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Shi N, Yang Z, Miao K, Tang L, Zhou N, Xie P, Wen G. Comparative analysis of the medicinal plant Polygonatum kingianum (Asparagaceae) with related verticillate leaf types of the Polygonatum species based on chloroplast genomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1202634. [PMID: 37680362 PMCID: PMC10482041 DOI: 10.3389/fpls.2023.1202634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 07/06/2023] [Indexed: 09/09/2023]
Abstract
Background Polygonatum kingianum has been widely used as a traditional Chinese medicine as well as a healthy food. Because of its highly variable morphology, this medicinal plant is often difficult to distinguish from other related verticillate leaf types of the Polygonatum species. The contaminants in P. kingianum products not only decrease the products' quality but also threaten consumer safety, seriously inhibiting the industrial application of P. kingianum. Methods Nine complete chloroplast (cp) genomes of six verticillate leaf types of the Polygonatum species were de novo assembled and systematically analyzed. Results The total lengths of newly sequenced cp genomes ranged from 155,437 to 155,977 bp, including 86/87 protein-coding, 38 tRNA, and 8 rRNA genes, which all exhibited well-conserved genomic structures and gene orders. The differences in the IR/SC (inverted repeats/single-copy) boundary regions and simple sequence repeats were detected among the verticillate leaf types of the Polygonatum cp genomes. Comparative cp genomes analyses revealed that a higher similarity was conserved in the IR regions than in the SC regions. In addition, 11 divergent hotspot regions were selected, providing potential molecular markers for the identification of the Polygonatum species with verticillate leaf types. Phylogenetic analysis indicated that, as a super barcode, plastids realized a fast and efficient identification that clearly characterized the relationships within the verticillate leaf types of the Polygonatum species. In brief, our results not only enrich the data on the cp genomes of the genus Polygonatum but also provide references for the P. kingianum germplasm resource protection, herbal cultivation, and drug production. Conclusion This study not only accurately identifies P. kingianum species, but also provides valuable information for the development of molecular markers and phylogenetic analyses of the Polygonatum species with verticillate leaf types.
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Affiliation(s)
- Naixing Shi
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Zefen Yang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Ke Miao
- Chinese Academy of Sciences (CAS) Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Lilei Tang
- College of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Nian Zhou
- Chinese Academy of Sciences (CAS) Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Pingxuan Xie
- College of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Guosong Wen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
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Liu K, Xie N. Pipeline for developing polymorphic microsatellites in species without reference genomes. 3 Biotech 2022; 12:248. [PMID: 36039078 PMCID: PMC9418399 DOI: 10.1007/s13205-022-03313-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/16/2022] [Indexed: 11/01/2022] Open
Abstract
Microsatellites, also known as simple sequence repeats (SSRs), are the preferred type of marker for many genetic applications. In conjunction with the ongoing development of next-generation sequencing, several bioinformatic tools have been developed for identifying SSRs from genomic or transcriptomic sequences. Although these tools are handy for generating polymorphic SSRs, their application almost always depends on an existing reference genome or self-assembly of the reference genome. With this in mind, we propose a pipeline for developing polymorphic SSRs that may be applied to species without reference genomes. Using a species without a reference genome (black Amur bream; Megalobrama terminalis Richardson, 1846) as a model, our pipeline was able to effectively discover polymorphic SSRs. Under different R parameters of a reference-free single nucleotide polymorphisms (SNPs) caller (ebwt2InDel), a total of 258, 208, 102, and 11 polymorphic SSRs were mined. To quantify the accuracy of the polymorphic SSRs detected using our pipeline, we analyzed 25 SSRs with PCR experiments. All primers were successfully amplified, and most SSRs (23 SSRs, 92%) were polymorphic. From the 36 individual black Amur bream, we acquired an average of 3.36 alleles per locus, ranging from one to 11. This demonstrates the effectiveness of our pipeline in identifying polymorphic SSRs and designing primers for SSR genotyping. Ultimately, our pipeline can effectively mine polymorphic SSRs for species without reference genomes, complementing SSR mining approaches based on reference genomes and helping to resolve biological issues that accompany these methods. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03313-0.
