Biodiv Sci ›› 2026, Vol. 34 ›› Issue (5): 25475. DOI: 10.17520/biods.2025475 cstr: 32101.14.biods.2025475
• Original Papers: Genetic Diversity • Previous Articles Next Articles
Shanshan Wang1,2, Qi Liu2,3, Yu Li2, Tianrui Wang2, Xiling Dai3, Gregor Kozlowski2,4,5, Jin Xu1,*(
), Yigang Song2,*(
)()
Received:2025-12-12
Accepted:2026-03-12
Online:2026-05-20
Published:2026-07-01
Contact:
Jin Xu, Yigang Song
Supported by:Shanshan Wang, Qi Liu, Yu Li, Tianrui Wang, Xiling Dai, Gregor Kozlowski, Jin Xu, Yigang Song. Cautions on using chloroplast genome-based phylogeny for species identification and biogeography: A case study of Pterocarya[J]. Biodiv Sci, 2026, 34(5): 25475.
| 物种 Species | 采集地 Location | 缩写 Abbreviation | 纬度 Latitude | 经度 Longitude | 海拔 Altitude (m) | 标本号 Specimen no. | 登录号 GenBank no. | 来源 Source |
|---|---|---|---|---|---|---|---|---|
| 水胡桃 P. rhoifolia | Niigata University Forest, Sado City, Niigata, Japan | PR_NS | 38.23° N | 138.40° E | 370 | NUF3 | PV130126 | 自测 This study |
| 甘肃枫杨 P. macroptera var. macroptera | 甘肃省天水市党川乡 Dangchuan Township, Tianshui City, Gansu Province, China | PMM_TS | 34.27° N | 106.06° E | 1,503 | DM15793-2 | PV130121 | 自测 This study |
| 甘肃枫杨 P. macroptera var. macroptera | 四川省冕宁县森荣乡 Senrong Township, Mianning County, Sichuan Province, China | PMM_MN | 28.35° N | 101.98° E | 2,620 | DM17327 | PV130122 | 自测 This study |
| 甘肃枫杨 P. macroptera var. macroptera | 四川省峨眉山景区 Emei Mountain Scenic Area, Sichuan Province, China | PMM_EM | 29.54° N | 103.34° E | 2,055 | LXC00013 | PV130125 | 自测 This study |
| 华西枫杨 P. macroptera var. insignis | 浙江省西天目山 West Tianmu Mountain, Zhejiang Province, China | PMI_TM | 28.35° N | 118.87° E | 950 | SYG00006-3 | PV130127 | 自测 This study |
| 云南枫杨 P. macroptera var. delavayi | 云南省迪庆藏族自治州维西傈僳族自治县 Weixi Lisu Autonomous County, Diqing Tibetan Autonomous Prefecture, Yunnan Province, China | PMD_DQ | 27.76° N | 99.02° E | 2,240 | DM21298 | PV130123 | 自测 This study |
| 云南枫杨 P. macroptera var. delavayi | 云南省怒江傈僳族自治州贡山独龙族怒族自治县 Gongshan Derung and Nu Autonomous County, Nujiang Lisu Autonomous Prefecture, Yunnan Province, China | PMD_NJ | 28.07° N | 98.74° E | 2,899 | DM21322 | PV130124 | 自测 This study |
Table 1 Basic information on field sampling of plant materials of Pterocarya
| 物种 Species | 采集地 Location | 缩写 Abbreviation | 纬度 Latitude | 经度 Longitude | 海拔 Altitude (m) | 标本号 Specimen no. | 登录号 GenBank no. | 来源 Source |
|---|---|---|---|---|---|---|---|---|
| 水胡桃 P. rhoifolia | Niigata University Forest, Sado City, Niigata, Japan | PR_NS | 38.23° N | 138.40° E | 370 | NUF3 | PV130126 | 自测 This study |
| 甘肃枫杨 P. macroptera var. macroptera | 甘肃省天水市党川乡 Dangchuan Township, Tianshui City, Gansu Province, China | PMM_TS | 34.27° N | 106.06° E | 1,503 | DM15793-2 | PV130121 | 自测 This study |
| 甘肃枫杨 P. macroptera var. macroptera | 四川省冕宁县森荣乡 Senrong Township, Mianning County, Sichuan Province, China | PMM_MN | 28.35° N | 101.98° E | 2,620 | DM17327 | PV130122 | 自测 This study |
| 甘肃枫杨 P. macroptera var. macroptera | 四川省峨眉山景区 Emei Mountain Scenic Area, Sichuan Province, China | PMM_EM | 29.54° N | 103.34° E | 2,055 | LXC00013 | PV130125 | 自测 This study |
