Complete chloroplast genome sequence of Rhododendron mariesii and comparative genomics of related species in the family Ericaeae
Rhododendron mariesii Hemsley et Wilson, 1907, a typical member of the family Ericaeae, possesses valuable medicinal and horticultural properties. In this research, the complete chloroplast (cp) genome of R. mariesii was sequenced and assembled, which proved to be a typical quadripartite structure w...
Saved in:
| Published in: | Comparative cytogenetics Vol. 17; no. 1; pp. 163 - 180 |
|---|---|
| Main Authors: | , , , , , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
Sofia
Pensoft Publishers
18-08-2023
|
| Subjects: | |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Abstract | Rhododendron mariesii
Hemsley et Wilson, 1907, a typical member of the family Ericaeae, possesses valuable medicinal and horticultural properties. In this research, the complete chloroplast (cp) genome of
R. mariesii
was sequenced and assembled, which proved to be a typical quadripartite structure with the length of 203,480 bp. In particular, the lengths of the large single copy region (LSC), small single copy region (SSC), and inverted repeat regions (IR) were 113,715 bp, 7,953 bp, and 40,918 bp, respectively. Among the 151 unique genes, 98 were protein-coding genes, 8 were tRNA genes, and 45 were rRNA genes. The structural characteristics of the
R. mariesii
cp genome was similar to other angiosperms. Leucine was the most representative amino acid, while cysteine was the lowest representative. Totally, 30 codons showed obvious codon usage bias, and most were A/U-ending codons. Six highly variable regions were observed, such as
trnK-pafI
and
atpE-rpoB
, which could serve as potential markers for future barcoding and phylogenetic research of
R. mariesii
species. Coding regions were more conserved than non-coding regions. Expansion and contraction in the IR region might be the main length variation in
R. mariesii
and related Ericaeae species. Maximum-likelihood (ML) phylogenetic analysis revealed that
R. mariesii
was relatively closed to the
R. simsii
Planchon, 1853 and
R. pulchrum
Sweet,1831. This research will supply rich genetic resource for
R. mariesii
and related species of the Ericaeae. |
|---|---|
| AbstractList | Rhododendron mariesii Hemsley et Wilson, 1907, a typical member of the family Ericaeae, possesses valuable medicinal and horticultural properties. In this research, the complete chloroplast (cp) genome of R. mariesii was sequenced and assembled, which proved to be a typical quadripartite structure with the length of 203,480 bp. In particular, the lengths of the large single copy region (LSC), small single copy region (SSC), and inverted repeat regions (IR) were 113,715 bp, 7,953 bp, and 40,918 bp, respectively. Among the 151 unique genes, 98 were protein-coding genes, 8 were tRNA genes, and 45 were rRNA genes. The structural characteristics of the R. mariesii cp genome was similar to other angiosperms. Leucine was the most representative amino acid, while cysteine was the lowest representative. Totally, 30 codons showed obvious codon usage bias, and most were A/U-ending codons. Six highly variable regions were observed, such as trnK-pafI and atpE-rpoB, which could serve as potential markers for future barcoding and