PHYLOGENY OF JUNCAGINACEAE IN CHINA BASED ON COMPLETE CHLOROPLAST GENOME
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摘要:
为探究水麦冬科(Juncaginaceae)系统发育上存在的争议, 并丰富水麦冬科物种的遗传信息资源, 研究对海韭菜(Triglochin maritima)和水麦冬(Triglochin palustris)叶绿体基因组进行测序、组装、注释和特征分析, 并重建其与相关类群的系统发育关系。海韭菜和水麦冬叶绿体基因组呈环状四分体结构, 全长分别为155881和155803 bp, 分别鉴定出了57和60个SSRs及49个长重复序列。海韭菜和水麦冬叶绿体基因组偏好使用以A/U结尾的密码子。系统发育分析表明水麦冬科两个物种聚为一支, 与其近缘类群遗传距离较远, 于78.67 MYA与眼子菜属(Potamogeton)、虾海藻属(Phyllospadix)、大叶藻属(Zostera)、二药藻属(Halodule)、针叶藻属(Syringodium)、川蔓藻属(Ruppia)构成的分支产生分化。结合物种生境与形态特征支持将水麦冬属上升为水麦冬科。研究将不仅为探究水麦冬科叶绿体基因组结构进化奠定理论基础, 也能为水麦冬科及相关类群物种保护和科学利用提供理论依据。
Abstract:To investigate the phylogeny of Juncaginaceae and enrich its genetic resources, the complete chloroplast genomes of Triglochin maritima and Triglochin palustris were sequenced, assembled, annotated, and characterized. In addition, the phylogenetic relationships of Juncaginaceae and closely related taxa were reconstructed. The results indicate that the chloroplast genomes of Triglochin maritima and Triglochin palustris exhibit circular structure with lengths of 155881 and 155803 bp, respectively, containing 57 and 60 SSRs and all 49 long repetitive sequences. In addition, Both genomes also show a preference for codons ending in A/U. Phylogenetic analysis shows that these two Juncaginaceae species form a single branch with a significant genetic distance from closely related taxa, diverging from Potamogeton, Phyllospadix, Zostera, Halodule, Syringodium, and Ruppia approximately 78.67 million years ago. In conjunction with the distributional habitat differences, this study supports the elevation of Triglochin to family status within Juncaginaceae. This study provides a theoretical foundation for investigating chloroplast genome structure evolution of Juncaginaceae and offers valuable insights for species conservation and scientific utilization of Juncaginaceae and its related taxa.
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Keywords:
- Juncaginaceae /
- Chloroplast genomes characteristics /
- Phylogeny /
- Divergence time
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图 1 水麦冬科叶绿体基因组图谱
A. 海韭菜Triglochin maritima; B. 水麦冬Triglochin palustris
Figure 1. Chloroplast genomes map of Juncaginaceae
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图 2 水麦冬科叶绿体基因组PR2-Plot、ENC-Plot和中性绘图分析
A. PR2-Plot; B. ENC-Plot; C. 中性绘图分析
Figure 2. Analysis of PR2-plot, ENC-plot, and neutrality plot of chloroplast genomes of Juncaginaceae
A. PR2-Plot; B. ENC-Plot; C. neutrality-plot
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图 3 水麦冬科叶绿体基因组RSCU分析与最优密码子
A. 海韭菜RSCU分析; B. 水麦冬RSCU分析; C. 最优密码子
Figure 3. Optimal codons analysis and RSCU analysis of chloroplast genomes of Juncaginaceae
A. RSCU analysis of Triglochin maritima; B. RSCU analysis of Triglochin palustris; C. Optimal codons
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图 4 水麦冬科植物基于RSCU的对应性分析
A. 海韭菜Triglochin maritima; B. 水麦冬Triglochin palustris
Figure 4. Corresponding analysis based on RSCU of Juncaginaceae
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图 5 水麦冬科叶绿体基因组长重复序列
A. 海韭菜Triglochin maritima; B. 水麦冬Triglochin palustris
