Pinellia discolor: A new cryptic species distinguished from P. cordata in Mainland China
Data files
Dec 05, 2023 version files 103.72 KB
Abstract
Pinellia cordata (Araceae) is a perennial herb species distributed in China and Japan. Several studies have shown that there are two types of this species, and chromosome counts have shown irregular variation among populations. In this study, we investigated the morphological characteristics, established the chromosome number in root tips, reconstructed phylogenetic relationship based on whole chloroplast genomes, and elucidated biogeographic patterns based on data collected from the Chinese Virtual Herbarium (CVH) and the Plant Photo Bank of China (PPBC) for the two types of P. cordata, including type I (greenish leaf blade) and type II (colored leaf blade). We found stable significant differences in morphometric characteristics (color of the leaf blade abaxially, petiole, spathe, and appendix) and the number of chromosomes. The results of the phylogenetic analysis showed that types I and II were located in different places in the evolutionary tree compared to the group. The distribution regions of these types of P. cordata were also slightly different in Mainland China. These findings suggested that P. cordata should be divided into P. cordata (Type I) and P. discolor (Type II, a cryptic species), and the latter is here described as a new species.
README: Pinellia discolor: A new cryptic species distinguished from P. cordata in Mainland China
https://doi.org/10.5061/dryad.8gtht76w0
Based on investigation of morphological characteristics, chromosome numbering, and phylogenetic analysis, a cryptic species, Pinellia discolor (Araceae), is identified from P. cordata. Geographic distribution of P. discolor is covered by P. cordata.
Description of the data and file structure
File List:
Supplementary Table S1. Morphological characteristics (n = 44) of P. cordata and P. discolor.xlsx
Supplementary Table S2. Chromosome number of P. cordata and P. discolor.xlsx
Supplementary Table S3. The list of genes found in the whole plastome of P. cordata and P. discolor.xlsx
Supplementary Table S4. The distribution of P. cordata and P. discolor in Mainland China.xlsx
Supplementary Figure S1. Chloroplast genome structure of P. discolor based on alignment with P. cordata.png
Supplementary Figure S2. Differences in LSC-IRb, IRb-SSC, SSC-IRa, and IRa-LSc between P. cordata and P. discolor.png
Supplementary Figure S3. Differences in simple sequence repeats (SSRs) between P. cordata and P. discolor.png
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DATA-SPECIFIC INFORMATION FOR: Supplementary Table S1. Morphological characteristics (n = 44) of P. cordata and P. discolor.xlsx
1. Number of variables: 47
2. Number of cases/rows: 95
3. Variable List:
- species: Pinellia cordata and P. discolor
- measurement time: measurement time of the study (2021.4.1-2021.5.15)
- sequence number: sequence number of P. cordata and P. discolor
- subterranean part: subterranean tuber of P. cordata and P. discolor
- tuber shape: tuber shape of P. cordata and P. discolor
- tuber diameter (cm): measure tuber size of P. cordata and P. discolor
- tuber surface: tuber surface had many fibrous root of P. cordata and P. discolor
- leaf number: leaf number of P. cordata and P. discolor
- petiole length (cm): measurement of petiole length
- petiole color: petiole color of P. cordata and P. discolor
- sheath at base of petiole: whether the petiole base contains the sheath (absent or existent)
- bulbil location: bulbil location at base of leaf blade or at basal part of petiole and blade
- leaf shape: leaf shape of P. cordata and P. discolor
- leaf blade adaxially color: leaf blade adaxially color of P. cordata and P. discolor
- leaf blade abaxially color: leaf blade abaxially color of P. cordata and P. discolor
- vein adaxially color: vein adaxially color of P. cordata and P. discolor
- vein abaxially color: vein abaxially color of P. cordata and P. discolor
- leaf blade apex shaped: leaf blade apex shaped of P. cordata and P. discolor
- leaf blade length (cm): measurement of leaf blade length
- leaf blade width (cm): measurement of leaf blade width
- vein number: vein number of P. cordata and P. discolor
- peduncle: length of peduncle compared to petiole (shorter or longer than petiole)
- peduncle length (cm): measurement of peduncle length
- spathe constriction: the degree of spathe constriction
- spathe shape: spathe shape of P. cordata and P. discolor
- the upper part of spathe: color of the upper part of spathe
- the lower part of spathe: color of the lower part of spathe
- spathe length (cm): measurement of spathe length
- spathe tube shape: spathe tube shape of P. cordata and P. discolor
- spathe tube length (cm): measurement of spathe tube length
- spathe tube width (cm): measurement of spathe tube width
- spathe limb shape: spathe limb shape of P. cordata and P. discolor
- spathe limb adaxially: color of the spathe limb adaxially
- spathe limb abaxially: color of the spathe limb abaxially
- spathe limb width (cm): measurement of spathe limb width
- spathe limb length (cm): measurement of spathe limb length
- spadix length (cm): measurement of spadix length