phylogenetic research of R. mariesii species. Coding regions were more conserved than non-coding regions. Expansion and contraction in the IR region might be the main length variation in R. mariesii and related Ericaeae species. Maximum-likelihood (ML) phylogenetic analysis revealed that R. mariesii was relatively closed to the R. simsii Planchon, 1853 and R. pulchrum Sweet,1831. This research will supply rich genetic resource for R. mariesii and related species of the Ericaeae. Rhododendron mariesii Hemsley et Wilson, 1907, a typical member of the family Ericaeae, possesses valuable medicinal and horticultural properties. In this research, the complete chloroplast (cp) genome of R. mariesii was sequenced and assembled, which proved to be a typical quadripartite structure with the length of 203,480 bp. In particular, the lengths of the large single copy region (LSC), small single copy region (SSC), and inverted repeat regions (IR) were 113,715 bp, 7,953 bp, and 40,918 bp, respectively. Among the 151 unique genes, 98 were protein-coding genes, 8 were tRNA genes, and 45 were rRNA genes. The structural characteristics of the R. mariesiicp genome was similar to other angiosperms. Leucine was the most representative amino acid, while cysteine was the lowest representative. Totally, 30 codons showed obvious codon usage bias, and most were A/U-ending codons. Six highly variable regions were observed, such as trnK-pafI and atpE-rpoB, which could serve as potential markers for future barcoding and phylogenetic research of R. mariesii species. Coding regions were more conserved than non-coding regions. Expansion and contraction in the IR region might be the main length variation in R. mariesii and related Ericaeae species. Maximum-likelihood (ML) phylogenetic analysis revealed that R. mariesii was relatively closed to the R. simsii Planchon, 1853 and R. pulchrum Sweet,1831. This research will supply rich genetic resource for R. mariesii and related species of the Ericaeae. Keywords: chloroplast genome, comparative genomics, conservation genetics, phylogeny, Rhododendron mariesii Rhododendron mariesii Hemsley et Wilson, 1907, a typical member of the family Ericaeae, possesses valuable medicinal and horticultural properties. In this research, the complete chloroplast (cp) genome of R. mariesii was sequenced and assembled, which proved to be a typical quadripartite structure with the length of 203,480 bp. In particular, the lengths of the large single copy region (LSC), small single copy region (SSC), and inverted repeat regions (IR) were 113,715 bp, 7,953 bp, and 40,918 bp, respectively. Among the 151 unique genes, 98 were protein-coding genes, 8 were tRNA genes, and 45 were rRNA genes. The structural characteristics of the R. mariesii cp genome was similar to other angiosperms. Leucine was the most representative amino acid, while cysteine was the lowest representative. Totally, 30 codons showed obvious codon usage bias, and most were A/U-ending codons. Six highly variable regions were observed, such as trnK-pafI and atpE-rpoB , which could serve as potential markers for future barcoding and phylogenetic research of R. mariesii species. Coding regions were more conserved than non-coding regions. Expansion and contraction in the IR region might be the main