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For: Davis JI, Soreng RJ. Migration of endpoints of two genes relative to boundaries between regions of the plastid genome in the grass family (Poaceae). Am J Bot 2010;97:874-92. [PMID: 21622452 DOI: 10.3732/ajb.0900228] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Number Cited by Other Article(s)
1
Li L, Wu Q, Zhai J, Wu K, Fang L, Li M, Zeng S, Li S. Comparative chloroplast genomics of 24 species shed light on the genome evolution and phylogeny of subtribe Coelogyninae (Orchidaceae). BMC PLANT BIOLOGY 2024;24:31. [PMID: 38182989 PMCID: PMC10768429 DOI: 10.1186/s12870-023-04665-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/05/2023] [Indexed: 01/07/2024]
2
Wang R, Zhang XJ, Guo XX, Xing Y, Qu XJ, Fan SJ. Plastid phylogenomics and morphological character evolution of Chloridoideae (Poaceae). FRONTIERS IN PLANT SCIENCE 2022;13:1002724. [PMID: 36407581 PMCID: PMC9666777 DOI: 10.3389/fpls.2022.1002724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
3
Lin P, Yin H, Wang K, Gao H, Liu L, Yao X. Comparative Genomic Analysis Uncovers the Chloroplast Genome Variation and Phylogenetic Relationships of Camellia Species. Biomolecules 2022;12:biom12101474. [PMID: 36291685 PMCID: PMC9599789 DOI: 10.3390/biom12101474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022]  Open
4
Wang R, Gao J, Feng J, Yang Z, Qi Z, Li P, Fu C. Comparative and Phylogenetic Analyses of Complete Chloroplast Genomes of Scrophularia incisa Complex (Scrophulariaceae). Genes (Basel) 2022;13:1691. [PMID: 36292576 PMCID: PMC9601301 DOI: 10.3390/genes13101691] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 10/14/2023]  Open
5
Turudić A, Liber Z, Grdiša M, Jakše J, Varga F, Šatović Z. Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats. Int J Mol Sci 2022;23:ijms231810804. [PMID: 36142721 PMCID: PMC9503105 DOI: 10.3390/ijms231810804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/01/2022] [Accepted: 09/13/2022] [Indexed: 12/31/2022]  Open
6
Jiao Y, Feng G, Huang L, Nie G, Li Z, Peng Y, Li D, Xiong Y, Hu Z, Zhang X. Complete Chloroplast Genomes of 14 Subspecies of D. glomerata: Phylogenetic and Comparative Genomic Analyses. Genes (Basel) 2022;13:genes13091621. [PMID: 36140789 PMCID: PMC9498378 DOI: 10.3390/genes13091621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/06/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022]  Open
7
Odago WO, Waswa EN, Nanjala C, Mutinda ES, Wanga VO, Mkala EM, Oulo MA, Wang Y, Zhang CF, Hu GW, Wang QF. Analysis of the Complete Plastomes of 31 Species of Hoya Group: Insights Into Their Comparative Genomics and Phylogenetic Relationships. FRONTIERS IN PLANT SCIENCE 2022;12. [DOI: https:/doi.org/10.3389/fpls.2021.814833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
8
Guo XX, Qu XJ, Zhang XJ, Fan SJ. Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae). BIOLOGY 2022;11:biology11010063. [PMID: 35053061 PMCID: PMC8773369 DOI: 10.3390/biology11010063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022]
9
Wang R, Liu K, Zhang XJ, Chen WL, Qu XJ, Fan SJ. Comparative Plastomes and Phylogenetic Analysis of Cleistogenes and Closely Related Genera (Poaceae). FRONTIERS IN PLANT SCIENCE 2021;12:638597. [PMID: 33841465 PMCID: PMC8030268 DOI: 10.3389/fpls.2021.638597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
10
Chloroplast genome sequence of Chongming lima bean (Phaseolus lunatus L.) and comparative analyses with other legume chloroplast genomes. BMC Genomics 2021;22:194. [PMID: 33736599 PMCID: PMC7977240 DOI: 10.1186/s12864-021-07467-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/23/2021] [Indexed: 11/16/2022]  Open
11
