Dataset Information

Characterization of the complete chloroplast genome of the Hongkong kumquat (Fortunella hindsii Swingle).

ABSTRACT: Hongkong qumquat (Fortunella hindsii Swingle) is a wild citrus species native to China. In this study, we firstly reporteded its complete chloroplast genome using BGISEQ-500 sequencing. The chloroplast genome is 160,145 bp in size, containing a large single copy region (87,467 bp), a small single copy region (18,730 bp), and a pair of IR regions (26,974 bp). The chloroplast genome contains 112 unique genes, including 79 protein-coding genes, 29 tRNAs, and 4 rRNAs. Phylogenetic maximum-likelihood analysis indicated that F. hindsii is closely related to Citrus species. The complete chloroplast genome would be subsequently used for citrus species researches.

SUBMITTER: Xu SR

PROVIDER: S-EPMC7706910 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Characterization of the complete chloroplast genome of the Hongkong kumquat (<i>Fortunella hindsii</i> Swingle).

Xu Shi-Rong SR Zhang Yong-Yan YY Liu Fan F Tian Na N Pan Dong-Ming DM Bei Xue-Jun XJ Cheng Chun-Zhen CZ

Mitochondrial DNA. Part B, Resources 20190717 2

Hongkong qumquat (<i>Fortunella hindsii</i> Swingle) is a wild citrus species native to China. In this study, we firstly reporteded its complete chloroplast genome using BGISEQ-500 sequencing. The chloroplast genome is 160,145 bp in size, containing a large single copy region (87,467 bp), a small single copy region (18,730 bp), and a pair of IR regions (26,974 bp). The chloroplast genome contains 112 unique genes, including 79 protein-coding genes, 29 tRNAs, and 4 rRNAs. Phylogenetic maximum-lik ...[more]

PMID: 33365649

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Project description:Recently, the systematic status of Fortunella Swingle and its taxonomy has attracted much attention. Flora of China incorporates Fortunella into Citrus Linn. and treats all species of the traditional Fortunella as one species, namely Citrus japonica (Thunb.) Swingle. Furthermore, F. venosa (Champ. ex Benth.) C. C. Huang and F. hindsii (Champ. ex Benth.) Swingle are currently considered as synonyms of C. japonica. In this paper, morphological, palynological, and phylogenetic analyses were used to systematically explore the taxonomic status of traditional Fortunella. The key morphological features that differed among the Fortunella species were the leaf and the petiole hence could be key in its taxonomic classification of the species. Additionally, pollen morphological analysis based on the pollen size, germination grooves, polar, and equatorial axes also supported the separation of the species. The results of the phylogenetic analysis showed that each of the three species clustered separately, hence strongly supporting the conclusion of independent species. In addition, the phylogenetic analysis showed that the two genera clustered closely together hence our results support the incorporation of Fortunella into Citrus. Based on the above, this article has revised the classification of the traditional Fortunella and determined that this genus has three species, namely; F. venosa, F. hindsii, and F. japonica. F. venosa and F. hindsii are placed in the Citrus as separate species, and their species names still use the previous specific epithet. The revised scientific names of the new combinations of F. venosa and F. hindsii are as follows: Citrus venosa (Champ. ex Benth.) K. M. Liu, X. Z. Cai, and G. W. Hu, comb. nov. and Citrus hindsii (Champ. ex Benth.) K. M. Liu, G. W. Hu, and X. Z. Cai, comb. nov. F. venosa is the original species of Fortunella, F. venosa and F. hindsii are both listed as the second-class key protected wild plants in China. Therefore, the establishment of the taxonomic status of F. venosa and F. hindsii not only deepens our understanding, importance, and the complexity of the systematic classification of Fortunella, but is also significant for global biodiversity conservation, genetic resources for breeding purposes, and population genetics.

Project description:Erigeron breviscapus is a famous medicinal plant. However, the limited chloroplast genome information of E. breviscapus, especially for the chloroplast DNA sequence resources, has hindered the study of E. breviscapus chloroplast genome transformation. Here, the complete chloroplast (cp) genome of E. breviscapus was reported. This genome was 152,164bp in length, included 37.2% GC content and was structurally arranged into two 24,699bp inverted repeats (IRs) and two single-copy areas. The sizes of the large single-copy region and the small single-copy region were 84,657 and 18,109bp, respectively. The E. breviscapus cp genome consisted of 127 coding genes, including 83 protein coding genes, 36 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. For those genes, 95 genes were single copy genes and 16 genes were duplicated in two inverted regions with seven tRNAs, four rRNAs, and five protein coding genes. Then, genomic DNA of E. breviscapus was used as a template, and the endogenous 5' and 3' flanking sequences of the trnI gene and trnA gene were selected as homologous recombinant fragments in vector construction and cloned through PCR. The endogenous 5' flanking sequences of the psbA gene and rrn16S gene, the endogenous 3' flanking sequences of the psbA gene, rbcL gene, and rps16 gene and one sequence element from the psbN-psbH chloroplast operon were cloned, and certain chloroplast regulatory elements were identified. Two homologous recombination fragments and all of these elements were constructed into the cloning vector pBluescript SK (+) to yield a series of chloroplast expression vectors, which harbored the reporter gene EGFP and the selectable marker aadA gene. After identification, the chloroplast expression vectors were transformed into Escherichia coli and the function of predicted regulatory elements was confirmed by a spectinomycin resistance test and fluorescence intensity measurement. The results indicated that aadA gene and EGFP gene were efficiently expressed under the regulation of predicted regulatory elements and the chloroplast expression vector had been successfully constructed, thereby providing a solid foundation for establishing subsequent E. breviscapus chloroplast transformation system and genetic improvement of E. breviscapus.

Dataset Information

Characterization of the complete chloroplast genome of the Hongkong kumquat (Fortunella hindsii Swingle).

Publications

Characterization of the complete chloroplast genome of the Hongkong kumquat (<i>Fortunella hindsii</i> Swingle).

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