length variation in R. mariesii and related Ericaeae species. Maximum-likelihood (ML) phylogenetic analysis revealed that R. mariesii was relatively closed to the R. simsii Planchon, 1853 and R. pulchrum Sweet,1831. This research will supply rich genetic resource for R. mariesii and related species of the Ericaeae. Rhododendron mariesii Hemsley et Wilson, 1907, a typical member of the family Ericaeae, possesses valuable medicinal and horticultural properties. In this research, the complete chloroplast (cp) genome of R. mariesii was sequenced and assembled, which proved to be a typical quadripartite structure with the length of 203,480 bp. In particular, the lengths of the large single copy region (LSC), small single copy region (SSC), and inverted repeat regions (IR) were 113,715 bp, 7,953 bp, and 40,918 bp, respectively. Among the 151 unique genes, 98 were protein-coding genes, 8 were tRNA genes, and 45 were rRNA genes. The structural characteristics of the R. mariesiicp genome was similar to other angiosperms. Leucine was the most representative amino acid, while cysteine was the lowest representative. Totally, 30 codons showed obvious codon usage bias, and most were A/U-ending codons. Six highly variable regions were observed, such as trnK-pafI and atpE-rpoB, which could serve as potential markers for future barcoding and phylogenetic research of R. mariesii species. Coding regions were more conserved than non-coding regions. Expansion and contraction in the IR region might be the main length variation in R. mariesii and related Ericaeae species. Maximum-likelihood (ML) phylogenetic analysis revealed that R. mariesii was relatively closed to the R. simsii Planchon, 1853 and R. pulchrum Sweet,1831. This research will supply rich genetic resource for R. mariesii and related species of the Ericaeae. |
| Audience | Academic |
| Author | Dong, Hongjin Zhang, Chunyu Huang, Zhiwei Yu, Jiaojun Wang, Shuzhen Li, Zhiliang Wan, Xuchun Zhang, Jialiang |
| Author_xml | – sequence: 1 givenname: Zhiliang surname: Li fullname: Li, Zhiliang – sequence: 2 givenname: Zhiwei surname: Huang fullname: Huang, Zhiwei – sequence: 3 givenname: Xuchun surname: Wan fullname: Wan, Xuchun – sequence: 4 givenname: Jiaojun surname: Yu fullname: Yu, Jiaojun – sequence: 5 givenname: Hongjin surname: Dong fullname: Dong, Hongjin – sequence: 6 givenname: Jialiang surname: Zhang fullname: Zhang, Jialiang – sequence: 7 givenname: Chunyu surname: Zhang fullname: Zhang, Chunyu – sequence: 8 givenname: Shuzhen surname: Wang fullname: Wang, Shuzhen |
| BookMark | eNptUtFqFDEUHaSCtfYThIDPuyaTzCTzWJaqhUKhKPgWMjc3u1lmkjFJhX3z0806UhVMHnK5nHO49-S8bi5CDNg0bxndcjXI9xDnBU4l7jFsmdwyykQrXzSXbBj4hkr19eK5luxVc53zkdbTCcUGetn82FX-hAUJHKaY4jKZXEgVizOSjN-eMACS6MjjIdpoMdgUA5lN8pi9JyZYcp7AJFP8d1yJHvKZkXAyBS3JC0JFEx9IOSBxZvbTidwmDwYNvmleOjNlvP79XjVfPtx-3n3a3D98vNvd3G9A9KxshEU7UtmN6FpDEXhn2lYxCu3IjULHRS1b4IqxEYSrJAQAw0ewQnRdy6-au1XXRnPUS_J1h5OOxutfjZj22qTiYUKNFqC644RjvRitGzo7cCVbQUerXMer1rtVa0mxOpSLPsanFOr4ulVdz7lQlP1B7U0V9cHFkgzMPoO-kbIfhp7KM2r7H1S9FquR9a-dr_1_CN1KgBRzTuiel2FUnyOh_4qEZlKvkeA_AZMwsOA |
| CitedBy_id | crossref_primary_10_1007_s13205_024_04006_6 crossref_primary_10_3390_horticulturae10050492 |
