Abstract
The present paper reports for the first time the characteristics of the complete plastid genome of Surianaceae (Suriana maritima L.) in the order Fabales. The circular complete plastid genome is 163,747 bp in length with a typical quadripartite organization containing 115 unique genes, of which 80 are protein-coding genes, 31 tRNA genes and four rRNA genes. The plastid genome of S. maritima is characterized by absence of intron in the atpF gene, which has never been reported for any other species of the Fabales. The gene content and their orders in the plastid genome of Surianaceae are similar to the basal lineages of the legume family (Cercidoideae, Detarioideae) and Quillajaceae, supporting a likely common ancestor for the three families. Phylogenetic analysis supported the sister relationship between Surianaceae and Leguminosae, with strongly supported by Bayesian method and moderately supported by likelihood method. The complete plastid genome of Surianaceae could provide potential benefit in resolving the long-standing unresolved interfamily relationships of Fabales when a more comprehensive sampling from Polygalaceae and Leguminosae is available for future studies.
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References
Bankevich A., Nurk S., Antipov D., Gurevich A. A., Dvorkin M., Kulikov A. S. et al. 2012 SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477.
Bello M. A., Rudall P. J. and Hawkins J. A. 2012 Combined phylogenetic analyses reveal interfamilial relationships and patterns of floral evolution in the eudicot order Fabales. Cladistics 28, 393–421.
Christenhusz M. J. M. and Byng J. W. 2016 The number of known plants species in the world and its annual increase. Phytotaxa 261, 201–217.
Claxton F., Banks H., Klitgaard B. B. and Crane P. R. 2005 Pollen morphology of families Quillajaceae and Surianaceae (Fabales). Rev. Palaeobot. Palyno. 133, 221–233.
Daniell H., Wurdack K. J., Kanagaraj A., Lee S. B., Saski C. and Jansen R. K. 2008 The complete nucleotide sequence of the cassava (manihot esculenta) chloroplast genome and the evolution of atpF in Malpighiales: RNA editing and multiple losses of a group II intron. Theor. Appl. Genet. 116, 723–737.
Darling A. C. E., Mau B., Blattner F. R. and Perna N. T. 2004 Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394–1403.
Doyle J. J. and Doyle J. L. 1987 A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11–15.
Dugas D. V., Hernandez D., Koenen E. J. M., Schwarz E., Straub S. and Hughes C. E. et al. 2015 Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP. Sci. Rep. 5, 16958.
Freudenthal J. A., Pfaff S., Terhoeven N., Korte A., Ankenbrand M. J. and Förster F. 2019 The landscape of chloroplast genome assembly tools (https://doi.org/10.1101/665869).
Jin J. J., Yu W. B., Yang J. B., Song Y., Yi T. S. and Li D. Z. 2018 GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data (https://doi.org/10.1101/256479).
Katoh K. and Standley D. M. 2013 MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780.
Kearse M., Moir R., Wilson A., Stones H. S., Cheung M., Sturrock S. et al. 2012 Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649.
Langmead B. and Salzberg S. L. 2012 Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359.
Liu J. F., Li S. C., Chen H. J., Tu T. Y. and Zhang D. X. 2018 A karyological study of Suriana maritima L. (Surianaceae) from Xisha Islands of South China Sea. Caryologia 71, 109–112.
LPWG-the legume phylogeny working group. 2017 A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny. Taxon 66, 44–77.
Qu X. J., Moore M. J., Li D. Z. and Yi T. S. 2019 PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes. Plant Methods 15, 50.
Ronquist F. and Huelsenbeck J. P. 2003 MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574.
Shaw J., Lickey E. B., Schilling E. E. and Small R. L. 2007 Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am. J. Bot. 94, 275–288.
Stamatakis A. 2014 RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313.
Sveinsson S. and Cronk Q. 2014 Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium). BMC Evol. Biol. 14, 228.
Thiel T., Michalek W., Varshney R. K. and Graner A. 2003 Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor. Appl. Genet. 106, 411–422.
Wick R. R., Schultz M. B., Zobel J. and Holt K. E. 2015 Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 31, 3350–3352.
Acknowledgements
This work was financially supported by the National Natural Science Foundation of China (grant 31270266), the Ministry of Science and Technology of China (2013FY111200) and the Strategic Priority Research Programme of the Chinese Academy of Sciences (XDA13020500). Science and Technology Planning Project of Guangdong Province (2019B030316020).
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Lai, Q., Zhu, C., Gu, S. et al. Complete plastid genome of Suriana maritima L. (Surianaceae) and its implications in phylogenetic reconstruction of Fabales. J Genet 98, 109 (2019). https://doi.org/10.1007/s12041-019-1157-3
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DOI: https://doi.org/10.1007/s12041-019-1157-3