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Additional file 13: Figure S12. Family relationships within the pruned angiosperm subdataset. In this tree, bootstrap/gCF/sCF scores are shown for each branch.

Additional file 14: Additional Text. Overview of angiosperm phylogeny at the familial level.

Additional file 10: Figure S9. Topologies of a pruned Maximum Likelihood phylogeny of 431 representative species (���ML431_pruned���) and ASTRAL analysis (���astral431_BS10���) of a 43-species subdataset of angiosperms using 80 plastid genes. The ML bootstrap percentages and ASTRAL local posterior probabilities are shown, respectively.

Additional file 7: Figure S6. Phylogenetic tree of 4792 plastomes of 445 families (including 12 gymnosperm families) of seed plants.

Additional file 9: Figure S8. Phylogenetic tree of 4792 plastomes with successive removal of the long branch forming a sister relationship with a ���clade��� of Mitrastemonaceae, Thismiaceae, Apodanthaceae, and Balanophoraceae.

Additional file 11: Figure S10. Family relationships within the pruned angiosperm phylogeny: nodes by Quartet Concordance (QC) scores for internal branches: green (QC > 0.2), blue (0.2 ��� QC > 0), orange (0 ��� QC ��� ���0.05, or red (QC < ���0.05). QC/Quartet Differential (QD)/Quartet Informativeness (QI) scores are shown for all internal branches.

Zingiberaceae are well known for their medicinal and economic significance across the world yet remained poorly known and studied and unfortunately considered one of the most threatened plant families in the Philippines. Such is the case for the genus Etlingera, where its taxonomy and nomenclature are much disputed particularly for several species in the archipelago that have been studied very little for over a century. Here, we report the seven newly sequenced Etlingera plastomes obtained through genome skimming using next generation sequencing. All plastomes displayed a typical quadripartite structure and their size ranges from 163,615–164,641 bp which encoded 113 different genes (80 protein-coding, 30 tRNA, and four rRNA genes) with 36.1% GC content. Gene content, gene order, and GC content were highly similar among these genomes. The maximum likelihood tree of the seven Etlingera within the family showed that plastomes can be used as a super-barcode to identify Etlingera spp. and provides an important reference and solid foundation in the establishment of species identification and phylogeny ofZingiberaceae. In addition, recent fieldwork in Mindanao resulted in the discovery of a new species (Etlingera dostseiana Naive, Demayo & Alejandro) and a new species record (E. pilosa A.D.Poulsen & Docot).

Additional file 3: Figure S2. Phylogenetic tree of 4782 plastomes of 445 families (including 12 gymnosperm families) of seed plants. Five problematic families (Rafflesiaceae, Apodanthaceae, Balanophoraceae, Mitrastemonaceae, and Thismiaceae) were added manually (see Results for details).

Additional file 8: Figure S7. Phylogenetic tree of 4792 plastomes of 4660 species of seed plants. All bootstrap values are shown.

Additional file 6: Figure S5. Phylogenetic tree of 4792 plastomes of 76 orders (including eight gymnosperm orders) of seed plants.

Additional file 5: Figure S4. Phylogenetic tree of 4782 plastomes (with ten plastomes of five problematic families excluded) of 4650 species of seed plants. Bootstrap values are shown.

Additional file 1: Figure S1. Reads mapping comparisons among the plastomes reassembled using GetOrganelle and NOVOPlasty, and the plastome from GenBank (KY085912) based on the same raw data SRR5602602 (Laurus nobilis L.). Figure S2. The covering positions and corresponding coverages at the plastome of newly captured reads during each round using GetOrganelle, with different arguments. A whole plastome and an rbcL region (right) from a gymnosperm species Gnetum parvifolium (Warb.) W.C.Cheng (GenBank nucleotide accession number: NC_011942.1) as the seed to assemble the plastome of an angiosperm species Haberlea rhodopensis from an online WGS dataset (GenBank SRA accession number: SRR4428742).

Additional file 3. Review history.

Zingiberaceae are well known for their medicinal and economic significance across the world yet remained to be poorly known and studied and unfortunately considered as one of the most threatened plant families in the Philippines. Included is the genus Etlingera, where its taxonomy and nomenclature are much disputed particularly for several species in the archipelago. Here, we report the seven newly sequenced Etlingera plastomes obtained through genome skimming using next generation sequencing. All plastomes displayed a typical quadripartite structure and their size ranges from 161,289–164,641 bp which encoded 115 different genes (79 protein-coding, 32 tRNA and four rRNA genes). Gene content, gene order, and GC content were highly similar among these genomes. Maximum likelihood tree of the seven Etlingera and other related species showed that the plastomes can be used as a super-barcode to identify Etlingera spp. and provides an important reference and solid foundation in the establishment of species identification and phylogeny of the family Zingiberaceae. In addition, recent fieldwork in Mindanao resulted in the discovery of a new species, Etlingera dostseii sp. nov., which is herein described and illustrated.