| Cites_doi | 10.1038/srep13957 10.1186/s12864-015-1498-0 10.1111/njb.02251 10.1186/s12864-021-08225-6 10.1101/gr.2289704 10.1371/journal.pone.0057533 10.3389/fpls.2016.00843 10.1270/jsbbs.18092 10.1007/s11295-020-01436-0 10.1007/s12298-021-00989-1 10.1093/bioinformatics/btu033 10.1186/s12870-020-02621-y 10.1186/s12864-020-07219-0 10.1093/gbe/evv069 10.1371/journal.pone.0233167 10.1186/s13059-016-1004-2 10.1016/j.ygeno.2020.12.016 10.1590/1678-4685-gmb-2017-0265 10.1186/s13059-020-02154-5 10.1038/srep08348 10.1371/journal.pcbi.1009244 10.1186/s12864-019-6253-5 10.1002/ajb2.1178 10.1080/23802359.2020.1714511 10.1186/s12870-016-0967-1 10.3390/ijms20051045 10.1186/1471-2164-13-715 10.1007/s00425-021-03812-z 10.3390/ijms19103142 10.1534/genetics.112.140178 10.1080/23802359.2021.1959458 10.1111/1755-0998.12585 10.3390/f11020158 10.1139/gen-2019-0153 10.1093/nar/gkz238 10.1007/s00239-021-10038-w 10.1093/bioinformatics/bty220 10.1080/23802359.2017.1390407 10.1093/gbe/evt063 10.1155/2022/3457806 |
| ContentType | Journal Article |
| Copyright | COPYRIGHT 2023 Pensoft Publishers 2023. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and conditions, you may use this content in accordance with the terms of the License. |
| Copyright_xml | – notice: COPYRIGHT 2023 Pensoft Publishers – notice: 2023. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and conditions, you may use this content in accordance with the terms of the License. |
| DBID | AAYXX CITATION 8FE 8FH ABUWG AFKRA ATCPS AZQEC BBNVY BENPR BHPHI CCPQU DWQXO GNUQQ HCIFZ LK8 M7P PATMY PIMPY PQEST PQQKQ PQUKI PYCSY DOA |
| DOI | 10.3897/compcytogen.17.101427 |
| DatabaseName | CrossRef ProQuest SciTech Collection ProQuest Natural Science Collection ProQuest Central (Alumni) ProQuest Central UK/Ireland Agricultural & Environmental Science Collection ProQuest Central Essentials Biological Science Collection ProQuest Central Natural Science Collection ProQuest One Community College ProQuest Central Korea ProQuest Central Student SciTech Premium Collection Biological Sciences Biological Science Database Environmental Science Database Publicly Available Content Database ProQuest One Academic Eastern Edition (DO NOT USE) ProQuest One Academic ProQuest One Academic UKI Edition Environmental Science Collection Directory of Open Access Journals |
| DatabaseTitle | CrossRef Publicly Available Content Database ProQuest Central Student ProQuest Biological Science Collection ProQuest Central Essentials ProQuest One Academic Eastern Edition ProQuest Central (Alumni Edition) SciTech Premium Collection ProQuest One Community College ProQuest Natural Science Collection Biological Science Database ProQuest SciTech Collection ProQuest Central Environmental Science Collection ProQuest One Academic UKI Edition Natural Science Collection ProQuest Central Korea Agricultural & Environmental Science Collection Biological Science Collection Environmental Science Database ProQuest One Academic |
| DatabaseTitleList | Publicly Available Content Database CrossRef |
| Database_xml | – sequence: 1 dbid: DOA name: Directory of Open Access Journals url: http://www.doaj.org/ sourceTypes: Open Website |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1993-078X |
| EndPage | 180 |
| ExternalDocumentID | oai_doaj_org_article_edcc819f4f164bdf95d9387240bd8f53 A776996071 10_3897_compcytogen_17_101427 |
