmann, Gretta L.; Chekhovskiy, Konstantin
- Plants, Vol. 8, Issue 12
The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae
journal, April 2018
- Amiryousefi, Ali; Hyvönen, Jaakko; Poczai, Péter
- PLOS ONE, Vol. 13, Issue 4