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Almerekova S, Yermagambetova M, Osmonali B, Vesselova P, Abugalieva S, Turuspekov Y. Characterization of the Plastid Genomes of Four Caroxylon Thunb. Species from Kazakhstan. PLANTS (BASEL, SWITZERLAND) 2024; 13:1332. [PMID: 38794403 PMCID: PMC11124919 DOI: 10.3390/plants13101332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024]
Abstract
The family Chenopodiaceae Vent. (Amaranthaceae s.l.) is known for its taxonomic complexity, comprising species of significant economic and ecological importance. Despite its significance, the availability of plastid genome data for this family remains limited. This study involved assembling and characterizing the complete plastid genomes of four Caroxylon Thunb. species within the tribe Salsoleae s.l., utilizing next-generation sequencing technology. We compared genome features, nucleotide diversity, and repeat sequences and conducted a phylogenetic analysis of ten Salsoleae s.l. species. The size of the plastid genome varied among four Caroxylon species, ranging from 150,777 bp (C. nitrarium) to 151,307 bp (C. orientale). Each studied plastid genome encoded 133 genes, including 114 unique genes. This set of genes includes 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Eight divergent regions (accD, atpF, matK, ndhF-ndhG, petB, rpl20-rpl22, rpoC2, and ycf3) were identified in ten Salsoleae s.l. plastid genomes, which could be potential DNA-barcoding markers. Additionally, 1106 repeat elements were detected, consisting of 814 simple sequence repeats, 92 tandem repeats, 88 forward repeats, 111 palindromic repeats, and one reverse repeat. The phylogenetic analysis provided robust support for the relationships within Caroxylon species. These data represent a valuable resource for future phylogenetic studies within the genus.
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Affiliation(s)
- Shyryn Almerekova
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (M.Y.); (S.A.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Moldir Yermagambetova
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (M.Y.); (S.A.)
| | - Bektemir Osmonali
- Institute of Botany and Phytointroduction, Almaty 050040, Kazakhstan; (B.O.); (P.V.)
| | - Polina Vesselova
- Institute of Botany and Phytointroduction, Almaty 050040, Kazakhstan; (B.O.); (P.V.)
| | - Saule Abugalieva
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (M.Y.); (S.A.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Yerlan Turuspekov
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (M.Y.); (S.A.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
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Wang D, Wei J, Yuan X, Chen Z, Wang L, Geng Y, Zhang J, Wang Y. Transcriptome and comparative chloroplast genome analysis of Taxus yunnanensis individuals with high and low paclitaxel yield. Heliyon 2024; 10:e27223. [PMID: 38455575 PMCID: PMC10918223 DOI: 10.1016/j.heliyon.2024.e27223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 02/10/2024] [Accepted: 02/26/2024] [Indexed: 03/09/2024] Open
Abstract
Paclitaxel is a potent anti-cancer drug that is mainly produced through semi-synthesis, which still requires plant materials as precursors. The content of paclitaxel and 10-deacetyl baccatin III (10-DAB) in Taxus yunnanensis has been found to differ from that of other Taxus species, but there is little research on the mechanism underlying the variation in paclitaxel content in T. yunnanensis of different provenances. In this experiment, the contents of taxoids and precursors in twigs between a high paclitaxel-yielding individual (TG) and a low paclitaxel-yielding individual (TD) of T. yunnanensis were compared, and comparative analyses of transcriptomes as well as chloroplast genomes were performed. High-performance liquid chromatography (HPLC) detection showed that 10-DAB and baccatin III contents in TG were 18 and 47 times those in TD, respectively. Transcriptomic analysis results indicated that genes encoding key enzymes in the paclitaxel biosynthesis pathway, such as taxane 10-β-hydroxylase (T10βH), 10-deacetylbaccatin III 10-O-acetyltransferase (DBAT), and debenzoyl paclitaxel N-benzoyl transferase (DBTNBT), exhibited higher expression levels in TG. Additionally, qRT-PCR showed that the relative expression level of T10βH and DBAT in TG were 29 and 13 times those in TD, respectively. In addition, six putative transcription factors were identified that may be involved in paclitaxel biosynthesis from transcriptome data. Comparative analysis of plastid genomes showed that the TD chloroplast contained a duplicate of rps12, leading to a longer plastid genome length in TD relative to TG. Fifteen mutation hotspot regions were identified between the two plastid genomes that can serve as candidate DNA barcodes for identifying high-paclitaxel-yield individuals. This experiment provides insight into the difference in paclitaxel accumulation among different provenances of T. yunnanensis individuals.
