Identification of High Molecular Variation Loci in Complete Chloroplast Genomes of Mammillaria (Cactaceae, Caryophyllales)
In plants, partial DNA sequences of chloroplasts have been widely used in evolutionary studies. However, the Cactaceae family (1500-1800 species) lacks molecular markers that allow a phylogenetic resolution between species and genera. In order to identify sequences with high variation levels, we com...
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| Veröffentlicht in: | Genes 2020-07, Vol.11 (7), p.830 |
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| creator | Chincoya, Delil A Sanchez-Flores, Alejandro Estrada, Karel Díaz-Velásquez, Clara E González-Rodríguez, Antonio Vaca-Paniagua, Felipe Dávila, Patricia Arias, Salvador Solórzano, Sofía |
| description | In plants, partial DNA sequences of chloroplasts have been widely used in evolutionary studies. However, the Cactaceae family (1500-1800 species) lacks molecular markers that allow a phylogenetic resolution between species and genera. In order to identify sequences with high variation levels, we compared previously reported complete chloroplast genomes of seven species of
. We identified repeated sequences (RSs) and two types of DNA variation: short sequence repeats (SSRs) and divergent homologous loci. The species with the highest number of RSs was
(256), whereas
contained the highest amount of SSRs (84). In contrast,
contained the lowest number (35) of both RSs and SSRs. In addition, five of the SSRs were found in the seven species, but only three of them showed variation. A total of 180 homologous loci were identified among the seven species. Out of these, 20 loci showed a molecular variation of 5% to 31%, and 12 had a length within the range of 150 to 1000 bp. We conclude that the high levels of variation at the reported loci represent valuable knowledge that may help to resolve phylogenetic relationships and that may potentially be convenient as molecular markers for population genetics and phylogeographic studies. |
| doi_str_mv | 10.3390/genes11070830 |
| format | Article |
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. We identified repeated sequences (RSs) and two types of DNA variation: short sequence repeats (SSRs) and divergent homologous loci. The species with the highest number of RSs was
(256), whereas
contained the highest amount of SSRs (84). In contrast,
contained the lowest number (35) of both RSs and SSRs. In addition, five of the SSRs were found in the seven species, but only three of them showed variation. A total of 180 homologous loci were identified among the seven species. Out of these, 20 loci showed a molecular variation of 5% to 31%, and 12 had a length within the range of 150 to 1000 bp. We conclude that the high levels of variation at the reported loci represent valuable knowledge that may help to resolve phylogenetic relationships and that may potentially be convenient as molecular markers for population genetics and phylogeographic studies.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes11070830</identifier><identifier>PMID: 32708269</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Cactaceae ; Cactus ; Caryophyllaceae - genetics ; Chloroplasts ; Deoxyribonucleic acid ; Divergence ; DNA ; Genetic Loci ; Genome, Chloroplast ; Genomes ; Genomics ; Mammillaria ; Microsatellite Repeats ; Nucleotide sequence ; Phylogenetics ; Phylogeny ; Polymorphism, Genetic ; Population genetics ; Population studies ; Species ; Taxonomy</subject><ispartof>Genes, 2020-07, Vol.11 (7), p.830</ispartof><rights>2020. This work is licensed under http://creativecommons.org/licenses/by/3.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2020 by the authors. 