Characterization and Comparative Analysis of Complete Chloroplast Genomes of Four Bromus (Poaceae, Bromeae) Species
(Poaceae Bromeae) is a forage grass with high adaptability and ecological and economic value. Here, we sequenced , , , and chloroplast genomes and compared them with four previously described species. The genome sizes of species ranged from 136,934 bp ( ) to 137,189 bp ( , ), with a typical quadripa...
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| Veröffentlicht in: | Genes 2024-06, Vol.15 (6), p.815 |
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| creator | Li, Shichao Tian, Chunyu Hu, Haihong Yang, Yanting Ma, Huiling Liu, Qian Liu, Lemeng Li, Zhiyong Wu, Zinian |
| description | (Poaceae Bromeae) is a forage grass with high adaptability and ecological and economic value. Here, we sequenced
,
,
, and
chloroplast genomes and compared them with four previously described species. The genome sizes of
species ranged from 136,934 bp (
) to 137,189 bp (
,
), with a typical quadripartite structure. The studied species had 129 genes, consisting of 83 protein-coding, 38 tRNA-coding, and 8 rRNA-coding genes. The highest GC content was found in the inverted repeat (IR) region (43.85-44.15%), followed by the large single-copy (LSC) region (36.25-36.65%) and the small single-copy (SSC) region (32.21-32.46%). There were 33 high-frequency codons, with those ending in A/U accounting for 90.91%. A total of 350 simple sequence repeats (SSRs) were identified, with single-nucleotide repeats being the most common (61.43%). A total of 228 forward and 141 palindromic repeats were identified. No reverse or complementary repeats were detected. The sequence identities of all sequences were very similar, especially with respect to the protein-coding and inverted repeat regions. Seven highly variable regions were detected, which could be used for molecular marker development. The constructed phylogenetic tree indicates that
is a monophyletic taxon closely related to Triticum. This comparative analysis of the chloroplast genome of
provides a scientific basis for species identification and phylogenetic studies. |
| doi_str_mv | 10.3390/genes15060815 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_11202509</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A799389516</galeid><sourcerecordid>A799389516</sourcerecordid><originalsourceid>FETCH-LOGICAL-c402t-db271a63d3a8f854472d8d74e888e0c5207077887a8472443df5d3aba61ccc6f3</originalsourceid><addsrcrecordid>eNqFkt9rFDEQxxdRbKl99FUWfGnBrfm5yT7JdbFVKCjYPodcdvYuJZusyW6h_evN3dXaE8HJQ4aZzwyTb6Yo3mJ0RmmDPq7AQ8Ic1Uhi_qI4JEjQijHCXz7zD4rjlG5RNoYIQvx1cUBlQ4Tg6LBI7VpHbSaI9kFPNvhS-65swzDm8GTvoFx47e6TTWXot3EHE5Tt2oUYRqfTVF6CDwNs8xdhjuV5DMOcypPvQRvQ8GEbyM5p-WMEYyG9KV712iU4fryPipuLz9ftl-rq2-XXdnFVmTzoVHVLIrCuaUe17CVnTJBOdoKBlBKQ4fmBSAgphZY5xRjtep7Zpa6xMabu6VHxadd3nJcDdAb8FLVTY7SDjvcqaKv2M96u1SrcKYwJIhw1ucPJY4cYfs6QJjXYZMA57SHMSVHMab0x-n8UCSIRZTXK6Pu_0NusW5Z5R1EiKeN_qJV2oKzvQ57RbJqqhWia_IUc15k6-weVTweDNcFDb3N8r6DaFZgYUorQP-mBkdosldpbqsy_ey7iE_17hegv80PGiQ</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>3072328345</pqid></control><display><type>article</type><title>Characterization and Comparative Analysis of Complete Chloroplast Genomes of Four Bromus (Poaceae, Bromeae) Species</title><source>MDPI - Multidisciplinary Digital Publishing Institute</source><source>MEDLINE</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central</source><source>PubMed Central Open Access</source><creator>Li, Shichao ; Tian, Chunyu ; Hu, Haihong ; Yang, Yanting ; Ma, Huiling ; Liu, Qian ; Liu, Lemeng ; Li, Zhiyong ; Wu, Zinian</creator><creatorcontrib>Li, Shichao ; Tian, Chunyu ; Hu, Haihong ; Yang, Yanting ; Ma, Huiling ; Liu, Qian ; Liu, Lemeng ; Li, Zhiyong ; Wu, Zinian</creatorcontrib><description>(Poaceae Bromeae) is a forage grass with high adaptability and ecological and economic value. Here, we sequenced
,
,
, and
chloroplast genomes and compared them with four previously described species. The genome sizes of
species ranged from 136,934 bp (
) to 137,189 bp (
,
