One size does not fit all: the risk of using amplicon size of chloroplast SSR marker for genetic relationship studies

Bang, Sun Woong; Chung, Sang-Min

doi:10.1007/s00299-015-1849-y

Cited by 4 publications

(4 citation statements)

References 8 publications

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“…Although SSRs have now almost become the standard analysis in cp genome research, their scope of application is still open to question. Bang et al have warned that attention must be paid to the risk of using amplicon-sized cpSSR markers for genetic relationship studies [37]. In our study, we found that there were more than 100 cpSSR loci in the B. platyphylla cp genome, but only one possible cpSSR locus among the three Betula species was predicted by CandiSSR.…”

Section: Discussionmentioning

confidence: 51%

Complete chloroplast genome sequence of Betula platyphylla: gene organization, RNA editing, and comparative and phylogenetic analyses

et al. 2018

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BackgroundBetula platyphylla is a common tree species in northern China that has high economic and medicinal value. Our laboratory has been devoted to genome research on B. platyphylla for approximately 10 years. As primary organelle genomes, the complete genome sequences of chloroplasts are important to study the divergence of species, RNA editing and phylogeny. In this study, we sequenced and analyzed the complete chloroplast (cp) genome sequence of B. platyphylla.ResultsThe complete cp genome of B. platyphylla was 160,518 bp in length, which included a pair of inverted repeats (IRs) of 26,056 bp that separated a large single copy (LSC) region of 89,397 bp and a small single copy (SSC) region of 19,009 bp. The annotation contained a total of 129 genes, including 84 protein-coding genes, 37 tRNA genes and 8 rRNA genes. There were 3 genes using alternative initiation codons. Comparative genomics showed that the sequence of the Fagales species cp genome was relatively conserved, but there were still some high variation regions that could be used as molecular markers. The IR expansion event of B. platyphylla resulted in larger cp genomes and rps19 pseudogene formation. The simple sequence repeat (SSR) analysis showed that there were 105 SSRs in the cp genome of B. platyphylla. RNA editing sites recognition indicated that at least 80 RNA editing events occurred in the cp genome. Most of the substitutions were C to U, while a small proportion of them were not. In particular, three editing loci on the rRNA were converted to more than two other bases that had never been reported. For synonymous conversion, most of them increased the relative synonymous codon usage (RSCU) value of the codons. The phylogenetic analysis suggested that B. platyphylla had a closer evolutionary relationship with B. pendula than B. nana.ConclusionsIn this study, we not only obtained and annotated the complete cp genome sequence of B. platyphylla, but we also identified new RNA editing sites and predicted the phylogenetic relationships among Fagales species. These findings will facilitate genomic, genetic engineering and phylogenetic studies of this important species.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5346-x) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 51%

Complete chloroplast genome sequence of Betula platyphylla: gene organization, RNA editing, and comparative and phylogenetic analyses

et al. 2018

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“…Though we chose to use microsatellites within the chloroplast genome to increase the likelihood of polymorphisms, we still found these regions to be well-conserved and with limited variation in our dataset. Therefore, we cannot rule out the possibility of fragment size homoplasy confounding results of low genetic diversity in some populations [ 46 ].…”

Section: Discussionmentioning

confidence: 99%

Genetic Structure of Invasive Baby’s Breath (Gypsophila paniculata L.) Populations in a Michigan Dune System

Leimbach-Maus

McCluskey

Locher

et al. 2020

Plants

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Coastal sand dunes are dynamic ecosystems with elevated levels of disturbance and are highly susceptible to plant invasions. One invasive plant that is of concern to the Great Lakes system is Gypsophila paniculata L. (perennial baby’s breath). The presence of G. paniculata negatively impacts native species and has the potential to alter ecosystem dynamics. Our research goals were to (1) estimate the genetic structure of invasive G. paniculata along the Michigan dune system and (2) identify landscape features that influence gene flow in this area. We analyzed 12 populations at 14 nuclear and two chloroplast microsatellite loci. We found strong genetic structure among populations (global FST = 0.228), and pairwise comparisons among all populations yielded significant FST values. Results from clustering analysis via STRUCTURE and discriminant analysis of principal components (DAPC) suggest two main genetic clusters that are separated by the Leelanau Peninsula, and this is supported by the distribution of chloroplast haplotypes. Land cover and topography better explained pairwise genetic distances than geographic distance alone, suggesting that these factors influence the genetic distribution of populations within the dunes system. Together, these data aid in our understanding of how invasive populations move through the dune landscape, providing valuable information for managing the spread of this species.

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“…All data generated by the MegaSSR pipeline are used to calculate a variety of statistical measures for post-processing and to generate tables and graphs. Bang and Chung (2015) reported that there is a risk in using length variation of SSR without sequence confirmation, even within a species. To avoid this risk, MegaSSR provides users with SSR flanking sequences as FASTA files.…”

Section: Methodsmentioning

confidence: 99%

MegaSSR: a web server for large scale microsatellite identification, classification, and marker development

Mokhtar,

Alsamman,

El Allali

2023

Front. Plant Sci.

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Next-generation sequencing technologies have opened new avenues for using genomic data to study and develop molecular markers and improve genetic resources. Simple Sequence Repeats (SSRs) as genetic markers are increasingly used in molecular diversity and molecular breeding programs that require bioinformatics pipelines to analyze the large amounts of data. Therefore, there is an ongoing need for online tools that provide computational resources with minimal effort and maximum efficiency, including automated development of SSR markers. These tools should be flexible, customizable, and able to handle the ever-increasing amount of genomic data. Here we introduce MegaSSR (https://bioinformatics.um6p.ma/MegaSSR), a web server and a standalone pipeline that enables the design of SSR markers in any target genome. MegaSSR allows users to design targeted PCR-based primers for their selected SSR repeats and includes multiple tools that initiate computational pipelines for SSR mining, classification, comparisons, PCR primer design, in silico PCR validation, and statistical visualization. MegaSSR results can be accessed, searched, downloaded, and visualized with user-friendly web-based tools. These tools provide graphs and tables showing various aspects of SSR markers and corresponding PCR primers. MegaSSR will accelerate ongoing research in plant species and assist breeding programs in their efforts to improve current genomic resources.

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One size does not fit all: the risk of using amplicon size of chloroplast SSR marker for genetic relationship studies

Cited by 4 publications

References 8 publications

Complete chloroplast genome sequence of Betula platyphylla: gene organization, RNA editing, and comparative and phylogenetic analyses

Complete chloroplast genome sequence of Betula platyphylla: gene organization, RNA editing, and comparative and phylogenetic analyses

Genetic Structure of Invasive Baby’s Breath (Gypsophila paniculata L.) Populations in a Michigan Dune System

MegaSSR: a web server for large scale microsatellite identification, classification, and marker development

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