2020</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3300-7e4e3a187b445cbddd8ce163fb4daabdffb06c131b44da782e3cea80223c4e53</citedby><cites>FETCH-LOGICAL-c3300-7e4e3a187b445cbddd8ce163fb4daabdffb06c131b44da782e3cea80223c4e53</cites><orcidid>0000-0002-7674-7050 ; 0000-0001-6251-0688 ; 0000-0003-0476-3139</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397273/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397273/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32708269$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chincoya, Delil A</creatorcontrib><creatorcontrib>Sanchez-Flores, Alejandro</creatorcontrib><creatorcontrib>Estrada, Karel</creatorcontrib><creatorcontrib>Díaz-Velásquez, Clara E</creatorcontrib><creatorcontrib>González-Rodríguez, Antonio</creatorcontrib><creatorcontrib>Vaca-Paniagua, Felipe</creatorcontrib><creatorcontrib>Dávila, Patricia</creatorcontrib><creatorcontrib>Arias, Salvador</creatorcontrib><creatorcontrib>Solórzano, Sofía</creatorcontrib><title>Identification of High Molecular Variation Loci in Complete Chloroplast Genomes of Mammillaria (Cactaceae, Caryophyllales)</title><title>Genes</title><addtitle>Genes (Basel)</addtitle><description>In plants, partial DNA sequences of chloroplasts have been widely used in evolutionary studies. However, the Cactaceae family (1500-1800 species) lacks molecular markers that allow a phylogenetic resolution between species and genera. In order to identify sequences with high variation levels, we compared previously reported complete chloroplast genomes of seven species of
. We identified repeated sequences (RSs) and two types of DNA variation: short sequence repeats (SSRs) and divergent homologous loci. The species with the highest number of RSs was
(256), whereas
contained the highest amount of SSRs (84). In contrast,
contained the lowest number (35) of both RSs and SSRs. In addition, five of the SSRs were found in the seven species, but only three of them showed variation. A total of 180 homologous loci were identified among the seven species. Out of these, 20 loci showed a molecular variation of 5% to 31%, and 12 had a length within the range of 150 to 1000 bp. We conclude that the high levels of variation at the reported loci represent valuable knowledge that may help to resolve phylogenetic relationships and that may potentially be convenient as molecular markers for population genetics and phylogeographic studies.</description><subject>Cactaceae</subject><subject>Cactus</subject><subject>Caryophyllaceae - genetics</subject><subject>Chloroplasts</subject><subject>Deoxyribonucleic acid</subject><subject>Divergence</subject><subject>DNA</subject><subject>Genetic Loci</subject><subject>Genome, Chloroplast</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Mammillaria</subject><subject>Microsatellite Repeats</subject><subject>Nucleotide sequence</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Polymorphism, Genetic</subject><subject>Population genetics</subject><subject>Population studies</subject><subject>Species</subject><subject>Taxonomy</subject><issn>2073-4425</issn><issn>2073-4425</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNpdkUFr3DAQhUVoaUKaY69B0EsKdSNp5JV9KRSTJoENvYRchSyPdxVky5XsQPrrq82mIakuErxvnubxCPnE2TeAmp1vcMTEOVOsAnZAjgRTUEgpynev3ofkJKV7lo9kgrHyAzkEkSfEqj4if647HGfXO2tmF0YaenrlNlt6EzzaxZtI70x0e20drKNupE0YJo8z0mbrQwyTN2mmlziGAdPO4MYMg_N-N0fPGmNnY9HgV9qY-Bim7WOWPKYvH8n73viEJ8_3Mbn9eXHbXBXrX5fXzY91YQEYKxRKBMMr1UpZ2rbrusoiX0Hfys6Ytuv7lq0sB571zqhKIOTvKiYEWIklHJPve9tpaQfsbI4bjddTdEPeRwfj9FtldFu9CQ9aQa2Egmxw9mwQw-8F06wHlyzmFCOGJWkhhRJ1WUue0c__ofdhiWNOt6NWNdT1k2Gxp2wMKUXsX5bhTO961W96zfzp6wQv9L8W4S8gn6EX</recordid><startdate>20200721</startdate><enddate>20200721</enddate><creator>Chincoya, Delil A</creator><creator>Sanchez-Flores, Alejandro</creator><creator>Estrada, Karel</creator><creator>Díaz-Velásquez, Clara E</creator><creator>González-Rodríguez, Antonio</creator><creator>Vaca-Paniagua, Felipe</creator><creator>Dávila, Patricia</creator><creator>Arias, Salvador</creator><creator>Solórzano, Sofía</creator><general>MDPI AG</general><general>MDPI</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-7674-7050</orcidid><orcidid>https://orcid.org/0000-0001-6251-0688</orcidid><orcidid>https://orcid.org/0000-0003-0476-3139</orcidid></search><sort><creationdate>20200721</creationdate><title>Identification of High Molecular Variation Loci in Complete Chloroplast Genomes of Mammillaria (Cactaceae, Caryophyllales)</title><author>Chincoya, Delil A ; Sanchez-Flores, Alejandro ; Estrada, Karel ; Díaz-Velásquez, Clara E ; González-Rodríguez, Antonio ; Vaca-Paniagua, Felipe ; Dávila, Patricia ; Arias, Salvador ; Solórzano, Sofía</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3300-7e4e3a187b445cbddd8ce163fb4daabdffb06c131b44da782e3cea80223c4e53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Cactaceae</topic><topic>Cactus</topic><topic>Caryophyllaceae - genetics</topic><topic>Chloroplasts</topic><topic>Deoxyribonucleic acid</topic><topic>Divergence</topic><topic>DNA</topic><topic>Genetic Loci</topic><topic>Genome, Chloroplast</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Mammillaria</topic><topic>Microsatellite Repeats</topic><topic>Nucleotide sequence</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Polymorphism, Genetic</topic><topic>Population genetics</topic><topic>Population studies</topic><topic>Species</topic><topic>Taxonomy</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chincoya, Delil A</creatorcontrib><creatorcontrib>Sanchez-Flores, Alejandro</creatorcontrib><creatorcontrib>Estrada, Karel</creatorcontrib><creatorcontrib>Díaz-Velásquez, Clara E</creatorcontrib><creatorcontrib>González-Rodríguez, Antonio</creatorcontrib><creatorcontrib>Vaca-Paniagua, Felipe</creatorcontrib><creatorcontrib>Dávila, Patricia</creatorcontrib><creatorcontrib>Arias, Salvador</creatorcontrib><creatorcontrib>Solórzano, Sofía</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genes</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chincoya, Delil A</au><au>Sanchez-Flores, Alejandro</au><au>Estrada, Karel</au><au>Díaz-Velásquez, Clara E</au><au>González-Rodríguez, Antonio</au><au>Vaca-Paniagua, Felipe</au><au>Dávila, Patricia</au><au>Arias, Salvador</au><au>Solórzano, Sofía</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of High Molecular Variation Loci in Complete Chloroplast Genomes of Mammillaria (Cactaceae, Caryophyllales)</atitle><jtitle>Genes</jtitle><addtitle>Genes (Basel)</addtitle><date>2020-07-21</date><risdate>2020</risdate><volume>11</volume><issue>7</issue><spage>830</spage><pages>830-</pages><issn>2073-4425</issn><eissn>2073-4425</eissn><abstract>In plants, partial DNA sequences of chloroplasts have been widely used in evolutionary studies. However, the Cactaceae family (1500-1800 species) lacks molecular markers that allow a phylogenetic resolution between species and genera. In order to identify sequences with high variation levels, we compared previously reported complete chloroplast genomes of seven species of
. We identified repeated sequences (RSs) and two types of DNA variation: short sequence repeats (SSRs) and divergent homologous loci. The species with the highest number of RSs was
(256), whereas
contained the highest amount of SSRs (84). In contrast,
contained the lowest number (35) of both RSs and SSRs. In addition, five of the SSRs were found in the seven species, but only three of them showed variation. A total of 180 homologous loci were identified among the seven species. Out of these, 20 loci showed a molecular variation of 5% to 31%, and 12 had a length within the range of 150 to 1000 bp. We conclude that the high levels of variation at the reported loci represent valuable knowledge that may help to resolve phylogenetic relationships and that may potentially be convenient as molecular markers for population genetics and phylogeographic studies.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>32708269</pmid><doi>10.3390/genes11070830</doi><orcidid>https://orcid.org/0000-0002-7674-7050</orcidid><orcidid>https://orcid.org/0000-0001-6251-0688</orcidid><orcidid>https://orcid.org/0000-0003-0476-3139</orcidid><oa>free_for_read</oa></addata></record> |
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| source | MDPI - Multidisciplinary Digital Publishing Institute; MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; PubMed Central Open Access |
| subjects | Cactaceae Cactus Caryophyllaceae - genetics Chloroplasts Deoxyribonucleic acid Divergence DNA Genetic Loci Genome, Chloroplast Genomes Genomics Mammillaria Microsatellite Repeats Nucleotide sequence Phylogenetics Phylogeny Polymorphism, Genetic Population genetics Population studies Species Taxonomy |
| title | Identification of High Molecular Variation Loci in Complete Chloroplast Genomes of Mammillaria (Cactaceae, Caryophyllales) |
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