Search

Primula xingshanensis, a new species of Primula endemic to Hubei Province, China, is described and illustrated. It is morphologically similar to two other species belonging to Primula sect. Auganthus, P. rupestris from West Hubei and South Shaanxi Provinces, and P. sinensis from Guizhou and Sichuan Provinces, but can be easily distinguished from the two by its obovate-spatulate to spatulate and pinnately lobed leaf blade, cuneate leaf base and shorter petioles that are 1.3–4.8 cm long.

Primula xingshanensis Y. B. Wang, sp. nov. (Fig. 1). Type.— CHINA. Hubei Province, Yichang City, Xingshan County, Xiakou Town, on rocks, elev. 360 m, 31°12´N, 110°51´E, 27 Feb 2022, Wang et al. ycmy152 (holotype, IBSC!, isotypes, PE!). Description:— Perennial herb, up to 30 cm tall, leaves and stems with dense long hairs. Roots dark brown or lilac, fleshy and brittle. Rhizomes brown, 3–22 cm long, sometimes branched, comparatively stout, with numerous dry leaf sheath, old and young leaves at apex. Leaves 5–12, rosette; petioles 1.3–4.8 cm long, green with copious multicellular white hairs, vaginate at base; blades obovate-spatulate to spatulate, 2–5 × 1–3 cm, fleshy, densely white villous on both sides, adaxially green, abaxially light green, pinnately lobed to ca. 1/3 of its width; lobes 7–10, oblong to subrotund, margin entire; cuneate at base, round at apex, lateral veins 4–6 pairs. Scapes 2–3 arising from each leaf rosette, 2.2–6.2 cm tall, densely white villous, umbels 1–3, superimposed, each umbel with 2–5 flowers; bracts linear to lanceolate, 0.3–1.5 cm long, acute at apex, densely white villous; pedicels 1.2–3.0 cm long, densely white villous. Flowers heterostylous; calyx bell-shaped, 6–9 mm long, 5–7 mm in diam., inflated at base in fruit, densely white villous, parted to 1/3, lobes triangular, margin entire, apex acute; corolla pink or pale lilac, funnel-shaped, with yellow spots at throat; limb 2.5–4.0 cm in diam., lobes 5, broadly elliptic, ca. 10 × 9 mm, glabrous, 2-lobed at apex, parted to 1/3. Pin flowers with corolla tube ca. 1–1.3 cm long, stamens inserted 3–4 mm from base of corolla tube, pillar length about 3/4 of corolla tube, 6–9 mm long, slightly higher than the calyx; thrum flowers with corolla tube 1.2–1.4 cm long, stamens inserted 6–8 mm from base of corolla tube, pillar 3 mm long. Stigma globular; ovary globular, glabrous, ca. 3.5 mm in diam., ovules many. Capsule subglobose, 5–6 mm in diam. Seeds many, ellipsoid, 1–2 mm long. Phenology:— The species was observed flowering from February to March, and fruiting from the end of March to April. Etymology:— The specific epithet refers to the Chinese pinyin of Xingshan County, where is the type locality. Distribution and ecology:— The new species is currently only known from Xiakou Town, Xingshan County, Yichang City, Hubei Province, China, growing on the rock ledges of rocky cliffs of limestone at about 360 m a.s.l., where there is without soil and moisture due to exposure to the sun. Companion species, such as Corydalis saxicola Bunting, Triaenophora shennongjiaensis X. D. Li, Y. Y. Zan & J. Q. Li, Silene dentipetala H. Chuang can be found around. Conservation status:— To date, only one population with ca. 1000 individuals of the new species has been found. The habitat is free from human disturbance, but the conditions are very poor (nearly without soil or moisture). Based on present survey and according to IUCN red list criteria (IUCN 2001), its conservation status is assessed as ‘Critically Endangered’ (CR)(B2abiii). Taxonomic Note:— According to Hu (1996), Primula xingshanensis should be placed in P. sect. Auganthus because of its distinctively broad and flat-bottomed calyx. Primula xingshanensis is morphologically most similar to P. rupestris in the broad and flat-bottomed calyx and rhizomes with persistent old leaves at the apex and has an overlapping geographical distribution with the latter (West Hubei versus West Hubei and South Shaanxi), but can be easily distinguished by leaf base (cuneate versus cordate or sub-truncate), leaf lobation pattern (pinnately lobed versus palmately lobed) and petiole length (1.3–4.8 cm versus 4–13 cm). The new species is also similar to P. sinensis from Guizhou and Sichuan, but P. xingshanensis clearly differs in its old leaves remaining at the apex of the rhizomes (versus without old leaves at apex), green petiole 1.3–4.8 cm long (versus purplish petiole 4–15 cm long), cuneate leaf base (versus cordate or sub-truncate) and pinnately lobed leaf blade (versus palmately lobed). Here, to facilitate its identification, we provided photographs (Figs. 1 & 2), a detailed morphological comparison (Table 1), as well as a key to the species of Primula sect. Auganthus., Published as part of Wang, Shi-Qin, Yan, Hai-Fei, Cheng, Zhi-Jie & Wang, Yu-Bing, 2023, Primula xingshanensis (Primulaceae), a new species from Hubei, China, pp. 158-162 in Phytotaxa 594 (2) on pages 158-160, DOI: 10.11646/phytotaxa.594.2.8, http://zenodo.org/record/7900653, {"references":["IUCN. (2001) IUCN red list categories and criteria, ver. 3. 1. IUCN Species Survival Commission. [https: // www. iucnredlist. org /]","Hu, C. M. & Kelso, S. (1996) Primulaceae. In: Wu, Z. Y. & Raven, P. H. (Eds.) Flora of China. Vol. 15. Science Press, Beijing & Missouri Botanical Garden Press, St. Louis, pp. 39 - 185."]}

