Complete Chloroplast Genome of Krascheninnikovia ewersmanniana : Comparative and Phylogenetic Analysis
is a dominant desert shrub in Xinjiang, China, with high economic and ecological value. However, molecular systematics research on is lacking. To resolve the genetic composition of within Amaranthaceae and its systematic relationship with related genera, we used a second-generation Illumina sequenci...
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| Veröffentlicht in: | Genes 2024-04, Vol.15 (5), p.546 |
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| creator | Wei, Peng Li, Youzheng Ke, Mei Hou, Yurong Aikebaier, Abudureyimu Wu, Zinian |
| description | is a dominant desert shrub in Xinjiang, China, with high economic and ecological value. However, molecular systematics research on
is lacking. To resolve the genetic composition of
within Amaranthaceae and its systematic relationship with related genera, we used a second-generation Illumina sequencing system to detect the chloroplast genome of
and analyze its assembly, annotation, and phylogenetics. Total length of the chloroplast genome of
reached 152,287 bp, with 84 protein-coding genes, 36 tRNAs, and eight rRNAs. Codon usage analysis showed the majority of codons ending with base A/U. Mononucleotide repeats were the most common (85.42%) of the four identified simple sequence repeats. A comparison with chloroplast genomes of six other Amaranthaceae species indicated contraction and expansion of the inverted repeat boundary region in
, with some genes (
,
,
) differing in length and distribution. Among the seven species, the variation in non-coding regions was greater. Phylogenetic analysis revealed
,
,
, and
to have a close monophyletic relationship. By sequencing the
chloroplast genome, this research resolves the relatedness among 35 Amaranthaceae species, providing molecular insights for germplasm utilization, and theoretical support for studying evolutionary relationships. |
| doi_str_mv | 10.3390/genes15050546 |
| format | Article |
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is lacking. To resolve the genetic composition of
within Amaranthaceae and its systematic relationship with related genera, we used a second-generation Illumina sequencing system to detect the chloroplast genome of
and analyze its assembly, annotation, and phylogenetics. Total length of the chloroplast genome of
reached 152,287 bp, with 84 protein-coding genes, 36 tRNAs, and eight rRNAs. Codon usage analysis showed the majority of codons ending with base A/U. Mononucleotide repeats were the most common (85.42%) of the four identified simple sequence repeats. A comparison with chloroplast genomes of six other Amaranthaceae species indicated contraction and expansion of the inverted repeat boundary region in
, with some genes (
,
,
) differing in length and distribution. Among the seven species, the variation in non-coding regions was greater. Phylogenetic analysis revealed
,
,
, and
to have a close monophyletic relationship. By sequencing the
chloroplast genome, this research resolves the relatedness among 35 Amaranthaceae species, providing molecular insights for germplasm utilization, and theoretical support for studying evolutionary relationships.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes15050546</identifier><identifier>PMID: 38790176</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Amaranthaceae ; Amaranthaceae - genetics ; Animal sciences ; China ; Chloroplasts ; Chloroplasts - genetics ; Codon Usage ; Codons ; Dysphania ; Evolution, Molecular ; Genome, Chloroplast ; Genomes ; Genomics ; Geographical distribution ; Germplasm ; Grasslands ; Inverted repeat ; Krascheninnikovia ; Microsatellite Repeats - genetics ; Molecular Sequence Annotation ; Phylogenetics ; Phylogeny ; Physiology ; Simple sequence repeats ; Software ; Taxonomy</subject><ispartof>Genes, 2024-04, Vol.15 (5), p.546</ispartof><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><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c316t-880021ea9434e5e340ed680f99348d42f06c0d85fd66bd595e06a1a878c525403</cites><orcidid>0000-0002-4121-4529</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38790176$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wei, Peng</creatorcontrib><creatorcontrib>Li, Youzheng</creatorcontrib><creatorcontrib>Ke, Mei</creatorcontrib><creatorcontrib>Hou, Yurong</creatorcontrib><creatorcontrib>Aikebaier, Abudureyimu</creatorcontrib><creatorcontrib>Wu, Zinian</creatorcontrib><title>Complete Chloroplast Genome of Krascheninnikovia ewersmanniana : Comparative and Phylogenetic Analysis</title><title>Genes</title><addtitle>Genes (Basel)</addtitle><description>is a dominant desert shrub in Xinjiang, China, with high economic and ecological value. However, molecular systematics research on
is lacking. To resolve the genetic composition of
within Amaranthaceae and its systematic relationship with related genera, we used a second-generation Illumina sequencing system to detect the chloroplast genome of
and analyze its assembly, annotation, and phylogenetics. Total length of the chloroplast genome of
reached 152,287 bp, with 84 protein-coding genes, 36 tRNAs, and eight rRNAs. Codon usage analysis showed the majority of codons ending with base A/U. Mononucleotide repeats were the most common (85.42%) of the four identified simple sequence repeats. A comparison with chloroplast genomes of six other Amaranthaceae species indicated contraction and expansion of the inverted repeat boundary region in
, with some genes (
,
,
) differing in length and distribution. Among the seven species, the variation in non-coding regions was greater. Phylogenetic analysis revealed
,
,
, and
to have a close monophyletic relationship. By sequencing the
