DOI: 10.5061/dryad.g79cnp62s
title: Data from: Two new species of <em>Primula</em> sect. <em>Auganthus</em> from Sichuan, China

description: In groups undergoing rapid radiations, species delimitation among
 phylogenetically close sister lineages has long been a challenge. During
 plant surveys in northwestern Sichuan, we unexpectedly discovered two
 putative new species of Primula that are morphologically similar
 yet distinct from each other. These species resemble P. xingshanensis,
 which has been assigned to sect. Auganthus based on morphological
 characters. To clarify the precise phylogenetic positions of the two
 putative new species and P. xingshanensis, we sampled related taxa and
 conducted phylogenetic analyses using chloroplast genomes and nuclear
 SNPs. The results showed that the two putative new species form sister
 clades and are closely related to P. sinensis, while P.
 xingshanensis is sister to P. rupestris. All belong to sect.
 Auganthus. Based on population genetic structure, morphological
 statistics, and artificial hybridization experiments, both putative new
 species should be accepted as distinct species, herein formally described
 as P. rongrong sp. nov and P. fujiangensis sp. nov. Based on our
 field surveys and in accordance with the IUCN criteria, we assess the
 conservation status of P. rongrong as Least Concern (LC) and P.
 fujiangensis as Critically Endangered (CR).
description: <strong>Morphological Data
 Acquisition:</strong><br> Thirty flowering individuals, with a
 minimum interval of two meters between any two, were randomly selected
 from each wild population for morphological observation. A single,
 moderately sized leaf was collected from each plant. Each leaf was
 photographed indoors on a black light-absorbing cloth with a scale bar for
 reference. A total of ten leaf morphological traits (Leaf Area, Leaf
 Perimeter, Leaf Shape Index, Leaf Length, Leaf Width, Petiole Length,
 Petiole Ratio, Primary Lobes Number, Total Serrations Number, Lateral
 Veins Number) were measured and counted from these digital images using
 ImageJ software (v. 1.54d). Six floral traits (Inflorescence Height,
 Pedicel Length, Bract Length, Calyx Tube Length) were measured in the
 field using a vernier caliper. The presence of nectar guides (coded as: 0
 = absent, 1 = present) and throat color (coded as: 0 = white, 1 = purple)
 were also recorded for each individual.
 <strong>Genomic SNP Data Acquisition and
 Bioinformatics:</strong><br> Genomic DNA was extracted from
 silica-gel-dried leaf tissue using a modified CTAB (cetyltrimethylammonium
 bromide) protocol. DNA quality and concentration were assessed using a
 NanoDrop 1000 Spectrophotometer and agarose gel electrophoresis. Library
 preparation, genome skimming (low-coverage whole-genome sequencing), and
 initial quality control (FastQC) were performed by Wuhan Frasergen Genetic
 Information Co., Ltd. (Wuhan, China) on an Illumina HiSeq 6000 platform.
 Approximately 3 Gb of raw paired-end sequencing data (150 bp) was
 generated per sample.<br> Raw sequencing reads were processed with
 SOAPnuke (v.2.1.7) to remove adapters and low-quality reads, producing
 clean reads. These clean reads were then aligned to the <em>Primula
 veris</em> reference genome using BWA-MEM (v.0.7.17-r1188) with
 default parameters. The resulting Sequence Alignment/Map (SAM) files were
 converted to Binary Alignment/Map (BAM) format, sorted, and processed with
 Picard-tools (https://broadinstitute.github.io/picard/) to mark and remove PCR duplicates. Mapping statistics (e.g., mapping rate, coverage depth) were calculated using SAMtools (v.1.9). Variant calling was performed on all samples simultaneously using the HaplotypeCaller tool in GATK (v.4.0). The initial raw SNP set was rigorously filtered using PLINK (v.1.07) with the following thresholds: a minor allele frequency (MAF) &gt; 0.05, a call rate &gt; 0.95, and pruning for linkage disequilibrium (LD). This process resulted in a final high-quality dataset of 150,248 independent SNP loci retained for downstream phylogenetic and population genetic structure analysis.
description: # Data from: Two new species of *Primula* sect. *Auganthus* from Sichuan,
 China Dataset DOI: [10.5061/dryad.g79cnp62s](10.5061/dryad.g79cnp62s) ##
 **Description:** This dataset contains the raw data used in the manuscript
 "Two New Species of *Primula* Sect. *Auganthus* from Sichuan,
 China". It comprises two main components: 1. **Morphometric data**
 for leaf and floral traits. 2. **Genomic data** in the form of a FASTA
 file containing aligned Single Nucleotide Polymorphism (SNP) sequences for
 phylogenetic and population genetic analysis. **File List:** This deposit
 contains the following two files: * `Morphological_Statistics_Table.csv`:
 Comma-separated values file containing morphological measurements for all
 sampled individuals. * `Single_Nucleotide_Polymorphisms_Matrix.fas`: A
 FASTA-formatted alignment file of SNP loci. **Data Dictionary:** **File:
 `Morphological_Statistics_Table.csv`**\ This file contains the
 morphological measurement data. Each row represents one individual plant.
 The columns are defined as follows: * **Leaf_Area (cm²)**: The
 two-dimensional area of a single side of the leaf. * **Leaf_Perimeter
 (cm)**: The total length of the leaf's outer boundary. *
 **Leaf_Shape_Index**: A dimensionless index calculated as Perimeter /
 Area. * **Leaf_Length (cm)**: The length of the leaf blade, excluding the
 petiole. * **Leaf_Width (cm)**: The maximum width of the leaf blade. *
 **Petiole_Length (cm)**: The length of the leaf stalk (petiole). *
 **Petiole_Ratio**: Ratio of petiole length to total leaf length:
 Petiole_Length / (Leaf_Length + Petiole_Length). *
 **Primary_Lobes_Number**: The count of primary lobes on the leaf. *
 **Total_Serrations_Number**: The total count of serrations on all leaf
 lobes. * **Lateral_Veins_Number**: The number of lateral veins on the
 leaf. * **Inflorescence_Height (cm)**: The height of the inflorescence
 from its base to the top. * **Pedicel_Length (cm)**: The length of the
 stalk of a single flower. * **Bract_Length (cm)**: The length of a
 randomly selected bract on the inflorescence. * **Calyx_Tube_Length
 (cm)**: The length of the calyx tube of a flower. * **Nectar_Guide**:
 Presence (1) or absence (0) of nectar guides on the flower. *
 **Throat_Color**: Color of the flower's throat (White: 0, Purple: 1).
 **File: `Single_Nucleotide_Polymorphisms_Matrix.fas`**\ This is a standard
 FASTA file containing SNP sequence data. * **Content:** It contains
 aligned SNP loci from a total of 17 individuals, including three
 previously described species and two newly described species in the
 associated study. * **Format:** Each sequence entry begins with a header
 line starting with a `&gt;` character, followed by the individual
 identifier (e.g., `&gt;Sample_ID_01`). The subsequent lines contain the
 nucleotide sequence for that individual. * **Correspondence:** All
 individual identifiers in the header lines correspond one-to-one with the
 numbering used in the paper. * **Bioinformatics:** This file is the
 product of a variant calling pipeline against the *Primula veris*
 reference genome, filtered to retain 150,248 high-quality SNP loci.
 **Usage Notes:** * For detailed descriptions of the methodologies used to
 collect morphological data and generate the SNP matrix, please see the
 **Methods** section of this dataset deposit.