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Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang China
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang China
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Yue J, Lu Q, Ni Y, Chen P, Liu C. Comparative analysis of the plastid and mitochondrial genomes of Artemisia giraldii Pamp. Sci Rep 2022; 12:13931. [PMID: 35978085 PMCID: PMC9385723 DOI: 10.1038/s41598-022-18387-2] [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: 02/05/2022] [Accepted: 08/10/2022] [Indexed: 12/30/2022] Open
Abstract
Artemisia giraldii Pamp. is an herbaceous plant distributed only in some areas in China. To understand the evolutionary relationship between plastid and mitochondria in A. giraldii, we sequenced and analysed the plastome and mitogenome of A. giraldii on the basis of Illumina and Nanopore DNA sequencing data. The mitogenome was 194,298 bp long, and the plastome was 151,072 bp long. The mitogenome encoded 56 genes, and the overall GC content was 45.66%. Phylogenetic analysis of the two organelle genomes revealed that A. giraldii is located in the same branching position. We found 13 pairs of homologous sequences between the plastome and mitogenome, and only one of them might have transferred from the plastid to the mitochondria. Gene selection pressure analysis in the mitogenome showed that ccmFc, nad1, nad6, atp9, atp1 and rps12 may undergo positive selection. According to the 18 available plastome sequences, we found 17 variant sites in two hypervariable regions that can be used in completely distinguishing 18 Artemisia species. The most interesting discovery was that the mitogenome of A. giraldii was only 43,226 bp larger than the plastome. To the best of our knowledge, this study represented one of the smallest differences between all sequenced mitogenomes and plastomes from vascular plants. The above results can provide a reference for future taxonomic and molecular evolution studies of Asteraceae species.
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Affiliation(s)
- Jingwen Yue
- grid.256111.00000 0004 1760 2876Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, National Engineering Research Center of Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, No.15, Shangxiadian Road, Fuzhou, 350002 Fujian People’s Republic of China ,grid.506261.60000 0001 0706 7839Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100193 People’s Republic of China
| | - Qianqi Lu
- grid.256111.00000 0004 1760 2876Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, National Engineering Research Center of Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, No.15, Shangxiadian Road, Fuzhou, 350002 Fujian People’s Republic of China
| | - Yang Ni
- grid.506261.60000 0001 0706 7839Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100193 People’s Republic of China
| | - Pinghua Chen
- grid.256111.00000 0004 1760 2876Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, National Engineering Research Center of Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, No.15, Shangxiadian Road, Fuzhou, 350002 Fujian People’s Republic of China
| | - Chang Liu
- grid.506261.60000 0001 0706 7839Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100193 People’s Republic of China
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AutomAted RepeaT Identifier (AARTI): A tool to identify common, polymorphic, and unique microsatellites. Mitochondrion 2022; 65:161-165. [PMID: 35738354 DOI: 10.1016/j.mito.2022.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/19/2022] [Indexed: 11/21/2022]
Abstract
Here we are presenting an automated computational pipeline used to mine 5976 mitochondrial genomes to identify common, polymorphic, and unique microsatellites also known as simple sequence repeats (SSRs). Microsatellites are repetitive motifs of 1-6 bases in a DNA sequence. Due to their abundance and highly polymorphic nature, microsatellites have become one of the widely used molecular/genetic markers valuable for many studies including gene tagging, genetic diversity, and species identification. Several computational tools dedicated to mine and categorize microsatellites in nucleotide sequences were developed; however, there is no tool which can identify unique, common and polymorphic microsatellites between each pair of nucleotide sequences. To explore such microsatellites, we have developed a fully automated computational pipeline named AutomAted RepeaT Identifier (AARTI). The AARTI is the only tool till date, which identifies common, polymorphic, and unique microsatellites between each pair of nucleotide sequences. The computational pipeline was constructed using the PERL programming language and the web server for the pipeline was developed with the help of PHP, HTML, CSS, and JavaScript. It was successfully tested to reproduce the results of previous study on 7 mitochondrial genomes of genus Orthotrichum. Moreover, the pipeline was also applied on 5846 (Metazoa) and 130 (Viridiplantae) mitochondrial genomes. The AARTI is freely available at https://lms.snu.edu.in/aarti/ and will certainly accelerate the studies of length variation in microsatellites between species. Additionally, it will be useful in comparative genomic studies, for the computational characterization of microsatellites, and has the potential to be a routine genome analysis pipeline for mitochondrial genomes.
