DOI: 10.57760/sciencedb.02943
title: The Fagus chienii is conspecific with F. hayatae based on molecular and morphological evidence: The original dataset of gene sequences and morphological measurements
title: The Fagus chienii is conspecific with F. hayatae based on molecular and morphological evidence: The original dataset of gene sequences and morphological measurements

description: Fagus chienii is only known from the type specimens collected in 1935 in Pingwu County of Sichuan Province, China. In this study, we reexamined the type specimens and conducted extensive field investigations in type locality of F. chienii. Through reconstructing the molecular phylogeny of Fagus species based on seven nuclear genes and statistical analyses of nine morphological characters using newly collected F. chienii materials, the results showed that F. chienii is conspecific with F. hayatae phylogenetically and morphologically.For the DNA sequence datasets, seven gene sequences (F128, F138, P4, P14, P37, P52, and P72) that could effectively distinguish all Fagus species were chosen in this research based on the phylogenetic framework in previous study (Jiang et al., 2022).In 2021, the total genomic DNA of 10 individuals of Fagus chienii and 10 individuals of F. hayatae we collected in China were isolated from silica gel-dried leaves, using a modified CTAB protocol. PCRs of the DNA fragments were carried out in 25μl total reaction volume containing 1μl 50ng of template DNA, 1μl 10μM of each forward and reverse primer and 22μl T3 Super PCR Mix (Tsingke, Beijing, China). The PCR programs were as follows: initial denaturation was 3 min at 98℃; followed by 35 cycles of 10s denaturation at 98℃, 10s annealing at 55℃ and extension for 10s at 72℃; a final extension for 2 min at 72℃ was carried out and stopped at 4℃. PCR products were checked for length and yield by gel electrophoresis on 1.5% agarose gels the sequenced on an ABI 3730XL sequencer (Applied Biosystems, Foster City, CA, USA) using the PCR primers. The rest of the gene sequences of Fagus species were downloaded from GenBank.The sequences obtained for each sample were manually checked and aligned using Sequencherv.5.4.6 and Bioedit v.7.0.5.3. All seven gene sequence datasets were stored in fasta format. The missing data in each of gene sequence files was because some individuals could not be amplified efficiently, but the missing data had no effect on the results. The gene sequence file sizes of F128, F138, P4, P14, P37, P52, and P72 are 41kb, 18kb, 36kb, 40kb, 40kb, 38kb, and 40kb, respectively.For the morphological measurements, digital images of Fagus. chienii, F. hayatae, F. longipetiolata and F. lucida examined in this study, were derived from the Chinese Virtual Herbarium (https://www.cvh.ac.cn/), the web of Plants of Taiwan (https://tai2.ntu.edu.tw), the Global Biodiversity Information Facility (https://www.gbif.org/) and JSTOR Global Plants (https://plants.jstor.org). For F. chienii, we examined twelve available specimens in total, seven of which were collected in this study from Pingwu County (the type locality), the rest five were holotype and isotypes with mature fruits deposited in the Royal Botanic Gardens, Kew, South China Botanical Garden, CAS, Chinese National Herbarium, Royal Botanic Garden Edinburgh and New York Botanic Garden, respectively. Additionally, we also measured 38 specimens of F. hayatae, and each 15 specimens of both F. longipetiolata and F. lucida.ImageJ software was applied to the examination of characters of leaf length (LL), leaf width (LW), ratio of leaf length/width (L/W), leaf petiole length (LPL), leaf teeth length (TL), number of secondary veins (NV), cupule peduncle length (CPL), bracts length (BL), and cupule length (CL). Three well-preserved leaves and/or fruits per specimen were randomly selected for examination, and the results were averaged.A total of 80 data items in the original measured values of morphological analyses were contained in an Excel file with a 18 kb file size. The species name appears in the first column, and columns two through four detail the information of specimens used for morphological measurements, including the location of the collection, the herbarium, and the voucher ID. The fifth column begins with specific measurements, including leaf length (LL, cm), leaf width (LW, cm), leaf petiole length (LPL, cm), cupule peduncle length (CPL, cm), cupule length (CL, cm), number of secondary veins (NV), ratio of leaf length/width (L/W), bracts length (BL, cm), and leaf teeth length (TL, cm). Missing data was a result of the specimens' lack of fruit morphology.ReferenceJiang, L., Bao, Q., He, W., et al., 2022. Phylogeny and biogeography of Fagus (Fagaceae) based on 28 nuclear single/low-copy loci. J. Syst. Evol., 60: 759–772. https://doi.org/10.1016/j.pld.2017.12.002
