Characterization of the complete chloroplast genome of <i>Allium kingdonii</i>

Yang, Xin; Xie, Deng-Feng; Zhou, Song‐Dong; He, Xing‐Jin

doi:10.1080/23802359.2019.1573118

Cited by 4 publications

(1 citation statement)

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“…The complete chloroplast (cp) genomes are reliable elements for deducing phylogeny and evolutionary history deriving from highly conserved gene structure and gene content, and the cp genomes are short of recombination with low mutation rate 8 . Recently, many cp genomes have been extensively applied for phylogenetic reconstruction, and especially in Allium species [9][10][11][12][13][14][15][16][17] . However, these researches were carried out according to a particular section.…”

Section: Introductionmentioning

confidence: 99%

The complete chloroplast genome of Allium mongolicum: insights into comparative and phylogenetic analyses with genus Allium

Jin

Zhang

Liu

et al. 2022

Preprint

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Allium mongolicum Regel is a wild and sandy vegetable with unique flavours. In this study, a complete chloroplast (cp) genome of A. mongolicum was obtained (Genbank accession number: OM630416), and contained 153,609 base pairs with the GC ratio as 36.8%. 130 genes were annotated including 84 protein-coding genes, 38 tRNA, and 8 rRNA genes. The large single-copy (LSC) region was 82,644 bp, and a small single-copy (SSC) region was 18,049 bp, which were separated by two inverted repeats (IRs, including IRa and IRb) of 26,458 bp. Comparative genome analyses of 55 Allium species suggested that genomic structure of genus Allium was conserved, and LSC and SSC regions were outstanding with high variability. Among them, more divergent loci were in the SSC region covering ycf1-rrn4.5 and ndhF-ccsA. Phylogenetic analysis on cp genomes of 55 Allium determined that all members were clustered into 13 clades with strong section-specificity, and A. mongolicum had close relationship with A. senescens. Corresponding analyses of four protein-coding genes (ycf1, ndhF, rpl32, and ccsA) in aforementioned divergent loci confirmed that ycf1 was finally chosen as the candidate gene for species identification and evolutionary classification of genus Allium. These data provide valuable genetic resources for future research on Allium.

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Section: Introductionmentioning

confidence: 99%

The complete chloroplast genome of Allium mongolicum: insights into comparative and phylogenetic analyses with genus Allium

Jin

Zhang

Liu

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Allium mongolicum

Jin¹,

Zhang²,

Liu³

et al. 2022

Sci Rep

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Allium mongolicum Regel is a wild and sandy vegetable with unique flavours. In this study, a complete chloroplast (cp) genome of A. mongolicum was obtained (Genbank accession number: OM630416), and contained 153,609 base pairs with the GC ratio as 36.8%. 130 genes were annotated including 84 protein-coding genes, 38 tRNA, and 8 rRNA genes. The large single-copy (LSC) region was 82,644 bp, and a small single-copy (SSC) region was 18,049 bp, which were separated by two inverted repeats (IRs, including IRa and IRb) of 26,458 bp. Comparative genome analyses of 55 Allium species suggested that genomic structure of genus Allium was conserved, and LSC and SSC regions were outstanding with high variability. Among them, more divergent loci were in the SSC region covering ycf1-rrn4.5 and ndhF-ccsA. Phylogenetic analysis on cp genomes of 55 Allium determined that all members were clustered into 13 clades, and A. mongolicum had close relationship with A. senescens. Corresponding analyses of four protein-coding genes (ycf1, ndhF, rpl32, and ccsA) in aforementioned divergent loci confirmed that ycf1 was finally chosen as the candidate gene for species identification and evolutionary classification of genus Allium. These data provide valuable genetic resources for future research on Allium.

show abstract