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Chen J, Li F, Wang M, Li J, Marquez-Lago TT, Leier A, Revote J, Li S, Liu Q, Song J. BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data. Front Big Data 2022; 4:727216. [PMID: 35118375 PMCID: PMC8805145 DOI: 10.3389/fdata.2021.727216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 12/13/2021] [Indexed: 11/22/2022] Open
Abstract
Background Simple Sequence Repeats (SSRs) are short tandem repeats of nucleotide sequences. It has been shown that SSRs are associated with human diseases and are of medical relevance. Accordingly, a variety of computational methods have been proposed to mine SSRs from genomes. Conventional methods rely on a high-quality complete genome to identify SSRs. However, the sequenced genome often misses several highly repetitive regions. Moreover, many non-model species have no entire genomes. With the recent advances of next-generation sequencing (NGS) techniques, large-scale sequence reads for any species can be rapidly generated using NGS. In this context, a number of methods have been proposed to identify thousands of SSR loci within large amounts of reads for non-model species. While the most commonly used NGS platforms (e.g., Illumina platform) on the market generally provide short paired-end reads, merging overlapping paired-end reads has become a common way prior to the identification of SSR loci. This has posed a big data analysis challenge for traditional stand-alone tools to merge short read pairs and identify SSRs from large-scale data. Results In this study, we present a new Hadoop-based software program, termed BigFiRSt, to address this problem using cutting-edge big data technology. BigFiRSt consists of two major modules, BigFLASH and BigPERF, implemented based on two state-of-the-art stand-alone tools, FLASH and PERF, respectively. BigFLASH and BigPERF address the problem of merging short read pairs and mining SSRs in the big data manner, respectively. Comprehensive benchmarking experiments show that BigFiRSt can dramatically reduce the execution times of fast read pairs merging and SSRs mining from very large-scale DNA sequence data. Conclusions The excellent performance of BigFiRSt mainly resorts to the Big Data Hadoop technology to merge read pairs and mine SSRs in parallel and distributed computing on clusters. We anticipate BigFiRSt will be a valuable tool in the coming biological Big Data era.