Yang Y, Zhou T, Qian Z, Zhao G. Phylogenetic relationships in Chinese oaks (Fagaceae, Quercus): Evidence from plastid genome using low-coverage whole genome sequencing. Genomics 2021;113:1438-1447. [PMID: 33744343 DOI: 10.1016/j.ygeno.2021.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 01/29/2023]
12
Liu K, Wang R, Guo XX, Zhang XJ, Qu XJ, Fan SJ. Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Eragrostideae (Chloridoideae, Poaceae). PLANTS 2021;10:plants10010109. [PMID: 33419221 PMCID: PMC7825611 DOI: 10.3390/plants10010109] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 11/24/2022]
13
Ruhlman TA, Jansen RK. Plastid Genomes of Flowering Plants: Essential Principles. Methods Mol Biol 2021;2317:3-47. [PMID: 34028761 DOI: 10.1007/978-1-0716-1472-3_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
14
Odago WO, Waswa EN, Nanjala C, Mutinda ES, Wanga VO, Mkala EM, Oulo MA, Wang Y, Zhang CF, Hu GW, Wang QF. Analysis of the Complete Plastomes of 31 Species of Hoya Group: Insights Into Their Comparative Genomics and Phylogenetic Relationships. FRONTIERS IN PLANT SCIENCE 2021;12:814833. [PMID: 35211136 PMCID: PMC8862764 DOI: 10.3389/fpls.2021.814833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/24/2021] [Indexed: 05/12/2023]
15
Adaptation Evolution and Phylogenetic Analyses of Species in Chinese Allium Section Pallasia and Related Species Based on Complete Chloroplast Genome Sequences. BIOMED RESEARCH INTERNATIONAL 2020;2020:8542797. [PMID: 32626767 PMCID: PMC7306069 DOI: 10.1155/2020/8542797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 05/22/2020] [Indexed: 11/20/2022]
16
Soto Gomez M, Lin Q, Silva Leal E, Gallaher TJ, Scherberich D, Mennes CB, Smith SY, Graham SW. A bi‐organellar phylogenomic study of Pandanales: inference of higher‐order relationships and unusual rate‐variation patterns. Cladistics 2020;36:481-504. [DOI: 10.1111/cla.12417] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/21/2022]  Open
17
Somaratne Y, Guan DL, Abbood NN, Zhao L, Wang WQ, Xu SQ. Comparison of the Complete Eragrostis pilosa Chloroplast Genome with Its Relatives in Eragrostideae (Chloridoideae; Poaceae). PLANTS (BASEL, SWITZERLAND) 2019;8:E485. [PMID: 31717580 PMCID: PMC6918254 DOI: 10.3390/plants8110485] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 10/30/2019] [Accepted: 11/06/2019] [Indexed: 01/18/2023]
18
Complete chloroplast genome sequences of four Allium species: comparative and phylogenetic analyses. Sci Rep 2019;9:12250. [PMID: 31439882 PMCID: PMC6706373 DOI: 10.1038/s41598-019-48708-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 08/09/2019] [Indexed: 11/26/2022]  Open
19
Saarela JM, Burke SV, Wysocki WP, Barrett MD, Clark LG, Craine JM, Peterson PM, Soreng RJ, Vorontsova MS, Duvall MR. A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions. PeerJ 2018;6:e4299. [PMID: 29416954 PMCID: PMC5798404 DOI: 10.7717/peerj.4299] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/08/2018] [Indexed: 12/23/2022]  Open
20
Yang Y, Zhu J, Feng L, Zhou T, Bai G, Yang J, Zhao G. Plastid Genome Comparative and Phylogenetic Analyses of the Key Genera in Fagaceae: Highlighting the Effect of Codon Composition Bias in Phylogenetic Inference. FRONTIERS IN PLANT SCIENCE 2018;9:82. [PMID: 29449857 PMCID: PMC5800003 DOI: 10.3389/fpls.2018.00082] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/15/2018] [Indexed: 05/10/2023]
21
Vining KJ, Johnson SR, Ahkami A, Lange I, Parrish AN, Trapp SC, Croteau RB, Straub SCK, Pandelova I, Lange BM. Draft Genome Sequence of Mentha longifolia and Development of Resources for Mint Cultivar Improvement. MOLECULAR PLANT 2017;10:323-339. [PMID: 27867107 DOI: 10.1016/j.molp.2016.10.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 10/28/2016] [Accepted: 10/29/2016] [Indexed: 05/08/2023]