Key to Primula sect. Auganthus (adapted from Hu & Kelso 1996): 1. Leaves pinnately lobed to midvein................................................................................................................................... P. filchnerae 1. Leaves pinnately or palmately lobed, lobes not reaching midvein 2. Old leaves falling off, petiole purplish................................................................................................................................ P. sinensis 2. Old leaves remaining, petiole green 3. Leaf blade base cuneate............................................................................................................................................. P. xingshanensis 3. Leaf blade base cordate to sub-truncate............................................................................................................................. P. rupestris, Published as part of Wang, Shi-Qin, Yan, Hai-Fei, Cheng, Zhi-Jie & Wang, Yu-Bing, 2023, Primula xingshanensis (Primulaceae), a new species from Hubei, China, pp. 158-162 in Phytotaxa 594 (2) on page 161, DOI: 10.11646/phytotaxa.594.2.8, http://zenodo.org/record/7900653, {"references":["Hu, C. M. & Kelso, S. (1996) Primulaceae. In: Wu, Z. Y. & Raven, P. H. (Eds.) Flora of China. Vol. 15. Science Press, Beijing & Missouri Botanical Garden Press, St. Louis, pp. 39 - 185."]}

Additional file 12: Fig. S12. Pie charts of the ratio of gene support, conflict, and non-informatic gene loci on each node of an ASTRAL maximum quartet support species tree (MQSST). The blue sector of the pie chart indicates the gene support for the shown topology. The green sector of the pie chart indicates the most common conflicting topologies. The red sector of the pie chart indicates all other supported conflicting topologies. The gray sector has no support for two conflict testing topologies. The number in parentheses represents the most common conflict (green) rather than all other gene tree conflicts (red).

Additional file 10: Fig. S10. The maximum quartet support species tree (MQSST) inferred by ASTRAL based on plastid regions. Local posterior probabilities (LPPs) are indicated along the branches.

Dataset for "Flora diversity survey and establishment of a plant DNA barcode database of Lomas ecosystems in Peru "

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).

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).

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.

Additional file 8: Fig. S8. The maximum likelihood tree (T3) of Lysimachia reconstructed based on IGS. The bootstrap support values are indicated along the branches.

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 1: Fig. S1. Comparison of LSC, IRs, and SSC junction positions among Lysimachia plastomes.

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%.

Additional file 9: Fig. S9. The maximum likelihood tree (T4) of Lysimachia reconstructed based on introns. The bootstrap support values are indicated along the branches.

Additional file 8: Figure S8. Correlation of NUMT length and Ericales mitogenome size.

Additional file 3: FigureS3. The inferred secondary structure of the ccmFc gene among the Ericales mitogenomes. Primula contains three Primula mitogenomes; Actinidia contains two kiwifruit mitogenomes.

Additional file 12: Table S12. Variability of 23 regions in Musaceae.

Additional file 8: Fig. S8. ML tree inferred from IQ-TREE based on unpartitioned CP-slope. CP-slope refers to CP after excluding saturated loci based on slopes of the linear regression. The support values of SH-aLRT (on the left) and UFBS (on the right) are shown on the branches, respectively.

Additional file 11: Fig. S11. Divergence times inferred from BEAST2. The red pentagrams refer to the fossil and secondary calibration points. The white numbers in black circles correspond to those in Fig. 2 and mentioned in the main text. The numbers and blue bars at nodes are divergence times before present and corresponding time intervals in the 95% highest posterior density (HPD).