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Affiliation(s)
- Dong Wang
- College of Forestry, Southwest Forestry University, Kunming, 650224, China
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Jiansheng Wei
- Haba Snow Mountain Provincial Nature Reserve Management and Protection Bureau, Diqing, 674402, China
| | - Xiaolong Yuan
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Zhonghua Chen
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Lei Wang
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Yunfen Geng
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Jinfeng Zhang
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Yi Wang
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
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Wei Z, Chen F, Ding H, Liu W, Yang B, Geng J, Chen S, Guo S. Comparative Analysis of Six Chloroplast Genomes in Chenopodium and Its Related Genera ( Amaranthaceae): New Insights into Phylogenetic Relationships and the Development of Species-Specific Molecular Markers. Genes (Basel) 2023; 14:2183. [PMID: 38137004 PMCID: PMC10743295 DOI: 10.3390/genes14122183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Species within the genus Chenopodium hold significant research interest due to their nutritional richness and salt tolerance. However, the morphological similarities among closely related species and a dearth of genomic resources have impeded their comprehensive study and utilization. In the present research, we conduct the sequencing and assembly of chloroplast (cp) genomes from six Chenopodium and related species, five of which were sequenced for the first time. These genomes ranged in length from 151,850 to 152,215 base pairs, showcased typical quadripartite structures, and encoded 85 protein-coding genes (PCGs), 1 pseudogene, 37 tRNA genes, and 8 rRNA genes. Compared with the previously published sequences of related species, these cp genomes are relatively conservative, but there are also some interspecific differences, such as inversion and IR region contraction. We discerned 929 simple sequence repeats (SSRs) and a series of highly variable regions across 16 related species, predominantly situated in the intergenic spacer (IGS) region and introns. The phylogenetic evaluations revealed that Chenopodium is more closely related to genera such as Atriplex, Beta, Dysphania, and Oxybase than to other members of the Amaranthaceae family. These lineages shared a common ancestor approximately 60.80 million years ago, after which they diverged into distinct genera. Based on InDels and SNPs between species, we designed 12 pairs of primers for species identification, and experiments confirmed that they could completely distinguish 10 related species.