| GroupedDBID | 53G 5GY 5VS 7XC 8FE 8FH AAFWJ AAHBH AAYXX ABDBF ADBBV AENEX AFKRA AFPKN ALMA_UNASSIGNED_HOLDINGS AOIJS ATCPS BAWUL BBNVY BCNDV BENPR BHPHI CCPQU CITATION DIK DU5 EBD EOJEC ESX GROUPED_DOAJ H13 HCIFZ HYE IAO IHR INH ITC K13 KQ8 LK8 M48 M7P OBODZ OK1 PATMY PGMZT PIMPY PROAC PYCSY QF4 QN7 RIG RNS RPM TR2 TUS ABUWG AZQEC DWQXO GNUQQ PQEST PQQKQ PQUKI |
| ID | FETCH-LOGICAL-c461t-4dedb075bef2a0ec35a22810c2b3a8ef340c22c3811bc4fc46eccca3bcd445523 |
| IEDL.DBID | DOA |
| ISSN | 1993-0771 |
| IngestDate | Tue Oct 22 15:05:25 EDT 2024 Thu Oct 10 18:12:52 EDT 2024 Wed Sep 25 17:18:47 EDT 2024 Tue Sep 24 04:06:54 EDT 2024 Thu Nov 21 22:11:52 EST 2024 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 1 |
| Language | English |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c461t-4dedb075bef2a0ec35a22810c2b3a8ef340c22c3811bc4fc46eccca3bcd445523 |
| OpenAccessLink | https://doaj.org/article/edcc819f4f164bdf95d9387240bd8f53 |
| PQID | 2856334801 |
| PQPubID | 2049308 |
| PageCount | 18 |
| ParticipantIDs | doaj_primary_oai_doaj_org_article_edcc819f4f164bdf95d9387240bd8f53 proquest_journals_2856334801 gale_infotracmisc_A776996071 gale_infotracacademiconefile_A776996071 crossref_primary_10_3897_compcytogen_17_101427 |
| PublicationCentury | 2000 |
| PublicationDate | 2023-08-18 |
| PublicationDateYYYYMMDD | 2023-08-18 |
| PublicationDate_xml | – month: 08 year: 2023 text: 2023-08-18 day: 18 |
| PublicationDecade | 2020 |
| PublicationPlace | Sofia |
| PublicationPlace_xml | – name: Sofia |
| PublicationTitle | Comparative cytogenetics |
| PublicationYear | 2023 |
| Publisher | Pensoft Publishers |
| Publisher_xml | – name: Pensoft Publishers |
| References | 101427_B40 101427_B26 101427_B27 101427_B24 101427_B25 101427_B22 101427_B23 101427_B20 101427_B21 101427_B4 101427_B5 101427_B2 101427_B3 101427_B8 101427_B9 101427_B6 101427_B28 101427_B7 101427_B29 101427_B1 101427_B30 101427_B15 101427_B37 101427_B16 101427_B38 101427_B13 101427_B35 101427_B14 101427_B36 101427_B11 101427_B33 101427_B12 101427_B34 101427_B31 101427_B10 101427_B32 101427_B19 101427_B17 101427_B39 101427_B18 |
| References_xml | – ident: 101427_B32 doi: 10.1038/srep13957 – ident: 101427_B14 doi: 10.1186/s12864-015-1498-0 – ident: 101427_B34 doi: 10.1111/njb.02251 – ident: 101427_B37 doi: 10.1186/s12864-021-08225-6 – ident: 101427_B7 doi: 10.1101/gr.2289704 – ident: 101427_B23 doi: 10.1371/journal.pone.0057533 – ident: 101427_B5 doi: 10.3389/fpls.2016.00843 – ident: 101427_B33 doi: 10.1270/jsbbs.18092 – ident: 101427_B35 doi: 10.1007/s11295-020-01436-0 – ident: 101427_B27 doi: 10.1007/s12298-021-00989-1 – ident: 101427_B3 doi: 10.1093/bioinformatics/btu033 – ident: 101427_B21 doi: 10.1186/s12870-020-02621-y – ident: 101427_B26 doi: 10.1186/s12864-020-07219-0 – ident: 101427_B31 doi: 10.1093/gbe/evv069 – ident: 101427_B19 doi: 10.1371/journal.pone.0233167 – ident: 101427_B6 doi: 10.1186/s13059-016-1004-2 – ident: 101427_B1 doi: 10.1016/j.ygeno.2020.12.016 – ident: 101427_B28 doi: 10.1590/1678-4685-gmb-2017-0265 – ident: 101427_B15 doi: 10.1186/s13059-020-02154-5 – ident: 101427_B9 doi: 10.1038/srep08348 – ident: 101427_B12 doi: 10.1371/journal.pcbi.1009244 – ident: 101427_B17 doi: 10.1186/s12864-019-6253-5 – ident: 101427_B11 doi: 10.1002/ajb2.1178 – ident: 101427_B36 doi: 