description: Fagus chienii is only known from the type specimens collected in 1935 in Pingwu County of Sichuan Province, China. In this study, we reexamined the type specimens and conducted extensive field investigations in type locality of F. chienii. Through reconstructing the molecular phylogeny of Fagus species based on seven nuclear genes and statistical analyses of nine morphological characters using newly collected F. chienii materials, the results showed that F. chienii is conspecific with F. hayatae phylogenetically and morphologically.For the DNA sequence datasets, seven gene sequences (F128, F138, P4, P14, P37, P52, and P72) that could effectively distinguish all Fagus species were chosen in this research based on the phylogenetic framework in previous study (Jiang et al., 2022).In 2021, the total genomic DNA of 10 individuals of Fagus chienii and 10 individuals of F. hayatae we collected in China were isolated from silica gel-dried leaves, using a modified CTAB protocol. PCRs of the DNA fragments were carried out in 25μl total reaction volume containing 1μl 50ng of template DNA, 1μl 10μM of each forward and reverse primer and 22μl T3 Super PCR Mix (Tsingke, Beijing, China). The PCR programs were as follows: initial denaturation was 3 min at 98℃; followed by 35 cycles of 10s denaturation at 98℃, 10s annealing at 55℃ and extension for 10s at 72℃; a final extension for 2 min at 72℃ was carried out and stopped at 4℃. PCR products were checked for length and yield by gel electrophoresis on 1.5% agarose gels the sequenced on an ABI 3730XL sequencer (Applied Biosystems, Foster City, CA, USA) using the PCR primers. The rest of the gene sequences of Fagus species were downloaded from GenBank.The sequences obtained for each sample were manually checked and aligned using Sequencherv.5.4.6 and Bioedit v.7.0.5.3. All seven gene sequence datasets were stored in fasta format. The missing data in each of gene sequence files was because some individuals could not be amplified efficiently, but the missing data had no effect on the results. The gene sequence file sizes of F128, F138, P4, P14, P37, P52, and P72 are 41kb, 18kb, 36kb, 40kb, 40kb, 38kb, and 40kb, respectively.For the morphological measurements, digital images of Fagus. chienii, F. hayatae, F. longipetiolata and F. lucida examined in this study, were derived from the Chinese Virtual Herbarium (https://www.cvh.ac.cn/), the web of Plants of Taiwan (https://tai2.ntu.edu.tw), the Global Biodiversity Information Facility (https://www.gbif.org/) and JSTOR Global Plants (https://plants.jstor.org). For F. chienii, we examined twelve available specimens in total, seven of which were collected in this study from Pingwu County (the type locality), the rest five were holotype and isotypes with mature fruits deposited in the Royal Botanic Gardens, Kew, South China Botanical Garden, CAS, Chinese National Herbarium, Royal Botanic Garden Edinburgh and New York Botanic Garden, respectively. Additionally, we also measured 38 specimens of F. hayatae, and each 15 specimens of both F. longipetiolata and F. lucida.ImageJ software was applied to the examination of characters of leaf length (LL), leaf width (LW), ratio of leaf length/width (L/W), leaf petiole length (LPL), leaf teeth length (TL), number of secondary veins (NV), cupule peduncle length (CPL), bracts length (BL), and cupule length (CL). Three well-preserved leaves and/or fruits per specimen were randomly selected for examination, and the results were averaged.A total of 80 data items in the original measured values of morphological analyses were contained in an Excel file with a 18 kb file size. The species name appears in the first column, and columns two through four detail the information of specimens used for morphological measurements, including the location of the collection, the herbarium, and the voucher ID. The fifth column begins with specific measurements, including leaf length (LL, cm), leaf width (LW, cm), leaf petiole length (LPL, cm), cupule peduncle length (CPL, cm), cupule length (CL, cm), number of secondary veins (NV), ratio of leaf length/width (L/W), bracts length (BL, cm), and leaf teeth length (TL, cm). Missing data was a result of the specimens' lack of fruit morphology.ReferenceJiang, L., Bao, Q., He, W., et al., 2022. Phylogeny and biogeography of Fagus (Fagaceae) based on 28 nuclear single/low-copy loci. J. Syst. Evol., 60: 759–772. https://doi.org/10.1016/j.pld.2017.12.002