The complete chloroplast genome sequence of the white strawberry Fragaria pentaphylla

被引：11

作者：

Bai, Li-jun ^{[1
]}

Ye, Yun-tian ^{[1
]}

Chen, Qing ^{[1
]}

Tang, Hao-ru ^{[1
]}

机构：

[1] Sichuan Agr Univ, Coll Hort, Chengdu 611130, Sichuan, Peoples R China

来源：

CONSERVATION GENETICS RESOURCES | 2017年 / 9卷 / 04期

关键词：

Chloroplast genome; Fragaria pentaphylla; Conservation genetics;

D O I：

10.1007/s12686-017-0713-5

中图分类号：

X176 [生物多样性保护];

学科分类号：

090705 ;

摘要：

Fragaria pentaphylla has fragmented distribution in southwest China, and its populations have been shrinking. In the present study, we report the complete chloroplast genome sequence of F. pentaphylla using next-generation sequencing technology. The complete chloroplast genome size is 155,640 bp. The genome contained 128 genes, including 30 tRNA genes, 78 protein-coding genes, and four rRNA genes, and multiple copies of 19 of these genes. Phylogenetic analysis based on nine complete chloroplast genomes revealed that F. pentaphylla is closely related to Fragaria vesca subsp. vesca. The complete chloroplast genome of F. pentaphylla would provide a good foundation for understanding the diversification and evolution of the genus Fragaria, and might help in conserving the precious natural populations of wild white strawberry.

引用

页码：659 / 661

页数：3

共 12 条

[1] Trimmomatic: a flexible trimmer for Illumina sequence data [J].

Bolger, Anthony M. ;

Lohse, Marc ;

Usadel, Bjoern .

BIOINFORMATICS, 2014, 30 (15) :2114-2120

[2]

Chen BingYi Chen BingYi, 2015, Journal of Fruit Science, V32, P51

[3]

Doyle JJ., 1987, PHYTOCHEMISTRY B, V19, P11

[4] ULTRA-BARCODING IN CACAO (THEOBROMA SPP.; MALVACEAE) USING WHOLE CHLOROPLAST GENOMES AND NUCLEAR RIBOSOMAL DNA [J].

Kane, Nolan ;

Sveinsson, Saemundur ;

Dempewolf, Hannes ;

Yang, Ji Yong ;

Zhang, Dapeng ;

Engels, Johannes M. M. ;

Cronk, Quentin .

AMERICAN JOURNAL OF BOTANY, 2012, 99 (02) :320-329

[5] MAFFT version 5: improvement in accuracy of multiple sequence alignment [J].

Katoh, K ;

Kuma, K ;

Toh, H ;

Miyata, T .

NUCLEIC ACIDS RESEARCH, 2005, 33 (02) :511-518

[6] OrganellarGenomeDRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets [J].

Lohse, Marc ;

Drechsel, Oliver ;

Kahlau, Sabine ;

Bock, Ralph .

NUCLEIC ACIDS RESEARCH, 2013, 41 (W1) :W575-W581

[7] Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing [J].

Njuguna, Wambui ;

Liston, Aaron ;

Cronn, Richard ;

Ashman, Tia-Lynn ;

Bassil, Nahla .

MOLECULAR PHYLOGENETICS AND EVOLUTION, 2013, 66 (01) :17-29

[8] From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes [J].

Ruhfel, Brad R. ;

Gitzendanner, Matthew A. ;

Soltis, Pamela S. ;

Soltis, Douglas E. ;

Burleigh, J. Gordon .

BMC EVOLUTIONARY BIOLOGY, 2014, 14

[9] BIOCLIMATIC, ECOLOGICAL, AND PHENOTYPIC INTERMEDIACY AND HIGH GENETIC ADMIXTURE IN A NATURAL HYBRID OF OCTOPLOID STRAWBERRIES [J].

Salamone, Isabella ;

Govindarajulu, Rajanikanth ;

Falk, Stacey ;

Parks, Matthew ;

Liston, Aaron ;

Ashman, Tia-Lynn .

AMERICAN JOURNAL OF BOTANY, 2013, 100 (05) :939-950

[10] The genome of woodland strawberry (Fragaria vesca) [J].

Shulaev, Vladimir ;

Sargent, Daniel J. ;

Crowhurst, Ross N. ;

Mockler, Todd C. ;

Folkerts, Otto ;

Delcher, Arthur L. ;

Jaiswal, Pankaj ;

Mockaitis, Keithanne ;

Liston, Aaron ;

Mane, Shrinivasrao P. ;

Burns, Paul ;

Davis, Thomas M. ;

Slovin, Janet P. ;

Bassil, Nahla ;

Hellens, Roger P. ;

Evans, Clive ;

Harkins, Tim ;

Kodira, Chinnappa ;

Desany, Brian ;

Crasta, Oswald R. ;

Jensen, Roderick V. ;

Allan, Andrew C. ;

Michael, Todd P. ;

Setubal, Joao Carlos ;

Celton, Jean-Marc ;

Rees, D. Jasper G. ;

Williams, Kelly P. ;

Holt, Sarah H. ;

Rojas, Juan Jairo Ruiz ;

Chatterjee, Mithu ;

Liu, Bo ;

Silva, Herman ;

Meisel, Lee ;

Adato, Avital ;

Filichkin, Sergei A. ;

Troggio, Michela ;

Viola, Roberto ;

Ashman, Tia-Lynn ;

Wang, Hao ;

Dharmawardhana, Palitha ;

Elser, Justin ;

Raja, Rajani ;

Priest, Henry D. ;

Bryant, Douglas W., Jr. ;

Fox, Samuel E. ;

Givan, Scott A. ;

Wilhelm, Larry J. ;

Naithani, Sushma ;

Christoffels, Alan ;

Salama, David Y. .

NATURE GENETICS, 2011, 43 (02) :109-116

← 1 2 →