Complete chloroplast genome of seven Fritillaria species, variable DNA markers identification and phylogenetic relationships within the genus

Abstract Saxifraga sinomontana J.-T. Pan & Gornall belongs to Saxifraga sect. Ciliatae subsect. Hirculoideae, a lineage containing ca. 110 species whose phylogenetic relationships are largely unresolved due to recent rapid radiations. Analyses of complete chloroplast genomes have the potential to significantly improve the resolution of phylogenetic relationships in this young plant lineage. The complete chloroplast genome of S. sinomontana was de novo sequenced, assembled and then compared with that of other six Saxifragaceae species. The S. sinomontana chloroplast genome is 147,240 bp in length with a typical quadripartite structure, including a large single-copy region of 79,310 bp and a small single-copy region of 16,874 bp separated by a pair of inverted repeats (IRs) of 25,528 bp each. The chloroplast genome contains 113 unique genes, including 79 protein-coding genes, four rRNAs and 30 tRNAs, with 18 duplicates in the IRs. The gene content and organization are similar to other Saxifragaceae chloroplast genomes. Sixty-one simple sequence repeats were identified in the S. sinomontana chloroplast genome, mostly represented by mononucleotide repeats of polyadenine or polythymine. Comparative analysis revealed 12 highly divergent regions in the intergenic spacers, as well as coding genes of matK, ndhK, accD, cemA, rpoA, rps19, ndhF, ccsA, ndhD and ycf1. Phylogenetic reconstruction of seven Saxifragaceae species based on 66 protein-coding genes received high bootstrap support values for nearly all identified nodes, suggesting a promising opportunity to resolve infrasectional relationships of the most species-rich section Ciliatae of Saxifraga.

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The Complete Chloroplast Genome Sequences of 14 Curcuma Species: Insights Into Genome Evolution and Phylogenetic Relationships Within Zingiberales

Frontiers in Genetics ◽

10.3389/fgene.2020.00802 ◽

2020 ◽

Vol 11 ◽

Cited By ~ 1

Author(s):

Heng Liang ◽

Yan Zhang ◽

Jiabin Deng ◽

Gang Gao ◽

Chunbang Ding ◽

...

Keyword(s):

Chloroplast Genome ◽

Genome Evolution ◽

Phylogenetic Relationships ◽

Genome Sequences ◽

Complete Chloroplast Genome

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Characterization of the complete chloroplast genome of Hevea brasiliensis reveals genome rearrangement, RNA editing sites and phylogenetic relationships

Gene ◽

10.1016/j.gene.2011.01.002 ◽

2011 ◽

Vol 475 (2) ◽

pp. 104-112 ◽

Cited By ~ 50

Author(s):

Sithichoke Tangphatsornruang ◽

Pichahpuk Uthaipaisanwong ◽

Duangjai Sangsrakru ◽

Juntima Chanprasert ◽

Thippawan Yoocha ◽

...

Keyword(s):

Chloroplast Genome ◽

Rna Editing ◽

Hevea Brasiliensis ◽

Phylogenetic Relationships ◽

Genome Rearrangement ◽

Complete Chloroplast Genome

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The Complete Chloroplast Genome Sequences of Fritillaria ussuriensis Maxim. and Fritillaria cirrhosa D. Don, and Comparative Analysis with Other Fritillaria Species

10.20944/preprints201703.0139.v1 ◽

2017 ◽

Cited By ~ 1

Author(s):

Inkyu Park ◽

Wook-Jin Kim ◽

Sang-Min Yeo ◽

Goya Choi ◽

Young-Min Kang ◽

...

Keyword(s):

Chloroplast Genome ◽

General Structure ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Genome Sequences ◽

Complete Chloroplast Genome ◽

Phylogenic Analysis ◽

Fritillaria Species ◽

Fritillaria Cirrhosa

The genus Fritillaria belongs to the widely distributed family Liliaceae. The bulbs of Fritillaria ussuriensis and Fritillaria cirrhosa are valuable herbaceous medicinal ingredients. However, they are still used indiscriminately in herbal medicine. Identification and molecular phylogenic analysis of Fritillaria species is therefore required. Here, we report the complete chloroplast (cp) genome sequences of F. ussuriensis and F. cirrhosa. The two Fritillaria cp genomes were 151,524 and 151,083 bp in length, respectively, including a pair of inverted repeat regions (52,678 and 52,156 bp) separated by a large single copy region (81,732 and 81,390 bp) and small single copy region (17,114 and 17,537 bp). A total of 111 genes in F. ussuriensis and 112 in F. cirrhosa comprised 77 protein-coding genes in F. ussuriensis and 78 in F. cirrhosa, 30 tRNA genes, and four rRNA genes. The gene order, content, and orientation of the two Fritillaria cp genomes exhibited the general structure of flowering plants, and were similar to those of other Fritillaria species. Comparison of the six Fritillaria species’ cp genomes indicated seven highly divergent regions in intergenic spacers and in the matK, rpoC1, rpoC2, ycf1, ycf2, ndhD, and ndhF coding regions. We established the position of the six species through phylogenic analysis. The complete chloroplast genome sequences of two Fritillaria species will be useful genomics resources for identification of Fritillaria species and for studying the phylogenetic relationship among Fritillaria species within the Liliaceae family.

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