), with a typical quadripartite structure. The studied species had 129 genes, consisting of 83 protein-coding, 38 tRNA-coding, and 8 rRNA-coding genes. The highest GC content was found in the inverted repeat (IR) region (43.85-44.15%), followed by the large single-copy (LSC) region (36.25-36.65%) and the small single-copy (SSC) region (32.21-32.46%). There were 33 high-frequency codons, with those ending in A/U accounting for 90.91%. A total of 350 simple sequence repeats (SSRs) were identified, with single-nucleotide repeats being the most common (61.43%). A total of 228 forward and 141 palindromic repeats were identified. No reverse or complementary repeats were detected. The sequence identities of all sequences were very similar, especially with respect to the protein-coding and inverted repeat regions. Seven highly variable regions were detected, which could be used for molecular marker development. The constructed phylogenetic tree indicates that
is a monophyletic taxon closely related to Triticum. This comparative analysis of the chloroplast genome of
provides a scientific basis for species identification and phylogenetic studies.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes15060815</identifier><identifier>PMID: 38927750</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Adaptability ; Amino acid sequence ; Base Composition - genetics ; Bromegrasses ; Bromus ; Bromus - genetics ; Bromus biebersteinii ; Bromus riparius ; Bromus rubens ; chloroplast genome ; Chloroplasts ; Ciliates ; Ciliophora ; Classification ; Codons ; Comparative analysis ; economic valuation ; Enzymes ; forage grasses ; Genes ; Genetic aspects ; genetic markers ; Genome, Chloroplast - genetics ; Genomes ; Genomic analysis ; Inverted repeat ; Microsatellite Repeats - genetics ; monophyly ; Morphology ; Nucleotide sequence ; Phylogenetics ; Phylogeny ; Physiological aspects ; Poaceae ; Proteins ; rRNA ; Simple sequence repeats ; Software ; Species ; species identification ; Taxonomy ; Transfer RNA ; Triticum ; tRNA</subject><ispartof>Genes, 2024-06, Vol.15 (6), p.815</ispartof><rights>COPYRIGHT 2024 MDPI AG</rights><rights>2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2024 by the authors. 2024</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c402t-db271a63d3a8f854472d8d74e888e0c5207077887a8472443df5d3aba61ccc6f3</cites><orcidid>0000-0002-4121-4529</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/PMC11202509/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11202509/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27903,27904,53769,53771</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38927750$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Shichao</creatorcontrib><creatorcontrib>Tian, Chunyu</creatorcontrib><creatorcontrib>Hu, Haihong</creatorcontrib><creatorcontrib>Yang, Yanting</creatorcontrib><creatorcontrib>Ma, Huiling</creatorcontrib><creatorcontrib>Liu, Qian</creatorcontrib><creatorcontrib>Liu, Lemeng</creatorcontrib><creatorcontrib>Li, Zhiyong</creatorcontrib><creatorcontrib>Wu, Zinian</creatorcontrib><title>Characterization and Comparative Analysis of Complete Chloroplast Genomes of Four Bromus (Poaceae, Bromeae) Species</title><title>Genes</title><addtitle>Genes (Basel)</addtitle><description>(Poaceae Bromeae) is a forage grass with high adaptability and ecological and economic value. Here, we sequenced
,
,
, and
chloroplast genomes and compared them with four previously described species. The genome sizes of
species ranged from 136,934 bp (
) to 137,189 bp (
,
), with a typical quadripartite structure. The studied species had 129 genes, consisting of 83 protein-coding, 38 tRNA-coding, and 8 rRNA-coding genes. The highest GC content was found in the inverted repeat (IR) region (43.85-44.15%), followed by the large single-copy (LSC) region (36.25-36.65%) and the small single-copy (SSC) region (32.21-32.46%). There were 33 high-frequency codons, with those ending in A/U accounting for 90.91%. A total of 350 simple sequence repeats (SSRs) were identified, with single-nucleotide repeats being the most common (61.43%). A total of 228 forward and 141 palindromic repeats were identified. No reverse or complementary repeats were detected. The sequence identities of all sequences were very similar, especially with respect to the protein-coding and inverted repeat regions. Seven highly variable regions were detected, which could be used for molecular marker development. The constructed phylogenetic tree indicates that