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Affiliation(s)
- Jinxiang Chen
- Department of Software Engineering, College of Information Engineering, Northwest A&F University, Yangling, China
| | - Fuyi Li
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- Monash Centre for Data Science, Monash University, Melbourne, VIC, Australia
- Department of Microbiology and Immunity, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Miao Wang
- Department of Software Engineering, College of Information Engineering, Northwest A&F University, Yangling, China
| | - Junlong Li
- Department of Software Engineering, College of Information Engineering, Northwest A&F University, Yangling, China
| | - Tatiana T. Marquez-Lago
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - André Leier
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jerico Revote
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Shuqin Li
- Department of Software Engineering, College of Information Engineering, Northwest A&F University, Yangling, China
| | - Quanzhong Liu
- Department of Software Engineering, College of Information Engineering, Northwest A&F University, Yangling, China
- Quanzhong Liu
| | - Jiangning Song
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- Monash Centre for Data Science, Monash University, Melbourne, VIC, Australia
- *Correspondence: Jiangning Song
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Automating microsatellite screening and primer design from multi-individual libraries using Micro-Primers. Sci Rep 2022; 12:295. [PMID: 34997147 PMCID: PMC8741888 DOI: 10.1038/s41598-021-04275-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/10/2021] [Indexed: 11/08/2022] Open
Abstract
Analysis of intra- and inter-population diversity has become important for defining the genetic status and distribution patterns of a species and a powerful tool for conservation programs, as high levels of inbreeding could lead into whole population extinction in few generations. Microsatellites (SSR) are commonly used in population studies but discovering highly variable regions across species' genomes requires demanding computation and laboratorial optimization. In this work, we combine next generation sequencing (NGS) with automatic computing to develop a genomic-oriented tool for characterizing SSRs at the population level. Herein, we describe a new Python pipeline, named Micro-Primers, designed to identify, and design PCR primers for amplification of SSR loci from a multi-individual microsatellite library. By combining commonly used programs for data cleaning and microsatellite mining, this pipeline easily generates, from a fastq file produced by high-throughput sequencing, standard information about the selected microsatellite loci, including the number of alleles in the population subset, and the melting temperature and respective PCR product of each primer set. Additionally, potential polymorphic loci can be identified based on the allele ranges observed in the population, to easily guide the selection of optimal markers for the species. Experimental results show that Micro-Primers significantly reduces processing time in comparison to manual analysis while keeping the same quality of the results. The elapsed times at each step can be longer depending on the number of sequences to analyze and, if not assisted, the selection of polymorphic loci from multiple individuals can represent a major bottleneck in population studies.
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Qin Q, Li J, Zeng S, Xu Y, Han F, Yu J. The complete plastomes of red fleshed pitaya ( Selenicereus monacanthus) and three related Selenicereus species: insights into gene losses, inverted repeat expansions and phylogenomic implications. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:123-137. [PMID: 35221575 PMCID: PMC8847515 DOI: 10.1007/s12298-021-01121-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 06/01/2023]
Abstract
UNLABELLED Selenicereus is a genus of perennial shrub from the family Cactaceae, and some of them play an important role in the food industry, pharmaceuticals, cosmetics and medicine. To date, there are few reports on Selenicereus plastomes, which limits our understanding of this genus. Here, we have reported the complete plastomes of four Selenicereus species (S. monacanthus, S. annthonyanus, S. grandifloras, and S. validus) and carried out a comprehensive comparative analysis. All four Selenicereus plastomes have a typical quartile structure. The plastome size ranged from 133,146 to 134,450 bp, and contained 104 unique genes, including 30 tRNA genes, 4 rRNA genes and 70 protein-coding genes. Comparative analysis showed that there were massive losses of ndh genes in Selenicereus. Besides, we observed the inverted repeat regions had undergone a dramatic expansion and formed a previously unreported small single copy/inverted repeat border in the intron region of the atpF gene. Furthermore, we identified 6 hypervariable regions (trnF-GAA-rbcL, ycf1, accD, clpP-trnS-GCU, clpP-trnT-CGU and rpl22-rps19) that could be used as potential DNA barcodes for the identification of Selenicereus species. Our study enriches the plastome in the family Cactaceae, and provides the basis for the reconstruction of phylogenetic relationships. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01121-z.