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Affiliation(s)
- Zixiang Wei
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Fangjun Chen
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Hongxia Ding
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Wenli Liu
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Bo Yang
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Jiahui Geng
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Shihua Chen
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Shanli Guo
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
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Su H, Ding X, Liao B, Zhang D, Huang J, Bai J, Xu S, Zhang J, Xu W, Qiu X, Gong L, Huang Z. Comparative chloroplast genomes provided insights into the evolution and species identification on the Datureae plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1270052. [PMID: 37941675 PMCID: PMC10628451 DOI: 10.3389/fpls.2023.1270052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Generally, chloroplast genomes of angiosperms are always highly conserved but carry a certain number of variation among species. In this study, chloroplast genomes of 13 species from Datureae tribe that are of importance both in ornamental gardening and medicinal usage were studied. In addition, seven chloroplast genomes from Datureae together with two from Solanaceae species retrieved from the National Center for Biotechnology Information (NCBI) were integrated into this study. The chloroplast genomes ranged in size from 154,686 to 155,979 and from 155,497 to 155,919 bp for species of Datura and Brugmansia, respectively. As to Datura and Brugmansia, a total of 128 and 132 genes were identified, in which 83 and 87 protein coding genes were identified, respectively; Furthermore, 37 tRNA genes and 8 rRNA genes were both identified in Datura and Brugmansia. Repeats analysis indicated that the number and type varied among species for Simple sequence repeat (SSR), long repeats, and tandem repeats ranged in number from 53 to 59, 98 to 99, and 22 to 30, respectively. Phylogenetic analysis based on the plastid genomes supported the monophyletic relationship among Datura and Brugmansia and Trompettia, and a refined phylogenic relationships among each individual was resolved. In addition, a species-specific marker was designed based on variation spot that resulted from a comparative analysis of chloroplast genomes and verified as effective maker for identification of D. stramonium and D. stramonium var. inermis. Interestingly, we found that 31 genes were likely to be under positive selection, including genes encoding ATP protein subunits, photosystem protein subunit, ribosome protein subunits, NAD(P)H dehydrogenase complex subunits, and clpP, petB, rbcL, rpoCl, ycf4, and cemA genes. These genes may function as key roles in the adaption to diverse environment during evolution. The diversification of Datureae members was dated back to the late Oligocene periods. These chloroplast genomes are useful genetic resources for taxonomy, phylogeny, and evolution for Datureae.
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Affiliation(s)
- He Su
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xiaoxia Ding
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Baosheng Liao
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Danchun Zhang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Juan Huang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Junqi Bai
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Subing Xu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jing Zhang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Wen Xu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xiaohui Qiu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Lu Gong
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Zhihai Huang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
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Gong L, Ding X, Guan W, Zhang D, Zhang J, Bai J, Xu W, Huang J, Qiu X, Zheng X, Zhang D, Li S, Huang Z, Su H. Comparative chloroplast genome analyses of Amomum: insights into evolutionary history and species identification. BMC PLANT BIOLOGY 2022; 22:520. [PMID: 36352400 PMCID: PMC9644571 DOI: 10.1186/s12870-022-03898-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Species in genus Amomum always have important medicinal and economic values. Classification of Amomum using morphological characters has long been a challenge because they exhibit high similarity. The main goals of this study were to mine genetic markers from cp genomes for Amomum species identification and discover their evolutionary history through comparative analysis. RESULTS Three species Amomum villosum, Amomum maximum and Amomum longipetiolatum were sequenced and annotated for the complete chloroplast (cp) genomes, and the cp genomes of A. longipetiolatum and A. maximum were the first reported. Three cp genomes exhibited typical quadripartite structures with 163,269-163,591 bp in length. Each genome encodes 130 functional genes including 79 protein-coding, 26 tRNAs and 3 rRNAs genes. 113-152 SSRs and 99 long repeats were identified in the three cp genomes. By designing specific primers, we amplified the highly variable loci and the mined genetic marker ccsA exhibited a relatively high species identification resolution in Amomum. The nonsynonymous and synonymous substitution ratios (Ka/Ks) in Amomum and Alpinia showed that most genes were subjected to a purifying selection. Phylogenetic analysis revealed the evolutionary relationships of Amomum and Alpinia species and proved that Amomum is paraphyletic. In addition, the sequenced sample of A. villosum was found to be a hybrid, becoming the first report of natural hybridization of this genus. Meanwhile, the high-throughput sequencing-based ITS2 analysis was proved to be an efficient tool for interspecific hybrid identification and with the help of the chloroplast genome, the hybrid parents can be also be determined. CONCLUSION The comparative analysis and mined genetic markers of cp genomes were conducive to species identification and evolutionary relationships of Amomum.
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Affiliation(s)
- Lu Gong
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiaoxia Ding
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Wan Guan
- Luqiao Hospital, Taizhou Enze Medical Center (Group), Taizhou, Zhejiang, China
| | - Danchun Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
| | - Jing Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Junqi Bai
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Wen Xu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Juan Huang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiaohui Qiu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiasheng Zheng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Danyan Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Shijie Li
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhihai Huang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China.
