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Additional file 11: Fig. S11. The results of quartet sampling analysis are based on the ASTRAL species tree using the whole plastid dataset. The three metrics are shown on each branch following the order of QC/QD/QI scores (QC: quartet concordance; QD: quartet differentiation; QI: quartet information). The QI score is a nonlinear elevation metric for quartet supports/conflicts. Heatmap of branches by Quartet Concordance (QC) scores for internal branches: dark green (QC > 0.2), light green (0.2 ≥ QC > 0), and dark orange (QC < −0.05).

Additional file 4: Fig. S4. Sequence identity plots of plastomes of Lysimachia by mVISTA using Lysimachia fortunei as the reference. The top line shows the orientation of genes. A cutoff of 70% identity was used for the plots, and the Y-scale represents the percentage identity ranging from 50 to 100%.

Here, we reported a haplotype-resolved and telomere-to-telomere genome assembly of M. acuminata using PacBio HiFi reads, Nanopore ultra-long reads and high-covered Hi-C data. This assembly represented a significantly high-quality reference assessed by contiguity (contig N50: 16.53Mb and 18.58Mb; LAI: 20.18 and 19.48), completeness (BUSCOs: 98.57% and 98.57%), and correctness (QV: 45.97 and 46.12). All centromeres and 36 of 44 telomeres had been captured. The mapping rates of HiFi and Illumina reads both exceeded 99.80%. In total, 40,889 and 38,269 protein-coding genes were annotated in the two haploid assemblies, respectively, of which 9.56% and 3.37% were newly annotated compared with previous databases. Gene BUSCOs reached up to 89.41% and 90.27%, respectively. Through comparing our assembly and the previously published genome of M. acuminata, we identified two large translocation regions with length of 3 Mb and 10 Mb, which were further confirmed by Hi-C heatmap and targeted-PCR gel electrophoresis. This haplotype-resolved and telomere-to-telomere reference genome of M. acuminata provides an excellent resource for further understanding the mechanisms of subgenome evolution, domestication history, and genetic breeding of banana.

Additional file 5: Fig. S2. Maximum likelihood phylogenetic tree of Arecaceae inferred from the complete-105 regions matrix. Bootstrap values inferior to 100% are shown, with dashes denoting a support inferior to 50%.

Lomas Landform, a fog "oasis island" in the desert belt of the west coast of South America, has a unique vegetation composition among the world's deserts. However, the conservation and plant diversity study has long been neglected, and there exists a severe gap in DNA sequence information. To address these questions, we conducted field species collection and laboratory DNA barcode sequencing to establish a DNA barcode reference library of Peruvian Lomas plants. This database provides 1,207 plant specimens and 3,130 DNA barcode data collected from 16 Lomas locations in Peru in 2017 and 2018. This database will facilitate both rapid species identification and basic studies on plant diversity, thereby further improving our understanding of Lomas flora’s composition and temporal variation, and providing valuable resources to conserve plant diversity and maintain the stability of the fragile Lomas ecosystems.

Additional file 2: Table S2. Accessions of the 49 genera with few plastid DNA regions available and therefore a large proportion of missing data in the incomplete-105 regions matrix, with GenBank accession numbers of sequences used in the present study. The character ‘—’ indicates that the sequence was unavailable from NCBI (https://www.ncbi.nlm.nih.gov/) and treated as missing data in the matrix.

Additional file 3: Table S3. Proportion of missing data for the 49 accessions (genera) with few DNA sequences available, compared to the total length of the incomplete-105 regions matrix, and bootstrap value for the stem nodes of these accessions (genera) obtained from maximum likelihood (ML) analysis of the incomplete-105 regions matrix (Fig. 1).

Additional file 6: Fig. S6. Comparisons of dN, dS, and dN/dS of the protein-coding genes in three main subg. Lysimachia clades. (a) The 53 protein-coding genes in subg. Palladia. (b) The 49 protein-coding genes in subg. Idiophyton. (c) The 51 protein-coding genes in subg. Lysimachia (Christinae clade).

Here, we reported a haplotype-resolved and telomere-to-telomere genome assembly of M. acuminata using PacBio HiFi reads, Nanopore ultra-long reads and high-covered Hi-C data. This assembly represented a significantly high-quality reference assessed by contiguity (contig N50: 16.53Mb and 18.58Mb; LAI: 20.18 and 19.48), completeness (BUSCOs: 98.57% and 98.57%), and correctness (QV: 45.97 and 46.12). All centromeres and 36 of 44 telomeres had been captured. The mapping rates of HiFi and Illumina reads both exceeded 99.80%. In total, 40,889 and 38,269 protein-coding genes were annotated in the two haploid assemblies, respectively, of which 9.56% and 3.37% were newly annotated compared with previous databases. Gene BUSCOs reached up to 89.41% and 90.27%, respectively. Through comparing our assembly and the previously published genome of M. acuminata, we identified two large translocation regions with length of 3 Mb and 10 Mb, which were further confirmed by Hi-C heatmap and targeted-PCR gel electrophoresis. This haplotype-resolved and telomere-to-telomere reference genome of M. acuminata provides an excellent resource for further understanding the mechanisms of subgenome evolution, domestication history, and genetic breeding of banana.

Additional file 5: Fig. S5. Comparison of nucleotide diversity (Pi) values in plastomes of four main Lysimachia clades. (a) The subg. Palladia (clade III). (b) The subg. Idiophyton (clade VI). (c) The subg. Lysimachia (clade I). (d) The subg. Lysimachia (clade IV).

Additional file 1: Table S1. List of accessions sampled, with voucher specimens, GenBank accession numbers and the length of plastomes newly sequenced. Sequences marked with ‘✱’ were obtained from NCBI (https://www.ncbi.nlm.nih.gov/).

Dataset for "Flora diversity survey and plants DNA barcode database establishment in Lomas ecosystem, Peru"

Additional file 7: Fig. S7. The maximum likelihood tree (T2) of Lysimachia reconstructed based on PCGs. The bootstrap support values are indicated along the branches.

Banana is among the most popular fruits worldwide. Cavendish-type bananas, which have a monospecific Musa acuminata origin (AAA), account for around half of the global banana production, thereby are of great significance for human societies. However, until now, the high-quality haplotype-resolved reference genome is still undecoded for banana cultivars. Here, we reported the telomere-to-telomere (T2T) and haplotype-resolved reference genome of ‘Baxijiao’ (Cavendish) consisting of three haploid assemblies. The sizes of the three haploid assemblies were estimated to be 477.16 Mb, 477.18 Mb and 469.57 Mb, respectively. Although with monospecific origins, the three haploid assemblies showed great differences with low levels of sequence collinearity. Several large reciprocal translocations were identified among chromosomes 1, 4 and 7. An expansion of gene families that might affect fruit quality and aroma was detected, such as those belonging to sucrose/disaccharide/oligosaccharide catabolic processes, sucrose metabolic process, starch metabolic process, and aromatic compound biosynthetic process. Besides, an expansion of gene families associated with anther and pollen development was observed, which could be related to parthenocarpy and sterility of the Cavendish cultivar. Finally, loss of resistance genes in the ‘Baxijiao’ genome was observed, particularly in the gene clusters in chromosomes 3 and 10, providing potential targets to investigate for molecular dissection of disease resistance in banana. This T2T haplotype-resolved reference genome will thus be a valuable genetic resource for biological studies, molecular breeding and genetic improvement of banana.