is a monophyletic taxon closely related to Triticum. This comparative analysis of the chloroplast genome of
provides a scientific basis for species identification and phylogenetic studies.</description><subject>Adaptability</subject><subject>Amino acid sequence</subject><subject>Base Composition - genetics</subject><subject>Bromegrasses</subject><subject>Bromus</subject><subject>Bromus - genetics</subject><subject>Bromus biebersteinii</subject><subject>Bromus riparius</subject><subject>Bromus rubens</subject><subject>chloroplast genome</subject><subject>Chloroplasts</subject><subject>Ciliates</subject><subject>Ciliophora</subject><subject>Classification</subject><subject>Codons</subject><subject>Comparative analysis</subject><subject>economic valuation</subject><subject>Enzymes</subject><subject>forage grasses</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>genetic markers</subject><subject>Genome, Chloroplast - genetics</subject><subject>Genomes</subject><subject>Genomic analysis</subject><subject>Inverted repeat</subject><subject>Microsatellite Repeats - genetics</subject><subject>monophyly</subject><subject>Morphology</subject><subject>Nucleotide sequence</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Physiological aspects</subject><subject>Poaceae</subject><subject>Proteins</subject><subject>rRNA</subject><subject>Simple sequence repeats</subject><subject>Software</subject><subject>Species</subject><subject>species identification</subject><subject>Taxonomy</subject><subject>Transfer RNA</subject><subject>Triticum</subject><subject>tRNA</subject><issn>2073-4425</issn><issn>2073-4425</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNqFkt9rFDEQxxdRbKl99FUWfGnBrfm5yT7JdbFVKCjYPodcdvYuJZusyW6h_evN3dXaE8HJQ4aZzwyTb6Yo3mJ0RmmDPq7AQ8Ic1Uhi_qI4JEjQijHCXz7zD4rjlG5RNoYIQvx1cUBlQ4Tg6LBI7VpHbSaI9kFPNvhS-65swzDm8GTvoFx47e6TTWXot3EHE5Tt2oUYRqfTVF6CDwNs8xdhjuV5DMOcypPvQRvQ8GEbyM5p-WMEYyG9KV712iU4fryPipuLz9ftl-rq2-XXdnFVmTzoVHVLIrCuaUe17CVnTJBOdoKBlBKQ4fmBSAgphZY5xRjtep7Zpa6xMabu6VHxadd3nJcDdAb8FLVTY7SDjvcqaKv2M96u1SrcKYwJIhw1ucPJY4cYfs6QJjXYZMA57SHMSVHMab0x-n8UCSIRZTXK6Pu_0NusW5Z5R1EiKeN_qJV2oKzvQ57RbJqqhWia_IUc15k6-weVTweDNcFDb3N8r6DaFZgYUorQP-mBkdosldpbqsy_ey7iE_17hegv80PGiQ</recordid><startdate>20240620</startdate><enddate>20240620</enddate><creator>Li, Shichao</creator><creator>Tian, Chunyu</creator><creator>Hu, Haihong</creator><creator>Yang, Yanting</creator><creator>Ma, Huiling</creator><creator>Liu, Qian</creator><creator>Liu, Lemeng</creator><creator>Li, Zhiyong</creator><creator>Wu, Zinian</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>RC3</scope><scope>7X8</scope><scope>7S9</scope><scope>L.6</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-4121-4529</orcidid></search><sort><creationdate>20240620</creationdate><title>Characterization and Comparative Analysis of Complete Chloroplast Genomes of Four Bromus (Poaceae, Bromeae) Species</title><author>Li, Shichao ; Tian, Chunyu ; Hu, Haihong ; Yang, Yanting ; Ma, Huiling ; Liu, Qian ; Liu, Lemeng ; Li, Zhiyong ; Wu, Zinian</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c402t-db271a63d3a8f854472d8d74e888e0c5207077887a8472443df5d3aba61ccc6f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Adaptability</topic><topic>Amino acid sequence</topic><topic>Base Composition - genetics</topic><topic>Bromegrasses</topic><topic>Bromus</topic><topic>Bromus - genetics</topic><topic>Bromus biebersteinii</topic><topic>Bromus riparius</topic><topic>Bromus rubens</topic><topic>chloroplast genome</topic><topic>Chloroplasts</topic><topic>Ciliates</topic><topic>Ciliophora</topic><topic>Classification</topic><topic>Codons</topic><topic>Comparative analysis</topic><topic>economic valuation</topic><topic>Enzymes</topic><topic>forage grasses</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>genetic markers</topic><topic>Genome, Chloroplast - genetics</topic><topic>Genomes</topic><topic>Genomic analysis</topic><topic>Inverted repeat</topic><topic>Microsatellite Repeats - genetics</topic><topic>monophyly</topic><topic>Morphology</topic><topic>Nucleotide sequence</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Physiological aspects</topic><topic>Poaceae</topic><topic>Proteins</topic><topic>rRNA</topic><topic>Simple sequence repeats</topic><topic>Software</topic><topic>Species</topic><topic>species identification</topic><topic>Taxonomy</topic><topic>Transfer RNA</topic><topic>Triticum</topic><topic>tRNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Shichao</creatorcontrib><creatorcontrib>Tian, Chunyu</creatorcontrib><creatorcontrib>Hu, Haihong</creatorcontrib><creatorcontrib>Yang, Yanting</creatorcontrib><creatorcontrib>Ma, Huiling</creatorcontrib><creatorcontrib>Liu, Qian</creatorcontrib><creatorcontrib>Liu, Lemeng</creatorcontrib><creatorcontrib>Li, Zhiyong</creatorcontrib><creatorcontrib>Wu, Zinian</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>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - 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>Li, Shichao</au><au>Tian, Chunyu</au><au>Hu, Haihong</au><au>Yang, Yanting</au><au>Ma, Huiling</au><au>Liu, Qian</au><au>Liu, Lemeng</au><au>Li, Zhiyong</au><au>Wu, Zinian</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Characterization and Comparative Analysis of Complete Chloroplast Genomes of Four Bromus (Poaceae, Bromeae) Species</atitle><jtitle>Genes</jtitle><addtitle>Genes (Basel)</addtitle><date>2024-06-20</date><risdate>2024</risdate><volume>15</volume><issue>6</issue><spage>815</spage><pages>815-</pages><issn>2073-4425</issn><eissn>2073-4425</eissn><abstract>(Poaceae Bromeae) is a forage grass with high adaptability and ecological and economic value. Here, we sequenced
,
,
, and
chloroplast genomes and compared them with four previously described species. The genome sizes of
species ranged from 136,934 bp (
) to 137,189 bp (
,
), with a typical quadripartite structure. The studied species had 129 genes, consisting of 83 protein-coding, 38 tRNA-coding, and 8 rRNA-coding genes. The highest GC content was found in the inverted repeat (IR) region (43.85-44.15%), followed by the large single-copy (LSC) region (36.25-36.65%) and the small single-copy (SSC) region (32.21-32.46%). There were 33 high-frequency codons, with those ending in A/U accounting for 90.91%. A total of 350 simple sequence repeats (SSRs) were identified, with single-nucleotide repeats being the most common (61.43%). A total of 228 forward and 141 palindromic repeats were identified. No reverse or complementary repeats were detected. The sequence identities of all sequences were very similar, especially with respect to the protein-coding and inverted repeat regions. Seven highly variable regions were detected, which could be used for molecular marker development. The constructed phylogenetic tree indicates that
is a monophyletic taxon closely related to Triticum. This comparative analysis of the chloroplast genome of
provides a scientific basis for species identification and phylogenetic studies.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>38927750</pmid><doi>10.3390/genes15060815</doi><orcidid>https://orcid.org/0000-0002-4121-4529</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 | Adaptability Amino acid sequence Base Composition - genetics Bromegrasses Bromus Bromus - genetics Bromus biebersteinii Bromus riparius Bromus rubens chloroplast genome Chloroplasts Ciliates Ciliophora Classification Codons Comparative analysis economic valuation Enzymes forage grasses Genes Genetic aspects genetic markers Genome, Chloroplast - genetics Genomes Genomic analysis Inverted repeat Microsatellite Repeats - genetics monophyly Morphology Nucleotide sequence Phylogenetics Phylogeny Physiological aspects Poaceae Proteins rRNA Simple sequence repeats Software Species species identification Taxonomy Transfer RNA Triticum tRNA |
| title | Characterization and Comparative Analysis of Complete Chloroplast Genomes of Four Bromus (Poaceae, Bromeae) Species |
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