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China.
| | - He Su
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China.
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China.
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Dong S, Zhou M, Zhu J, Wang Q, Ge Y, Cheng R. The complete chloroplast genomes of Tetrastigma hemsleyanum (Vitaceae) from different regions of China: molecular structure, comparative analysis and development of DNA barcodes for its geographical origin discrimination. BMC Genomics 2022; 23:620. [PMID: 36028808 PMCID: PMC9412808 DOI: 10.1186/s12864-022-08755-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tetrastigma hemsleyanum is a valuable traditional Chinese medicinal plant widely distributed in the subtropical areas of China. It belongs to the Cayratieae tribe, family Vitaceae, and exhibited significant anti-tumor and anti-inflammatory activities. However, obvious differences were observed on the quality of T. hemsleyanum root from different regions, requiring the discrimination strategy for the geographical origins. RESULT This study characterized five complete chloroplast (cp) genomes of T. hemsleynum samples from different regions, and conducted a comparative analysis with other representing species from family Vitaceae to reveal the structural variations, informative markers and phylogenetic relationships. The sequenced cp genomes of T. hemsleyanum exhibited a conserved quadripartite structure with full length ranging from 160,124 bp of Jiangxi Province to 160,618 bp of Zhejiang Province. We identified 112 unique genes (80 protein-coding, 28 tRNA and 4 rRNA genes) in the cp genomes of T. hemsleyanum with highly similar gene order, content and structure. The IR contraction/expansion events occurred on the junctions of ycf1, rps19 and rpl2 genes with different degrees, causing the differences of genome sizes in T. hemsleyanum and Vitaceae plants. The number of SSR markers discovered in T. hemsleyanum was 56-57, exhibiting multiple differences among the five geographic groups. Phylogenetic analysis based on conserved cp genome proteins strongly grouped the five T. hemsleyanum species into one clade, showing a sister relationship with T. planicaule. Comparative analysis of the cp genomes from T. hemsleyanum and Vitaceae revealed five highly variable spacers, including 4 intergenic regions and one protein-coding gene (ycf1). Furthermore, five mutational hotspots were observed among T. hemsleyanum cp genomes from different regions, providing data for designing DNA barcodes trnL and trnN. The combination of molecular markers of trnL and trnN clustered the T. hemsleyanum samples from different regions into four groups, thus successfully separating specimens of Sichuan and Zhejiang from other areas. CONCLUSION Our study obtained the chloroplast genomes of T. hemsleyanum from different regions, and provided a potential molecular tracing tool for determining the geographical origins of T. hemsleyanum, as well as important insights into the molecular identification approach and and phylogeny in Tetrastigma genus and Vitaceae family.
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Affiliation(s)
- Shujie Dong
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China.,School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Manjia Zhou
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jinxing Zhu
- Bureau of Agricultural and Rural Affairs of Suichang, Suichang, China
| | - Qirui Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuqing Ge
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China.
| | - Rubin Cheng
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China. .,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China.