| 华西枫杨 P. macroptera var. insignis | 浙江省西天目山 West Tianmu Mountain, Zhejiang Province, China | PMI_TM | 28.35° N | 118.87° E | 950 | SYG00006-3 | PV130127 | 自测 This study |
| 云南枫杨 P. macroptera var. delavayi | 云南省迪庆藏族自治州维西傈僳族自治县 Weixi Lisu Autonomous County, Diqing Tibetan Autonomous Prefecture, Yunnan Province, China | PMD_DQ | 27.76° N | 99.02° E | 2,240 | DM21298 | PV130123 | 自测 This study |
| 云南枫杨 P. macroptera var. delavayi | 云南省怒江傈僳族自治州贡山独龙族怒族自治县 Gongshan Derung and Nu Autonomous County, Nujiang Lisu Autonomous Prefecture, Yunnan Province, China | PMD_NJ | 28.07° N | 98.74° E | 2,899 | DM21322 | PV130124 | 自测 This study |
Fig. 1 Genomic map of the Pterocarya rhoifolia chloroplast genome (the chloroplast genome maps of other six individuals are similar). The outer circle shows the gene structure on the plastome. Genes outside the circle are transcribed counterclockwise, while genes inside the circle are transcribed clockwise. Genes are color-coded according to their functional categories.
| 基因组特征 Genome characteristics | 水胡桃 PR_NS | 甘肃枫杨PMM_TS | 甘肃枫杨PMM_MN | 甘肃枫杨PMM_EM | 华西枫杨PMI_TM | 云南枫杨PMD_DQ | 云南枫杨PMD_NJ |
|---|---|---|---|---|---|---|---|
| 序列全长 Genome size (bp) | 160,209 | 160,210 | 160,238 | 160,318 | 160,236 | 160,176 | 160,232 |
| 大单拷贝区长度 Large single copy (LSC) length (bp) | 89,708 | 89,731 | 89,770 | 89,810 | 89,768 | 89,701 | 89,757 |
| 小单拷贝区长度 Small single copy (SSC) length (bp) | 18,459 | 18,451 | 18,412 | 18,446 | 18,412 | 18,443 | 18,443 |
| 反向重复区长度 Inverted repeat (IR) length (bp) | 26,021 | 26,014 | 26,028 | 26,031 | 26,028 | 26,016 | 26,016 |
| GC含量 GC content (%) | 36.20 | 36.20 | 36.20 | 36.10 | 36.20 | 36.20 | 36.20 |
| 大单拷贝区GC含量 GC content of LSC (%) | 33.77 | 33.77 | 33.78 | 33.72 | 33.72 | 33.77 | 33.79 |
| 小单拷贝区GC含量 GC content of SSC (%) | 29.86 | 29.86 | 29.86 | 29.85 | 29.85 | 29.89 | 29.87 |
| 反向重复区GC含量 GC content of IR (%) | 42.57 | 42.57 | 42.56 | 42.57 | 42.57 | 42.54 | 42.55 |
| A碱基占比 A base content (%) | 31.60 | 31.50 | 31.60 | 31.60 | 31.60 | 31.50 | 31.60 |
| T碱基占比 T base content (%) | 32.30 | 32.30 | 32.30 | 32.30 | 32.30 | 32.30 | 32.30 |
| C碱基占比 C base content (%) | 18.40 | 18.40 | 18.40 | 18.40 | 18.40 | 18.40 | 18.40 |
| G碱基占比 G base content (%) | 17.80 | 17.80 | 17.80 | 17.80 | 17.80 | 17.80 | 17.80 |
| 基因总数 No. of total genes | 131 | 131 | 131 | 131 | 131 | 131 | 131 |
| 蛋白质编码基因数 No. of protein coding genes | 86 | 86 | 86 | 86 | 86 | 86 | 86 |
| tRNA基因数 No. of tRNA genes | 37 | 37 | 37 | 37 | 37 | 37 | 37 |
| rRNA基因数 No. of rRNA genes | 8 | 8 | 8 | 8 | 8 | 8 | 8 |
Table 2 Comparison of chloroplast genomic characteristics of seven newly sequenced individuals in this study
| 基因组特征 Genome characteristics | 水胡桃 PR_NS | 甘肃枫杨PMM_TS | 甘肃枫杨PMM_MN | 甘肃枫杨PMM_EM | 华西枫杨PMI_TM | 云南枫杨PMD_DQ | 云南枫杨PMD_NJ |
|---|---|---|---|---|---|---|---|
| 序列全长 Genome size (bp) | 160,209 | 160,210 | 160,238 | 160,318 | 160,236 | 160,176 | 160,232 |
| 大单拷贝区长度 Large single copy (LSC) length (bp) | 89,708 | 89,731 | 89,770 | 89,810 | 89,768 | 89,701 | 89,757 |