- female zone length (cm): measurement of female zone length
- pistil number: count the number of pistils
- pistil shape: pistil shape of P. cordata and P. discolor
- style: the presence or absence of style
- stigma shape: stigma shape of P. cordata and P. discolor
- sterile zone length (cm): measurement of sterile zone length
- male zone length (cm): measurement of male zone length
- appendix shape: appendix shape of P. cordata and P. discolor
- appendix color: appendix color of P. cordata and P. discolor
- appendix length (cm): measurement of appendix length
4. Blank cell: None
5. Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: Supplementary Table S2. Chromosome number of P. cordata and P. discolor.xlsx
1. Number of variables: 18
2. Number of cases/rows: 65
3. Variable List:
- Species: Pinellia cordata and P. discolor
- Roo tip: sequence number of root tip
- 2n = 26: chromosome number of 2n = 26
- 2n = 30: chromosome number of 2n = 30
- 2n = 32: chromosome number of 2n = 32
- 2n = 34: chromosome number of 2n = 34
- 2n = 36: chromosome number of 2n = 36
- 2n = 38: chromosome number of 2n = 38
- 2n = 39: chromosome number of 2n = 39
- 2n = 40: chromosome number of 2n = 40
- 2n = 64: chromosome number of 2n = 64
- 2n = 66: chromosome number of 2n = 66
- 2n = 70: chromosome number of 2n = 70
- 2n = 72: chromosome number of 2n = 72
- 2n = 74: chromosome number of 2n = 74
- 2n = 76: chromosome number of 2n = 76
- 2n = 78: chromosome number of 2n = 78
- Numbers of Cell Type (With differential Chromosome No.): chromosome number types of per root tip
4. Blank cell: indicate null values in the data (data not available)
5. Specialized formats or other abbreviations used: No. = number
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DATA-SPECIFIC INFORMATION FOR: Supplementary Table S3. The list of genes found in the whole plastome of P. cordata and P. discolor.xlsx
1. Number of variables: 6
2. Number of cases/rows: 226
3. Variable List:
- Species: Pinellia cordata and P. discolor
- Gene name: gene name of the chloroplast genome
- Gene location: gene location in the chloroplast genome
- Gene length: base number of the gene
- Intron location: Intron location of the gene
- Intron length: Intron length of the gene
4. Blank cell: indicate null values in the data (data not available)
5. Specialized formats or other abbreviations used: "" Gene with one intron; "*" Gene with two introns; "x2" Gene located in the inverted repeats
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DATA-SPECIFIC INFORMATION FOR: Supplementary Table S4. The distribution of P. cordata and P. discolor in Mainland China.xlsx
1. Number of variables: 5
2. Number of cases/rows: 112
3. Variable List:
- Species: Pinellia cordata and P. discolor
- Longitude: longitude of the geographic location
- Latitude: latitude of the geographic location
- Location: location of P. cordata and P. discolor
- Data sources: geographic distribution sources of P. cordata and P. discolor
4. Blank cell: None
5. Specialized formats or other abbreviations used: "()" represents library barcode of Chinese Virtual Herbarium
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DATA-SPECIFIC INFORMATION FOR: Supplementary Figure S1. Chloroplast genome structure of P. discolor based on alignment with P. cordata.png
Note: The vertical scale represents the sequence identity varying between 50% and 100%; Arrows indicate genes and their transcriptional directions; CNS: Conserved non-coding sequences; UTRs: Untranslated regions.
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DATA-SPECIFIC INFORMATION FOR: Supplementary Figure S2. Differences in LSC-IRb, IRb-SSC, SSC-IRa, and IRa-LSc between P. cordata and P. discolor.png
Note: Numbers of base pair showed length from genes to junction sites.
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DATA-SPECIFIC INFORMATION FOR: Supplementary Figure S3. Differences in simple sequence repeats (SSRs) between P. cordata and P. discolor.png
Note: A: Numbers of SSRs in different regions (LSC, IRs, and SSC). B: Numbers of SSRs for different kinds of repeats.
Methods
Morphometric analyses: Mature individuals during sexual reproductive stage (43 for Pinellia cordata and 52 for P. discolor, from the end of March to the middle of May, 2021) were used to determine 44 morphological characteristics. Statistical analysis should be carried out with Excel 2010® based on 18 quantitative traits among these 44 determined characteristics. Chromosome numbering: Root tips were used to chromosome preparation: stained and crushed in carbol fuchsin, and then were observed and photographed (Olympus® BX53) (Liu et al., 1987). Chloroplast genome analysis and phylogenetic analyses: The complete chloroplast genome annotation (Tillich et al., 2017) and SSRs analysis (Thiel et al., 2003) for P. discolor were carried out. Furthermore, whole chloroplast genome comparision between P. discolor and P. cordata (MT863558, Luo et al., 2021) were executed on the basis of re-annotation. Biogeographic pattern analysis: Chinese Virtual Herbarium (CVH, https://www.cvh.ac.cn/) and Plant Photo Bank of China (PPBC, http://ppbc.iplant.cn/) were used to collected geographic distribution information of P. cordata and P. discolor in field.