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Targeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio. Sci Rep 2021; 11:19751. [PMID: 34611187 PMCID: PMC8492636 DOI: 10.1038/s41598-021-98402-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 09/06/2021] [Indexed: 02/08/2023] Open
Abstract
We developed novel miRNA-based markers based on salt responsive miRNA sequences to detect polymorphisms in miRNA sequences and locations. The validation of 76 combined miRNA + miRNA and miRNA + ISSR markers in the three extreme pistachio populations led to the identification of three selected markers that could link salt tolerance phenotype to genotype and divided pistachio genotypes and Pistacia species into three clusters. This novel functional marker system, in addition to more efficient performance, has higher polymorphisms than previous miRNA-based marker systems. The functional importance of the target gene of five miRNAs in the structure of the three selected markers in regulation of different genes such as ECA2, ALA10, PFK, PHT1;4, PTR3, KUP2, GRAS, TCP, bHLH, PHD finger, PLATZ and genes involved in developmental, signaling and biosynthetic processes shows that the polymorphism associated with these selected miRNAs can make a significant phenotypic difference between salt sensitive and tolerant pistachio genotypes. The sequencing results of selected bands showed the presence of conserved miRNAs in the structure of the mitochondrial genome. Further notable findings of this study are that the sequences of PCR products of two selected markers were annotated as Gypsy and Copia retrotransposable elements. The transposition of retrotransposons with related miRNAs by increasing the number of miRNA copies and changing their location between nuclear and organellar genomes can affect the regulatory activity of these molecules. These findings show the crucial role of retrotransposon-derived miRNAs as mobile epigenetic regulators between intracellular genomes in regulating salt stress responses as well as creating new and tolerant phenotypes for adaptation to environmental conditions.
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Song H, Liu F, Li Z, Xu Q, Chen Y, Yu Z, Chen N. Development of a high-resolution molecular marker for tracking Phaeocystis globosa genetic diversity through comparative analysis of chloroplast genomes. HARMFUL ALGAE 2020; 99:101911. [PMID: 33218437 DOI: 10.1016/j.hal.2020.101911] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
The phytoplankton Phaeocystis globosa thrives in a wide range of marine regions and plays an important role in climate control. It can also form harmful algal blooms (HABs) that threaten environments and impact important coastal infrastructures. Mechanisms underlying the formation of P. globosa blooms still remain poorly understood. Accumulating evidence suggests that P. globosa has high genetic diversity and different P. globosa strains may have differential contributions to the development of P. globosa blooms. However, due to the lack of molecular markers with adequate resolution for distinguishing P. globosa genetic diversity, such differential contributions by different P. globosa strains could not be accurately ascertained. As such, high-resolution molecular markers need to be developed and applied to distinguish P. globosa genetic diversity. In this study, we undertook to define high-resolution molecular marker by assembling and comparing the whole chloroplast genomes of P. globosa strains isolated from different regions of the world. Through comparative analysis of P. globosa cpDNAs and detection of single nucleotide variations (SNVs), a molecular marker pgcp1 with improved resolution was developed. The pgcp1 demonstrated the highest resolution compared with other regions including 18S rDNA V4 region, 28S rDNA D1-D2 region and rbcL region, through genetic distance and phylogenetic analysis of 13 P. globosa strains. Molecular analysis of environmental samples and strains collected in multiple expeditions from a wide range of ocean regions including multiple regions in China, Vietnam, Thailand and Western Pacific using pgcp1 as the molecular marker displayed high genetic diversity of P. globosa with at least four major P. globosa clades. In conclusion, we have developed pgcp1 as a high-resolution molecular marker for the harmful algal bloom species P. globosa, which can be used to track intra-species genetic diversity and dynamics of P. globosa during bloom development.
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Affiliation(s)
- Huiyin Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Feng Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zelin Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Ocean University of China, Qingdao 266100, China
| | - Qing Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiming Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada.