chloroplast genome, this research resolves the relatedness among 35 Amaranthaceae species, providing molecular insights for germplasm utilization, and theoretical support for studying evolutionary relationships.</description><subject>Amaranthaceae</subject><subject>Amaranthaceae - genetics</subject><subject>Animal sciences</subject><subject>China</subject><subject>Chloroplasts</subject><subject>Chloroplasts - genetics</subject><subject>Codon Usage</subject><subject>Codons</subject><subject>Dysphania</subject><subject>Evolution, Molecular</subject><subject>Genome, Chloroplast</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Geographical distribution</subject><subject>Germplasm</subject><subject>Grasslands</subject><subject>Inverted repeat</subject><subject>Krascheninnikovia</subject><subject>Microsatellite Repeats - genetics</subject><subject>Molecular Sequence Annotation</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Physiology</subject><subject>Simple sequence repeats</subject><subject>Software</subject><subject>Taxonomy</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>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNpdkc1Lw0AQxRdRbKk9epUFL16ik-xHEm-laBULetBz2CYTuzXZjbtJpf-9CVVRZw4zAz8ej3mEnIZwyVgKV69o0IcC-ubygIwjiFnAeSQOf-0jMvV-A31xiADEMRmxJE4hjOWYlHNbNxW2SOfryjrbVMq3dIHG1khtSR-c8vkajTZGv9mtVhQ_0Pla9bcyil7TQUA51eotUmUK-rTeVXYw1uqczoyqdl77E3JUqsrj9GtOyMvtzfP8Llg-Lu7ns2WQs1C2QZIARCGqlDOOAhkHLGQCZZoynhQ8KkHmUCSiLKRcFSIVCFKFKomTXESCA5uQi71u4-x7h77Nau1zrCpl0HY-YyCBxVwA69Hzf-jGdq73O1C9dCiFGKhgT-XOeu-wzBqna-V2WQjZkEH2J4OeP_tS7VY1Fj_098fZJ4lfgeY</recordid><startdate>20240425</startdate><enddate>20240425</enddate><creator>Wei, Peng</creator><creator>Li, Youzheng</creator><creator>Ke, Mei</creator><creator>Hou, Yurong</creator><creator>Aikebaier, Abudureyimu</creator><creator>Wu, Zinian</creator><general>MDPI AG</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><orcidid>https://orcid.org/0000-0002-4121-4529</orcidid></search><sort><creationdate>20240425</creationdate><title>Complete Chloroplast Genome of Krascheninnikovia ewersmanniana : Comparative and Phylogenetic Analysis</title><author>Wei, Peng ; Li, Youzheng ; Ke, Mei ; Hou, Yurong ; Aikebaier, Abudureyimu ; Wu, Zinian</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c316t-880021ea9434e5e340ed680f99348d42f06c0d85fd66bd595e06a1a878c525403</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Amaranthaceae</topic><topic>Amaranthaceae - genetics</topic><topic>Animal sciences</topic><topic>China</topic><topic>Chloroplasts</topic><topic>Chloroplasts - genetics</topic><topic>Codon Usage</topic><topic>Codons</topic><topic>Dysphania</topic><topic>Evolution, Molecular</topic><topic>Genome, Chloroplast</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Geographical distribution</topic><topic>Germplasm</topic><topic>Grasslands</topic><topic>Inverted repeat</topic><topic>Krascheninnikovia</topic><topic>Microsatellite Repeats - genetics</topic><topic>Molecular Sequence Annotation</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Physiology</topic><topic>Simple sequence repeats</topic><topic>Software</topic><topic>Taxonomy</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wei, Peng</creatorcontrib><creatorcontrib>Li, Youzheng</creatorcontrib><creatorcontrib>Ke, Mei</creatorcontrib><creatorcontrib>Hou, Yurong</creatorcontrib><creatorcontrib>Aikebaier, Abudureyimu</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><jtitle>Genes</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wei, Peng</au><au>Li, Youzheng</au><au>Ke, Mei</au><au>Hou, Yurong</au><au>Aikebaier, Abudureyimu</au><au>Wu, Zinian</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Complete Chloroplast Genome of Krascheninnikovia ewersmanniana : Comparative and Phylogenetic Analysis</atitle><jtitle>Genes</jtitle><addtitle>Genes (Basel)</addtitle><date>2024-04-25</date><risdate>2024</risdate><volume>15</volume><issue>5</issue><spage>546</spage><pages>546-</pages><issn>2073-4425</issn><eissn>2073-4425</eissn><abstract>is a dominant desert shrub in Xinjiang, China, with high economic and ecological value. However, molecular systematics research on
is lacking. To resolve the genetic composition of
within Amaranthaceae and its systematic relationship with related genera, we used a second-generation Illumina sequencing system to detect the chloroplast genome of
and analyze its assembly, annotation, and phylogenetics. Total length of the chloroplast genome of
reached 152,287 bp, with 84 protein-coding genes, 36 tRNAs, and eight rRNAs. Codon usage analysis showed the majority of codons ending with base A/U. Mononucleotide repeats were the most common (85.42%) of the four identified simple sequence repeats. A comparison with chloroplast genomes of six other Amaranthaceae species indicated contraction and expansion of the inverted repeat boundary region in
, with some genes (
,
,
) differing in length and distribution. Among the seven species, the variation in non-coding regions was greater. Phylogenetic analysis revealed
,
,
, and
to have a close monophyletic relationship. By sequencing the
chloroplast genome, this research resolves the relatedness among 35 Amaranthaceae species, providing molecular insights for germplasm utilization, and theoretical support for studying evolutionary relationships.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>38790176</pmid><doi>10.3390/genes15050546</doi><orcidid>https://orcid.org/0000-0002-4121-4529</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Amaranthaceae Amaranthaceae - genetics Animal sciences China Chloroplasts Chloroplasts - genetics Codon Usage Codons Dysphania Evolution, Molecular Genome, Chloroplast Genomes Genomics Geographical distribution Germplasm Grasslands Inverted repeat Krascheninnikovia Microsatellite Repeats - genetics Molecular Sequence Annotation Phylogenetics Phylogeny Physiology Simple sequence repeats Software Taxonomy |
| title | Complete Chloroplast Genome of Krascheninnikovia ewersmanniana : Comparative and Phylogenetic Analysis |
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