The complete chloroplast genome of the threatened Napa False Indigo Amorpha californica var. napensis Jeps. 1925 (Fabaceae) from Northern California, USA
Amorpha californica var. napensis Jeps. 1925, the Napa false indigo, is a threatened shrub endemic to northern California. Here the complete chloroplast genome of topotype material of var. napensis was assembled and characterized to contribute to the bioinformatics, systematics, and conservation of...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2022-01-01
|
| Series: | Mitochondrial DNA. Part B. Resources |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/23802359.2022.2029605 |
| _version_ | 1797638675248447488 |
|---|---|
| author | Hartnell College Genomics Group Ivan D. Agudelo Griselda Aldaco Angel Brito-Pizano Kimberly G. Chavez Karina G. Cortina Jorge Flores Alejandro Fuentes Adam N. Garcia Alejandro Garcia Daniel Gonzalez-Martinez Jennifer Hernandez Ramos Jeffery R. Hughey Fernando R. Katada Felix A. Leon Maleny P. Lopez Sandra Z. Lopez Aileen G. Mendoza Maritta Molina Asmahan Muhrram Daisy Ortiz-Matias Tonantzin E. Ortiz Alicia Pacheco Nandini Patel Paz M. Ramirez Jennifer L. Scaramuzzino Alexandria Soto Richard A. Stabler Jessica M. Vidauri Jose Villicana James A. Yhip |
| author_facet | Hartnell College Genomics Group Ivan D. Agudelo Griselda Aldaco Angel Brito-Pizano Kimberly G. Chavez Karina G. Cortina Jorge Flores Alejandro Fuentes Adam N. Garcia Alejandro Garcia Daniel Gonzalez-Martinez Jennifer Hernandez Ramos Jeffery R. Hughey Fernando R. Katada Felix A. Leon Maleny P. Lopez Sandra Z. Lopez Aileen G. Mendoza Maritta Molina Asmahan Muhrram Daisy Ortiz-Matias Tonantzin E. Ortiz Alicia Pacheco Nandini Patel Paz M. Ramirez Jennifer L. Scaramuzzino Alexandria Soto Richard A. Stabler Jessica M. Vidauri Jose Villicana James A. Yhip |
| author_sort | Hartnell College Genomics Group |
| collection | DOAJ |
| description | Amorpha californica var. napensis Jeps. 1925, the Napa false indigo, is a threatened shrub endemic to northern California. Here the complete chloroplast genome of topotype material of var. napensis was assembled and characterized to contribute to the bioinformatics, systematics, and conservation of this variety. The chloroplast genome (GenBank accession OK274088) is 158,294 base pairs (bp) in length, encodes 130 genes including 85 protein-coding, 37 tRNA, 8 rRNA, and shows a high-level of gene synteny to other Papilionoideae. Phylogenetic analysis fully resolved var. napensis in a clade with A. fruticosa L. and A. roemeriana Scheele, sister to the Dalbergieae. The newly sequenced chloroplast genome shows that the genetic differences between var. napensis and Amorpha californica Nutt. var. californica are greater than the variation observed between var. napensis and many other Amorpha spp. sequences deposited in GenBank. These data suggest that var. napensis should be elevated to full species rank. |
| first_indexed | 2024-03-11T13:07:02Z |
| format | Article |
| id | doaj.art-ee30e7761e59436085a88207740cfcd8 |
| institution | Directory Open Access Journal |
| issn | 2380-2359 |
| language | English |
| last_indexed | 2024-03-11T13:07:02Z |
| publishDate | 2022-01-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Mitochondrial DNA. Part B. Resources |
| spelling | doaj.art-ee30e7761e59436085a88207740cfcd82023-11-03T14:36:01ZengTaylor & Francis GroupMitochondrial DNA. Part B. Resources2380-23592022-01-017128328510.1080/23802359.2022.20296052029605The complete chloroplast genome of the threatened Napa False Indigo Amorpha californica var. napensis Jeps. 1925 (Fabaceae) from Northern California, USAHartnell College Genomics Group0Ivan D. Agudelo1Griselda Aldaco2Angel Brito-Pizano3Kimberly G. Chavez4Karina G. Cortina5Jorge Flores6Alejandro Fuentes7Adam N. Garcia8Alejandro Garcia9Daniel Gonzalez-Martinez10Jennifer Hernandez Ramos11Jeffery R. Hughey12Fernando R. Katada13Felix A. Leon14Maleny P. Lopez15Sandra Z. Lopez16Aileen G. Mendoza17Maritta Molina18Asmahan Muhrram19Daisy Ortiz-Matias20Tonantzin E. Ortiz21Alicia Pacheco22Nandini Patel23Paz M. Ramirez24Jennifer L. Scaramuzzino25Alexandria Soto26Richard A. Stabler27Jessica M. Vidauri28Jose Villicana29James A. Yhip30Division of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeCounty of SonomaDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeDivision of Mathematics, Science, and Engineering, Hartnell CollegeAmorpha californica var. napensis Jeps. 1925, the Napa false indigo, is a threatened shrub endemic to northern California. Here the complete chloroplast genome of topotype material of var. napensis was assembled and characterized to contribute to the bioinformatics, systematics, and conservation of this variety. The chloroplast genome (GenBank accession OK274088) is 158,294 base pairs (bp) in length, encodes 130 genes including 85 protein-coding, 37 tRNA, 8 rRNA, and shows a high-level of gene synteny to other Papilionoideae. Phylogenetic analysis fully resolved var. napensis in a clade with A. fruticosa L. and A. roemeriana Scheele, sister to the Dalbergieae. The newly sequenced chloroplast genome shows that the genetic differences between var. napensis and Amorpha californica Nutt. var. californica are greater than the variation observed between var. napensis and many other Amorpha spp. sequences deposited in GenBank. These data suggest that var. napensis should be elevated to full species rank.http://dx.doi.org/10.1080/23802359.2022.2029605amorphaamorpha californicaamorpha californica var. californicachloroplast genomepapilionoideae |
| spellingShingle | Hartnell College Genomics Group Ivan D. Agudelo Griselda Aldaco Angel Brito-Pizano Kimberly G. Chavez Karina G. Cortina Jorge Flores Alejandro Fuentes Adam N. Garcia Alejandro Garcia Daniel Gonzalez-Martinez Jennifer Hernandez Ramos Jeffery R. Hughey Fernando R. Katada Felix A. Leon Maleny P. Lopez Sandra Z. Lopez Aileen G. Mendoza Maritta Molina Asmahan Muhrram Daisy Ortiz-Matias Tonantzin E. Ortiz Alicia Pacheco Nandini Patel Paz M. Ramirez Jennifer L. Scaramuzzino Alexandria Soto Richard A. Stabler Jessica M. Vidauri Jose Villicana James A. Yhip The complete chloroplast genome of the threatened Napa False Indigo Amorpha californica var. napensis Jeps. 1925 (Fabaceae) from Northern California, USA Mitochondrial DNA. Part B. Resources amorpha amorpha californica amorpha californica var. californica chloroplast genome papilionoideae |