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9
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He S, Yang Y, Li Z, Wang X, Guo Y, Wu H. Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment. PeerJ 2020; 8:e9132. [PMID: 32509453 PMCID: PMC7247528 DOI: 10.7717/peerj.9132] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/14/2020] [Indexed: 11/20/2022] Open
Abstract
The horticulturally important genus Zantedeschia (Araceae) comprises eight species of herbaceous perennials. We sequenced, assembled and analyzed the chloroplast (cp) genomes of four species of Zantedeschia (Z. aethiopica, Z. odorata, Z. elliottiana, and Z. rehmannii) to investigate the structure of the cp genome in the genus. According to our results, the cp genome of Zantedeschia ranges in size from 169,065 bp (Z. aethiopica) to 175,906 bp (Z. elliottiana). We identified a total of 112 unique genes, including 78 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Comparison of our results with cp genomes from other species in the Araceae suggests that the relatively large sizes of the Zantedeschia cp genomes may result from inverted repeats (IR) region expansion. The sampled Zantedeschia species formed a monophylogenetic clade in our phylogenetic analysis. Furthermore, the long single copy (LSC) and short single copy (SSC) regions in Zantedeschia are more divergent than the IR regions in the same genus, and non-coding regions showed generally higher divergence than coding regions. We identified a total of 410 cpSSR sites from the four Zantedeschia species studied. Genetic diversity analyses based on four polymorphic SSR markers from 134 cultivars of Zantedeschia suggested that high genetic diversity (I = 0.934; Ne = 2.371) is present in the Zantedeschia cultivars. High genetic polymorphism from the cpSSR region suggests that cpSSR could be an effective tool for genetic diversity assessment and identification of Zantedeschia varieties.
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Affiliation(s)
- Shuilian He
- College of Horticulture and Landscape, Yunnan Agricuture University, Kunming, Yunnan, China
| | - Yang Yang
- College of Science, Yunnan Agricuture University, Kunming, Yunnan, China
| | - Ziwei Li
- College of Horticulture and Landscape, Yunnan Agricuture University, Kunming, Yunnan, China
| | - Xuejiao Wang
- College of Horticulture and Landscape, Yunnan Agricuture University, Kunming, Yunnan, China
| | - Yanbing Guo
- College of Horticulture and Landscape, Yunnan Agricuture University, Kunming, Yunnan, China
| | - Hongzhi Wu
- College of horticulture and landscape, Yunnan Agricultural University, Kunming, Yunnan, China
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10
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Shi C, Han K, Li L, Seim I, Lee SMY, Xu X, Yang H, Fan G, Liu X. Complete Chloroplast Genomes of 14 Mangroves: Phylogenetic and Comparative Genomic Analyses. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8731857. [PMID: 32462024 PMCID: PMC7225854 DOI: 10.1155/2020/8731857] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/20/2020] [Accepted: 04/02/2020] [Indexed: 11/17/2022]
Abstract
Mangroves are a group of plant species that occupy the coastal intertidal zone and are major components of this ecologically important ecosystem. Mangroves belong to about twenty diverse families. Here, we sequenced and assembled chloroplast genomes of 14 mangrove species from eight families spanning five rosid orders and one asterid order: Fabales (Pongamia pinnata), Lamiales (Avicennia marina), Malpighiales (Excoecaria agallocha, Bruguiera sexangula, Kandelia obovata, Rhizophora stylosa, and Ceriops tagal), Malvales (Hibiscus tiliaceus, Heritiera littoralis, and Thespesia populnea), Myrtales (Laguncularia racemosa, Sonneratia ovata, and Pemphis acidula), and Sapindales (Xylocarpus moluccensis). These chloroplast genomes range from 149 kb to 168 kb in length. A conserved structure of two inverted repeats (IRa and IRb, ~25.8 kb), one large single-copy region (LSC, ~89.0 kb), and one short single-copy region (SSC, ~18.9 kb) as well as ~130 genes (85 protein-coding, 37 tRNAs, and 8 rRNAs) was observed. We found the lowest divergence in the IR regions among the four regions. We also identified simple sequence repeats (SSRs), which were found to be variable in numbers. Most chloroplast genes are highly conserved, with only four genes under positive selection or relaxed pressure. Combined with publicly available chloroplast genomes, we carried out phylogenetic analysis and confirmed the previously reported phylogeny within rosids, including the positioning of obscure families in Malpighiales. Our study reports 14 mangrove chloroplast genomes and illustrates their genome features and evolution.