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Affiliation(s)
- Qiulin Qin
- College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400716 China
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400716 China
| | - Siyuan Zeng
- College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400716 China
| | | | - Fang Han
- College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400716 China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400716 China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, 400716 China
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Li J, Xu Y, Shan Y, Pei X, Yong S, Liu C, Yu J. Assembly of the complete mitochondrial genome of an endemic plant, Scutellaria tsinyunensis, revealed the existence of two conformations generated by a repeat-mediated recombination. PLANTA 2021; 254:36. [PMID: 34302538 DOI: 10.1007/s00425-021-03684-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
We assembled the complete mitochondrial genome of Scutellaria tsinyunensis in this study. Repeat-mediated recombination resulted in the formation of two conformations of the mitochondrial genome in S. tsinyunensis. Scutellaria tsinyunensis belongs to the family Lamiaceae, distributed only in the Jinyun Mountain, Chongqing, China. As a valuable endemic and small population species, it is regarded as a natural resource potentially with significant economic and ecological importance. In this study, we assembled a complete and gap-free mitochondrial genome of S. tsinyunensis. This genome had a length of 354,073 bp and the base composition of the genome was A (27.44%), T (27.30%), C (22.58%), and G (22.68%). This genome encodes 59 genes, including 32 protein-coding genes, 24 tRNA genes, and 3 rRNA genes. The Sanger sequencing and Oxford Nanopore sequencing confirmed a pair of direct repeats had mediated genome recombination, resulting in the formation of two conformations. The gene conversation between plastome and mitochondrial genome was also observed in S. tsinyunensis by detecting gene migration, including six tRNA genes (namely, trnW-CCA, trnI-CAU, trnH-UUU, trnD-GUC, trnN-GUU, and trnM-CAU), five protein-coding gene fragments, and the fragments from 2 rRNA genes. Moreover, the dN/dS analysis revealed the atp9 gene had undergone strong negative selection, and four genes (atp4, mttB, ccmFc, and ccmB) probably had undergone positive selection during evolution in Lamiales. This work reported the first mitochondrial genome of S. tsinyunensis, which could be used as a reference genome for the important medicinal plants of the genus Scutellaria, and also provide much-desired information for molecular breeding.
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Affiliation(s)
- Jingling Li
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Yicen Xu
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Yuanyu Shan
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Xiaoying Pei
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Shunyuan Yong
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China.
| | - Jie Yu
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China.
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Li J, Tang J, Zeng S, Han F, Yuan J, Yu J. Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea. BMC PLANT BIOLOGY 2021; 21:25. [PMID: 33413130 PMCID: PMC7792329 DOI: 10.1186/s12870-020-02793-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 12/09/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca 'Greizy', Pilea peperomioides and Pilea serpyllacea 'Globosa') and performed comprehensive comparative analysis. RESULTS The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae. CONCLUSION Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.
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Affiliation(s)
- Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jianmin Tang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Siyuan Zeng
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Fang Han
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jing Yuan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, 400716, China.
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Gou X, Shi H, Yu S, Wang Z, Li C, Liu S, Ma J, Chen G, Liu T, Liu Y. SSRMMD: A Rapid and Accurate Algorithm for Mining SSR Feature Loci and Candidate Polymorphic SSRs Based on Assembled Sequences. Front Genet 2020; 11:706. [PMID: 32849772 PMCID: PMC7398111 DOI: 10.3389/fgene.2020.00706] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/10/2020] [Indexed: 12/16/2022] Open
Abstract
Microsatellites or simple sequence repeats (SSRs) are short tandem repeats of DNA widespread in genomes and transcriptomes of diverse organisms and are used in various genetic studies. Few software programs that mine SSRs can be further used to mine polymorphic SSRs, and these programs have poor portability, have slow computational speed, are highly dependent on other programs, and have low marker development rates. In this study, we develop an algorithm named Simple Sequence Repeat Molecular Marker Developer (SSRMMD), which uses improved regular expressions to rapidly and exhaustively mine perfect SSR loci from any size of assembled sequence. To mine polymorphic SSRs, SSRMMD uses a novel three-stage method to assess the conservativeness of SSR flanking sequences and then uses the sliding window method to fragment each assembled sequence to assess its uniqueness. Furthermore, molecular biology assays support the polymorphic SSRs identified by SSRMMD. SSRMMD is implemented using the Perl programming language and can be downloaded from https://github.com/GouXiangJian/SSRMMD.
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Affiliation(s)
- Xiangjian Gou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.,Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Haoran Shi
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shifan Yu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhiqiang Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Caixia Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shihang Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Tao Liu
- College of Information Engineering, Sichuan Agricultural University, Ya'an, China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
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