| title | The complete chloroplast genome of the threatened Napa False Indigo Amorpha californica var. napensis Jeps. 1925 (Fabaceae) from Northern California, USA |
| title_full | The complete chloroplast genome of the threatened Napa False Indigo Amorpha californica var. napensis Jeps. 1925 (Fabaceae) from Northern California, USA |
| title_fullStr | The complete chloroplast genome of the threatened Napa False Indigo Amorpha californica var. napensis Jeps. 1925 (Fabaceae) from Northern California, USA |
| title_full_unstemmed | The complete chloroplast genome of the threatened Napa False Indigo Amorpha californica var. napensis Jeps. 1925 (Fabaceae) from Northern California, USA |
| title_short | The complete chloroplast genome of the threatened Napa False Indigo Amorpha californica var. napensis Jeps. 1925 (Fabaceae) from Northern California, USA |
| title_sort | complete chloroplast genome of the threatened napa false indigo amorpha californica var napensis jeps 1925 fabaceae from northern california usa |
| topic | amorpha amorpha californica amorpha californica var. californica chloroplast genome papilionoideae |
| url | http://dx.doi.org/10.1080/23802359.2022.2029605 |
| work_keys_str_mv | AT hartnellcollegegenomicsgroup thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT ivandagudelo thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT griseldaaldaco thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT angelbritopizano thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT kimberlygchavez thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT karinagcortina thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT jorgeflores thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT alejandrofuentes thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT adamngarcia thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT alejandrogarcia thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT danielgonzalezmartinez thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT jenniferhernandezramos thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT jefferyrhughey thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT fernandorkatada thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT felixaleon thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT malenyplopez thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT sandrazlopez thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT aileengmendoza thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT marittamolina thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT asmahanmuhrram thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT daisyortizmatias thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT tonantzineortiz thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT aliciapacheco thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT nandinipatel thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT pazmramirez thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT jenniferlscaramuzzino thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT alexandriasoto thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT richardastabler thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT jessicamvidauri thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT josevillicana thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT jamesayhip thecompletechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT hartnellcollegegenomicsgroup completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT ivandagudelo completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT griseldaaldaco completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT angelbritopizano completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT kimberlygchavez completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT karinagcortina completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT jorgeflores completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT alejandrofuentes completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT adamngarcia completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT alejandrogarcia completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT danielgonzalezmartinez completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT jenniferhernandezramos completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT jefferyrhughey completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT fernandorkatada completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT felixaleon completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT malenyplopez completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT sandrazlopez completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT aileengmendoza completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT marittamolina completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT asmahanmuhrram completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT daisyortizmatias completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT tonantzineortiz completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT aliciapacheco completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT nandinipatel completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT pazmramirez completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT jenniferlscaramuzzino completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT alexandriasoto completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT richardastabler completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT jessicamvidauri completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT josevillicana completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa AT jamesayhip completechloroplastgenomeofthethreatenednapafalseindigoamorphacalifornicavarnapensisjeps1925fabaceaefromnortherncaliforniausa |