22
Wu M, Lan S, Cai B, Chen S, Chen H, Zhou S. The Complete Chloroplast Genome of Guadua angustifolia and Comparative Analyses of Neotropical-Paleotropical Bamboos. PLoS One 2015;10:e0143792. [PMID: 26630488 PMCID: PMC4668023 DOI: 10.1371/journal.pone.0143792] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 11/10/2015] [Indexed: 11/19/2022]  Open
23
Complete Plastid Genome Sequencing of Four Tilia Species (Malvaceae): A Comparative Analysis and Phylogenetic Implications. PLoS One 2015;10:e0142705. [PMID: 26566230 PMCID: PMC4643919 DOI: 10.1371/journal.pone.0142705] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 10/26/2015] [Indexed: 12/02/2022]  Open
24
Evidence for horizontal transfer of mitochondrial DNA to the plastid genome in a bamboo genus. Sci Rep 2015;5:11608. [PMID: 26100509 PMCID: PMC4477325 DOI: 10.1038/srep11608] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 06/01/2015] [Indexed: 11/08/2022]  Open
25
Saarela JM, Wysocki WP, Barrett CF, Soreng RJ, Davis JI, Clark LG, Kelchner SA, Pires JC, Edger PP, Mayfield DR, Duvall MR. Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes. AOB PLANTS 2015;7:plv046. [PMID: 25940204 PMCID: PMC4480051 DOI: 10.1093/aobpla/plv046] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/21/2015] [Indexed: 05/08/2023]
26
Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae. Mol Phylogenet Evol 2014;80:169-85. [PMID: 25109653 DOI: 10.1016/j.ympev.2014.07.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 07/18/2014] [Accepted: 07/21/2014] [Indexed: 11/21/2022]
27
Huang H, Shi C, Liu Y, Mao SY, Gao LZ. Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships. BMC Evol Biol 2014;14:151. [PMID: 25001059 PMCID: PMC4105164 DOI: 10.1186/1471-2148-14-151] [Citation(s) in RCA: 238] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 06/20/2014] [Indexed: 12/23/2022]  Open
28
Ruhlman TA, Jansen RK. The plastid genomes of flowering plants. Methods Mol Biol 2014;1132:3-38. [PMID: 24599844 DOI: 10.1007/978-1-62703-995-6_1] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
29
Zhao L, Zhang N, Ma PF, Liu Q, Li DZ, Guo ZH. Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae. PLoS One 2013;8:e64642. [PMID: 23734211 PMCID: PMC3667173 DOI: 10.1371/journal.pone.0064642] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/16/2013] [Indexed: 11/23/2022]  Open
30
Kelchner SA. Higher level phylogenetic relationships within the bamboos (Poaceae: Bambusoideae) based on five plastid markers. Mol Phylogenet Evol 2013;67:404-13. [DOI: 10.1016/j.ympev.2013.02.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 11/14/2012] [Accepted: 02/06/2013] [Indexed: 01/24/2023]
31
Cohen JI. Continuous characters in phylogenetic analyses: patterns of corolla tube length evolution in LithospermumL. (Boraginaceae). Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01938.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
32
Polyphyly of the grass tribe Hainardieae (Poaceae: Pooideae): identification of its different lineages based on molecular phylogenetics, including morphological and cytogenetic characteristics. ORG DIVERS EVOL 2012. [DOI: 10.1007/s13127-012-0077-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
33
Zhang YJ, Ma PF, Li DZ. High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae). PLoS One 2011;6:e20596. [PMID: 21655229 PMCID: PMC3105084 DOI: 10.1371/journal.pone.0020596] [Citation(s) in RCA: 194] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 05/05/2011] [Indexed: 11/25/2022]  Open
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