| 小单拷贝区长度 Small single copy (SSC) length (bp) | 18,459 | 18,451 | 18,412 | 18,446 | 18,412 | 18,443 | 18,443 |
| 反向重复区长度 Inverted repeat (IR) length (bp) | 26,021 | 26,014 | 26,028 | 26,031 | 26,028 | 26,016 | 26,016 |
| GC含量 GC content (%) | 36.20 | 36.20 | 36.20 | 36.10 | 36.20 | 36.20 | 36.20 |
| 大单拷贝区GC含量 GC content of LSC (%) | 33.77 | 33.77 | 33.78 | 33.72 | 33.72 | 33.77 | 33.79 |
| 小单拷贝区GC含量 GC content of SSC (%) | 29.86 | 29.86 | 29.86 | 29.85 | 29.85 | 29.89 | 29.87 |
| 反向重复区GC含量 GC content of IR (%) | 42.57 | 42.57 | 42.56 | 42.57 | 42.57 | 42.54 | 42.55 |
| A碱基占比 A base content (%) | 31.60 | 31.50 | 31.60 | 31.60 | 31.60 | 31.50 | 31.60 |
| T碱基占比 T base content (%) | 32.30 | 32.30 | 32.30 | 32.30 | 32.30 | 32.30 | 32.30 |
| C碱基占比 C base content (%) | 18.40 | 18.40 | 18.40 | 18.40 | 18.40 | 18.40 | 18.40 |
| G碱基占比 G base content (%) | 17.80 | 17.80 | 17.80 | 17.80 | 17.80 | 17.80 | 17.80 |
| 基因总数 No. of total genes | 131 | 131 | 131 | 131 | 131 | 131 | 131 |
| 蛋白质编码基因数 No. of protein coding genes | 86 | 86 | 86 | 86 | 86 | 86 | 86 |
| tRNA基因数 No. of tRNA genes | 37 | 37 | 37 | 37 | 37 | 37 | 37 |
| rRNA基因数 No. of rRNA genes | 8 | 8 | 8 | 8 | 8 | 8 | 8 |
Fig. 2 Simple sequence repeat (SSRs) analysis of the chloroplast genomes of 17 individuals. (A) Number of SSRs in different types; (B) Number of SSRs in the large single copy (LSC), inverted repeats (IRs) and small single copy (SSC); (C) Number of SSRs in the intergenic spacer (IGS), coding sequence (CDS) and intron regions.
Fig. 3 Analysis of repeat sequences in the chloroplast genomes of 17 individuals, including tandem and dispersed repeats. (A) Distribution and counts of different repeat sequence types; (B) Counts of tandem repeats across different length ranges; (C) Counts of dispersed repeats across different length ranges.
Fig. 4 Analysis of the contraction and expansion of the inverted repeat (IR) region boundaries in the chloroplast genomes of Pterocarya species: IRa/LSC (JLA), LSC/IRb (JLB), IRb/SSC (JSB), SSC/IRa (JSA). LSC, Large single copy; SSC, Small single copy; IRa, Inverted repeat a; IRb, Inverted repeat b.
Fig. 5 Visualization of the eight chloroplast genomes of Pterocarya with Pterocarya stenoptera as a reference using mVISTA. The gray arrows above show the position of the reference sequence genes, in either the forward or reverse direction. Alignment similarity percentages are shown on the right side of the figure (vertical axis).
Fig. 6 Sliding window analysis of chloroplast genome of Pterocarya. The X-axis represents the nucleotide positions and the Y-axis represents the value of nucleotide diversity (Pi) per window. SNP, Single nucleotide polymorphism.
Fig. 7 Maximum likelihood phylogenetic trees of Pterocarya based on different datasets. (A) Based on the complete chloroplast genomes of 17 individuals of Pterocarya; (B) Based on the coding sequences (CDS) of 17 individuals of Pterocarya; (C) Based on the highly variable ndhF region sequences of 17 individuals of Pterocarya. The bootstrap support values (BS) are labeled at branches in the evolutionary tree.
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