10.1080/23802359.2020.1714511 – ident: 101427_B38 doi: 10.1186/s12870-016-0967-1 – ident: 101427_B18 doi: 10.3390/ijms20051045 – ident: 101427_B20 doi: 10.1186/1471-2164-13-715 – ident: 101427_B40 doi: 10.1007/s00425-021-03812-z – ident: 101427_B39 doi: 10.3390/ijms19103142 – ident: 101427_B2 doi: 10.1534/genetics.112.140178 – ident: 101427_B22 doi: 10.1080/23802359.2021.1959458 – ident: 101427_B29 doi: 10.1111/1755-0998.12585 – ident: 101427_B30 doi: 10.3390/f11020158 – ident: 101427_B13 doi: 10.1139/gen-2019-0153 – ident: 101427_B10 doi: 10.1093/nar/gkz238 – ident: 101427_B24 doi: 10.1007/s00239-021-10038-w – ident: 101427_B4 doi: 10.1093/bioinformatics/bty220 – ident: 101427_B16 doi: 10.1080/23802359.2017.1390407 – ident: 101427_B8 doi: 10.1093/gbe/evt063 – ident: 101427_B25 doi: 10.1155/2022/3457806 |
| SSID | ssj0000548190 |
| Score | 2.3250115 |
| Snippet | Rhododendron mariesii
Hemsley et Wilson, 1907, a typical member of the family Ericaeae, possesses valuable medicinal and horticultural properties. In this... Rhododendron mariesii Hemsley et Wilson, 1907, a typical member of the family Ericaeae, possesses valuable medicinal and horticultural properties. In this... |
| SourceID | doaj proquest gale crossref |
| SourceType | Open Website Aggregation Database |
| StartPage | 163 |
| SubjectTerms | Amino acids Angiosperms Chloroplasts Codons Genes Genetic aspects Genomes Genomics Inverted repeat Leucine Nucleotide sequence Phylogenetics Phylogeny Rhododendron RpoB protein rRNA tRNA |
| Title | Complete chloroplast genome sequence of Rhododendron mariesii and comparative genomics of related species in the family Ericaeae |
| URI | https://www.proquest.com/docview/2856334801 https://doaj.org/article/edcc819f4f164bdf95d9387240bd8f53 |
| Volume | 17 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://sdu.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV07bxQxELYgEhINSniIgxC5QKLaZL1rr31lQhJRUfCQ6Cx7PFauyG50tynS8dOZWe-FS4Fo0q28tmTNwzOf5flGiI-YgjJRhcpg7ioNqatcE1yFTqmuyZRgt1MT2-_26y93fsE0OfetvvhNWKEHLoI7wQRAUSvrTIl9THlp0rJ1lgJRTC6bwvNZdztgqrB6aw51pWSHYrI94RfacDcOpJZjZRm0au4ksxOMJs7-f53MU7i53Bcv5jxRnpb9HYgn2L8Uz0rnyLtX4jf7MYkcJVwR4h5uKAkeJROuXqPcPo-WQ5bfrgh30tmS1kMvrydgvFrJ0CcJf3m_y8IVbHjFVN2CSXINJs2Wq15SkijLTYiczk0M-Fr8vLz48flLNTdTqEB3aqx0whQpP4iYm1AjtCY0jVM1NLENDnOr6bMBCuAqgs60iJQLoY2QtDYEV9-IvX7o8a2QgKquo9GIBGmXaCjzJZzV5tTaGOsIC3G8laq_KZwZnrAGq8HvqMEr64saFuKMZX8_mSmvpwEyBD8bgv-fISzEJ9acZ8cc1wHCXF9Ae2aKK39qbcdUNFYtxOGDmeRQ8PD3Vvd-duiNb5zpuGi5Vu8eY7PvxXPuW8-X08odir1xfYsfxNNNuj2aDPkPUdD8XA |
| link.rule.ids | 315,782,786,866,2106,27933,27934 |
| linkProvider | Directory of Open Access Journals |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Complete+chloroplast+genome+sequence+of+Rhododendron+mariesii+and+comparative+genomics+of+related+species+in+the+family+Ericaeae&rft.jtitle=Comparative+cytogenetics&rft.au=Li%2C+Zhiliang&rft.au=Huang%2C+Zhiwei&rft.au=Wan%2C+Xuchun&rft.au=Yu%2C+Jiaojun&rft.date=2023-08-18&rft.pub=Pensoft+Publishers&rft.issn=1993-0771&rft.eissn=1993-078X&rft.volume=17&rft.spage=163&rft_id=info:doi/10.3897%2Fcompcytogen.17.101427 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1993-0771&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1993-0771&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1993-0771&client=summon |