Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

[1] Daniell H(2016)Chloroplast genomes: diversity, evolution and applications in genetic engineering Genome Biol 17 134-179

[2] Lin CS(2009)Phylogeny and classification of Eucalyptus subgenus Eudesmia (Myrtaceae) based on nuclear ribosomal DNA chloroplast DNA and morphology Aus Syst Botany 22 158-329

[3] Yu M(2009)Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes BMC Biol 7 84-716

[4] Chang WJ(2012)Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA Am J Bot 99 320-334

[5] Gibbs AK(2013)Chloroplast genome analysis of Australian eucalypts--Eucalyptus, Corymbia, angophora, Allosyncarpia and Stockwellia (Myrtaceae) Mol Phylogenet Evol 69 704-297

[6] Udovicic F(2013)Chloroplast phylogeny of Cucurbita: evolution of the domesticated and wild species J Syst Evol 51 326-970

[7] Drinnan AN(2016)A large-scale chloroplast phylogeny of the Lamiaceae sheds new light on its subfamilial classification Sci Rep 6 34343-442

[8] Ladiges PY(2017)Population genetic structure and Phylogeography of Camellia flavida (Theaceae) based on Chloroplast and nuclear DNA sequences Front Plant Sci 8 718-1217

[9] Parks M(2011)The evolution of the plastid chromosome in land plants: gene content, gene order gene function Plant Mol Biol 76 273-2190

[10] Cronn R(2017)Inferring the evolutionary mechanism of the chloroplast genome size by comparing whole-chloroplast genome sequences in seed plants Sci Rep 7 1555-2049

[1] Daniell H(2016)Chloroplast genomes: diversity, evolution and applications in genetic engineering Genome Biol 17 134-179

[2] Lin CS(2009)Phylogeny and classification of Eucalyptus subgenus Eudesmia (Myrtaceae) based on nuclear ribosomal DNA chloroplast DNA and morphology Aus Syst Botany 22 158-329

[3] Yu M(2009)Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes BMC Biol 7 84-716

[4] Chang WJ(2012)Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA Am J Bot 99 320-334

[5] Gibbs AK(2013)Chloroplast genome analysis of Australian eucalypts--Eucalyptus, Corymbia, angophora, Allosyncarpia and Stockwellia (Myrtaceae) Mol Phylogenet Evol 69 704-297

[6] Udovicic F(2013)Chloroplast phylogeny of Cucurbita: evolution of the domesticated and wild species J Syst Evol 51 326-970

[7] Drinnan AN(2016)A large-scale chloroplast phylogeny of the Lamiaceae sheds new light on its subfamilial classification Sci Rep 6 34343-442

[8] Ladiges PY(2017)Population genetic structure and Phylogeography of Camellia flavida (Theaceae) based on Chloroplast and nuclear DNA sequences Front Plant Sci 8 718-1217

[9] Parks M(2011)The evolution of the plastid chromosome in land plants: gene content, gene order gene function Plant Mol Biol 76 273-2190

[10] Cronn R(2017)Inferring the evolutionary mechanism of the chloroplast genome size by comparing whole-chloroplast genome sequences in seed plants Sci Rep 7 1555-2049