Additional file 13: Table S13. The indel polymorphism of some pairwise species with minimal interspecific K2P distance based on the combination of four most variable markers.

Additional file 6: FigureS6. Gene clusters of each Ericales mitogenome. The red cell indicates the existence of one specific gene cluster.

Additional file 5: Figure S5. The three longest LCBs and their distribution in Primula taxa.

Additional file 10: Table S10. Distribution of tandem repeats in Musaceae plastomes.

Additional file 6: Fig. S6. ML tree inferred from IQ-TREE based on partitioned NPCG. The support values of SH-aLRT (on the left) and UFBS (on the right) are shown on the branches.

Additional file 3: Table S3. The indexes of the codon usage bias in Musaceae plastomes.

Additional file 5: Figure S5. The three longest LCBs and their distribution in Primula taxa.

Additional file 6: Table S6. Frequency of short dispersed repeats (SDRs).

Additional file 9: Figure S9. Correlation of NUMTs, MTPTs, and repeat length and Ericales mitogenome size after removing outlier mitogenomes. (a) NUMT length and Ericales mitogenome size after removing the Aegiceras corniculatum mitogenome; (b) repeat length and Ericales mitogenome size after removing the kiwifruit mitogenomes; (c) MTPT length and Ericales mitogenome size after removing the Rhododendron simsii and Monotropa hypopitys mitogenomes.

Additional file 6: FigureS6. Gene clusters of each Ericales mitogenome. The red cell indicates the existence of one specific gene cluster.

Additional file 7: Fig. S7. Saturation indices for 197 loci shown as density plots. (a) Slopes of the linear regression between patristic and uncorrected pairwise distances. (b) R2 of the linear regression between patristic and uncorrected pairwise distances. The vertical and dashed lines indicate starting shoulder value. Loci that may be saturated are colored in red; the numbers of saturated loci are indicated aside.

Additional file 1: Table S1. Classification and species list of Musaceae.

Additional file 5: Fig. S5. ML tree inferred from IQ-TREE based on partitioned PCG. The support values of SH-aLRT (on the left) and UFBS (on the right) are shown on the branches.

Additional file 2: Table S2. List of genes present in the plastomes of Musaceae species generated in this study.

Additional file 15: Table S15. The primers used for PCR in current study.

Additional file 11: Table S11. The estimation of substitution rate and dN/dS.

Additional file 8: Table S8. Distribution of simple sequence repeats (SSRs) in Musaceae plastomes.

Additional file 3: Fig. S3. ML tree inferred from IQ-TREE based on unpartitioned non-protein coding genes (NPCG). The support values of SH-aLRT (on the left) and UFBS (on the right) are shown on the branches.

Additional file 15: Fig. S15. The single-chain MCMC diagnostics for a CoMET analysis. The blue bars and dots indicate passed tests, while red bars and dots refer to failed convergence.

Additional file 5: Table S5. Codons exhibited higher usages (RSCU) and lower usages (RSCU) in Musacompared to Ensete and Musella.

Additional file 4: Fig. S4. ML tree inferred from IQ-TREE based on partitioned genes of complete plastomes (CP). The support values of SH-aLRT (on the left) and UFBS (on the right) are shown on the branches.

Additional file 7: Figure S7. The newly identified gene clusters of each Ericales mitogenome. The red cell indicates the existence of one specific gene cluster.

Additional file 1: Fig. S1. Complete plastid genome map of tribe Perseeae. Different genes are color coded.

Additional file 9: Table S9. Frequency of tandem repeats by length.

Additional file 16: Table S16. The sequences of PCR products generated in this study with their accession names in Science DB (available at https://www.doi.org/10.11922/sciencedb.01436 ).

Additional file 4: Table S4. Codon usage in Musaceae plastomes.

Additional file 2: Fig. S2. ML tree inferred from IQ-TREE based on unpartitioned protein coding genes (PCG). The support values of Shimodaira-Hasegawa-like approximate likelihood ratio test (SH-aLRT; on the left) and ultrafast bootstrap (UFBS; on the right) are shown on the branches, respectively.

Additional file 14: Table S14. List of taxa and sources of plant material analyzed, and GenBank accession numbers of plastome of taxa used in the present study.

Additional file 10: Fig. S10. Number of gaps in each locus. The locus with the highest number of gaps (ccsA-trnLUAG) is marked.

Additional file 17: Table S17. Partition scheme of 79 coding sequences (CDSs) used in this study.