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Affiliation(s)
- Chengcheng Shi
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 101408, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Kai Han
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Liangwei Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Inge Seim
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing 210046, China
- Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Woolloongabba 4102, Australia
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Xun Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Huanming Yang
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 101408, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
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11
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Cheng J, Zhao Z, Li B, Qin C, Wu Z, Trejo-Saavedra DL, Luo X, Cui J, Rivera-Bustamante RF, Li S, Hu K. A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum. Sci Rep 2016; 6:18919. [PMID: 26739748 PMCID: PMC4703971 DOI: 10.1038/srep18919] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/30/2015] [Indexed: 02/05/2023] Open
Abstract
The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum.
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Affiliation(s)
- Jiaowen Cheng
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zicheng Zhao
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Bo Li
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Cheng Qin
- Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou 563102, China
| | - Zhiming Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Diana L. Trejo-Saavedra
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav)-Unidad Irapuato, Irapuato 36821, México
| | - Xirong Luo
- Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou 563102, China
| | - Junjie Cui
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Rafael F. Rivera-Bustamante
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav)-Unidad Irapuato, Irapuato 36821, México
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Kailin Hu
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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12
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Nazareno AG, Carlsen M, Lohmann LG. Complete Chloroplast Genome of Tanaecium tetragonolobum: The First Bignoniaceae Plastome. PLoS One 2015; 10:e0129930. [PMID: 26103589 PMCID: PMC4478014 DOI: 10.1371/journal.pone.0129930] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/13/2015] [Indexed: 12/13/2022] Open
Abstract
Bignoniaceae is a Pantropical plant family that is especially abundant in the Neotropics. Members of the Bignoniaceae are diverse in many ecosystems and represent key components of the Tropical flora. Despite the ecological importance of the Bignoniaceae and all the efforts to reconstruct the phylogeny of this group, whole chloroplast genome information has not yet been reported for any members of the family. Here, we report the complete chloroplast genome sequence of Tanaecium tetragonolobum (Jacq.) L.G. Lohmann, which was reconstructed using de novo and referenced-based assembly of single-end reads generated by shotgun sequencing of total genomic DNA in an Illumina platform. The gene order and organization of the chloroplast genome of T. tetragonolobum exhibits the general structure of flowering plants, and is similar to other Lamiales chloroplast genomes. The chloroplast genome of T. tetragonolobum is a circular molecule of 153,776 base pairs (bp) with a quadripartite structure containing two single copy regions, a large single copy region (LSC, 84,612 bp) and a small single copy region (SSC, 17,586 bp) separated by inverted repeat regions (IRs, 25,789 bp). In addition, the chloroplast genome of T. tetragonolobum has 38.3% GC content and includes 121 genes, of which 86 are protein-coding, 31 are transfer RNA, and four are ribosomal RNA. The chloroplast genome of T. tetragonolobum presents a total of 47 tandem repeats and 347 simple sequence repeats (SSRs) with mononucleotides being the most common and di-, tri-, tetra-, and hexanucleotides occurring with less frequency. The results obtained here were compared to other chloroplast genomes of Lamiales available to date, providing new insight into the evolution of chloroplast genomes within Lamiales. Overall, the evolutionary rates of genes in Lamiales are lineage-, locus-, and region-specific, indicating that the evolutionary pattern of nucleotide substitution in chloroplast genomes of flowering plants is complex. The discovery of tandem repeats within T. tetragonolobum and the presence of divergent regions between chloroplast genomes of Lamiales provides the basis for the development of markers at various taxonomic levels. The newly developed markers have the potential to greatly improve the resolution of molecular phylogenies.
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Affiliation(s)
- Alison Gonçalves Nazareno
- Universidade de São Paulo, Instituto de Biociências, Departamento de Botânica, São Paulo, São Paulo, Brazil
- * E-mail: (AGN); (LGL)
| | - Monica Carlsen
- University of Missouri-St. Louis, Biology Department, St. Louis, Missouri, United States of America
| | - Lúcia Garcez Lohmann
- Universidade de São Paulo, Instituto de Biociências, Departamento de Botânica, São Paulo, São Paulo, Brazil
- * E-mail: (AGN); (LGL)
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