Figure 5. Long repeat sequences of chloroplast genomes of Juncaginaceae
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图 6 水麦冬科叶绿体基因组选择压力分析
Figure 6. Selective pressure analysis of chloroplast genomes of Juncaginaceae
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图 7 水麦冬科及近缘类群叶绿体基因组共线性分析
Figure 7. Collinearity analysis of chloroplast genomes of Juncaginaceae and closely related tax
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图 8 水麦冬科及近缘类群时间度量树
Figure 8. Time metric tree of Juncaginaceae and closely related taxa
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图 9 水麦冬科及近缘类群叶绿体基因组遗传距离
Figure 9. Genetic distance of Juncaginaceae and closely related taxa based on chloroplst genomes
表 1 海韭菜叶绿体基因组注释基因
Table 1 Genes contained of Triglochin maritima chloroplast genome
基因功能Gene function 基因类型Gene type 基因名称Gene name 光合作用相关基因
Genes for photosynthesis光系统Ⅰ Photosystem Ⅰ psaA, psaB, psaC, psaI, psaJ 光系统ⅡPhotosystem Ⅱ psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN(pbf1), psbT, psbZ 细胞色素b/f 复合物Cytochrome b/f complex petA, petB*, petD*, petG, petL, petN ATP 合成酶ATP synthase atpA, atpB, atpE, atpF*, atpH, atpI NADH 脱氢酶NADH dehydrogenase ndhA*, ndhB*(2), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK 二磷酸核酮糖羧化酶大亚基Rubisco large subunit rbcL 自我复制Self-replication 核糖体RNA Ribosomal RNAs rrn16(2), rrn23(2), rrn4.5(2), rrn5(2) RNA 聚合酶亚基Subunits of RNA polymerase rpoA, rpoB, rpoC1*, rpoC2 核糖体小亚基(SSU)Small subunit of rubisco rps11, rps12**(2), rps14, rps15, rps16*, rps18, rps19, rps2, rps3, rps4, rps7(2), rps8 核糖体大亚基(LSU)Large subunit of rubisco rpl14, rpl16*, rpl2*(2), rpl20, rpl22, rpl23(2), rpl32, rpl33, rpl36 转运RNA Transfer RNAs trnA-UGC*(2), trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-GCC, trnG-UCC*, trnH-GUG, trnI-CAU(2), trnI-GAU*(2), trnK-UUU*, trnL-CAA(2), trnL-UAA*, trnL-UAG, trnM-AUG, trnN-GUU(2), trnP-UGG, trnQ-UUG, trnR-ACG(2), trnR-UCU, trnS-GCU, trnS-UCC, trnS-UGA, trnT-ACA, trnT-GGU, trnV-GAC(2), trnV-UAC*, trnW-CCA, trnY-GUA, trnfM-CAU 其他基因Other genes 成熟酶Maturase matK 被膜蛋白Envelop membrane protein cemA(2) 乙酰辅酶A羧化酶Acetyl-CoA carboxylase accD c-型细胞色素合成基因
c-type cytochrome synthesis geneccsA 蛋白酶Protease clpP1** 转录启动因子Transcription promoter infA 未知功能基因
Unknown function genes假定的保守叶绿体开放阅读框
Conserved hypothetical chloroplast Reading Framesycf1, ycf2(2), ycf3(pafI)**, ycf4(pafII) 注: Gene*. 此基因含有一个内含子; Gene**. 此基因含有两个内含子; Gene(2). 基因多拷贝数Note: Gene*. Gene with one intron; Gene**. Gene with two introns; Gene(2). Number of copies of multi-copy genes 
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表 2 水麦冬科叶绿体基因组简单重复序列
Table 2 Simple repeat sequences of chloroplast genomes of Juncaginaceae
重复类型
Repetitive type重复碱基
Repetitive
bases数量
Repeat最大重复单元
Maximum
repeat size单核苷酸重复
Single-nucleotide repeatA 24/30 16/15 C 1/1 10/10 G 1/0 11/0 T 26/25 15/18 二核苷酸重复
Dinucleotide repeatAT 3/1 7/7 TA 2/3 8/6 注: “/”前为海韭菜核苷酸重复数量或最大重复单元, 后为水麦冬核苷酸重复数量或最大重复单元Note: “/” is preceded by the repeats or maximum repeat size of nucleotide repeats in Triglochin maritima, followed by the repeats or maximum repeat size of nucleotide repeats in Triglochin palustris
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