Complete Chloroplast Genome Sequence of Broomcorn Millet (Panicum miliaceum L.) and Comparative Analysis with Other Panicoideae Species

Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated cereals worldwide, holding significant agricultural, historical, and evolutionary importance. However, our genomic knowledge of it is rather limited at present, hampering further genetic and evolutionary studies. Here, we sequenced and assembled the chloroplast genome (cp) of broomcorn millet and compared it with five other Panicoideae species. Results showed that the cp genome of broomcorn millet was 139,826 bp in size, with a typical quadripartite structure. In total, 108 genes were annotated and 18 genes were duplicated in the IR (inverted region) region, which was similar to other Panicoideae species. Comparative analysis showed a rather conserved genome structure between them, with three common regions. Furthermore, RNA editing, codon usage, and expansion of the IR, as well as simple sequence repeat (SSR) elements, were systematically investigated and 13 potential DNA markers were developed for Panicoideae species identification. Finally, phylogenetic analysis implied that broomcorn millet was a sister species to Panicum virgatum within the tribe Paniceae, and supported a monophyly of the Panicoideae. This study has reported for the first time the genome organization, gene content, and structural features of the chloroplast genome of broomcorn millet, which provides valuable information for genetic and evolutionary studies in the genus Panicum and beyond.

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Comparative analysis of drought-responsive physiological and transcriptome in broomcorn millet (Panicum miliaceum L.) genotypes with contrasting drought tolerance

Industrial Crops and Products ◽

10.1016/j.indcrop.2021.114498 ◽

2022 ◽

Vol 177 ◽

pp. 114498

Author(s):

Yuhao Yuan ◽

Long Liu ◽

Yongbin Gao ◽

Qinghua Yang ◽

Kongjun Dong ◽

...

Keyword(s):

Comparative Analysis ◽

Drought Tolerance ◽

Panicum Miliaceum ◽

Broomcorn Millet

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Complete sequence of the chloroplast genome from pear (Pyrus pyrifolia): genome structure and comparative analysis

Tree Genetics & Genomes ◽

10.1007/s11295-012-0469-8 ◽

2012 ◽

Vol 8 (4) ◽

pp. 841-854 ◽

Cited By ~ 47

Author(s):

Shingo Terakami ◽

Yuichiro Matsumura ◽

Kanako Kurita ◽

Hiroyuki Kanamori ◽

Yuichi Katayose ◽

...

Keyword(s):

Comparative Analysis ◽

Chloroplast Genome ◽

Genome Structure ◽

Complete Sequence ◽

Pyrus Pyrifolia

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Comparative Chloroplast Genome Analysis of Medicinally Important Veratrum (Melanthiaceae) in China: Insights into Genomic Characterization and Phylogenetic Relationships

10.21203/rs.3.rs-117897/v1 ◽

2020 ◽

Author(s):

Ying-min Zhang ◽

Li-jun Han ◽

Ying-Ying Liu ◽

Cong-wei Yang ◽

Xing Tian ◽

...

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Blood Stasis ◽

Genome Comparison ◽

Phylogenetic Study ◽

Species Classification ◽

Chloroplast Genomes ◽

Genomic Characterization ◽

Cp Genome

Abstract Background: Veratrum is a genus of perennial herbs that are widely used as traditional Chinese medicine for emetic, resolving blood stasis and relieve pain. However, the species classification and the phylogenetic relationship of the genus Veratrum have long been controversial due to the complexity of morphological variations. Knowledge on the infrageneric relationships of the genus Veratrum can be obtained from their chloroplast genome sequences and increase the taxonomic and phylogenetic resolution.Methods: Total DNA was extracted from ten species of Veratrum and subjected to next-generation sequencing. The cp genome was assembled by NOVOPlasty. Genome annotation was conducted using the online tool DOGMA and subsequently corrected by Geneious Prime. Then, genomic characterization of the Veratrum plastome and genome comparison with closely related species was analyzed by corresponding software. Moreover, phylogenetical trees were reconstructed, based on the 29 plastomes by maximum likelihood (ML) and Bayesian inference (BI) methods.Results: The whole plastomes of Veratrum species possess a typical quadripartite structure, ranging from 151,597 bp to 153,711 bp in size and comprising 135 genes. The gene order, content, and genome structure were nearly identical with a few exceptions across the Veratrum chloroplast genomes. The total number of simple sequence repeats (SSRs) ranged from 31 to 35, and of large sequence repeats (LSRs) ranged from 65 to 71. Seven highly divergent regions (rpoB-trnC, trnT-trnL, trnS-trnG, psbC-psbZ, psbI, ycf1, and ndhF) were identified that can be used for DNA barcoding in the genus of Veratrum. Phylogenetic analyses based on 29 plastomes strongly supported the monophyly of Veratrum. The circumscription and relationships of infrageneric taxa of Veratrum were well evaluated with high resolutions. Conclusions: Our study identified and analyzed the cp genome features of ten Veratrum species, and suggested high effectivity of chloroplast complete genome in resolving generic circumscription in Veratrum. These results will facilitate the identification, taxonomy, and utilization of Veratrum plants as well as the phylogenetic study of Melanthiaceae simultaneously.

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Complete Chloroplast Genome Sequence of Justicia flava: Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae

BioMed Research International ◽

10.1155/2019/4370258 ◽

2019 ◽

Vol 2019 ◽

pp. 1-17 ◽

Cited By ~ 4

Author(s):

Samaila S. Yaradua ◽

Dhafer A. Alzahrani ◽

Enas J. Albokhary ◽

Abidina Abba ◽

Abubakar Bello

Keyword(s):

Comparative Analysis ◽

Chloroplast Genome ◽

Phylogenetic Relationships ◽

Inverted Repeat ◽

Gc Content ◽

Single Copy ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Protein Coding Genes ◽

Cp Genome

The complete chloroplast genome of J. flava, an endangered medicinal plant in Saudi Arabia, was sequenced and compared with cp genome of three Acanthaceae species to characterize the cp genome, identify SSRs, and also detect variation among the cp genomes of the sampled Acanthaceae. NOVOPlasty was used to assemble the complete chloroplast genome from the whole genome data. The cp genome of J. flava was 150, 888bp in length with GC content of 38.2%, and has a quadripartite structure; the genome harbors one pair of inverted repeat (IRa and IRb 25, 500bp each) separated by large single copy (LSC, 82, 995 bp) and small single copy (SSC, 16, 893 bp). There are 132 genes in the genome, which includes 80 protein coding genes, 30 tRNA, and 4 rRNA; 113 are unique while the remaining 19 are duplicated in IR regions. The repeat analysis indicates that the genome contained all types of repeats with palindromic occurring more frequently; the analysis also identified total number of 98 simple sequence repeats (SSR) of which majority are mononucleotides A/T and are found in the intergenic spacer. The comparative analysis with other cp genomes sampled indicated that the inverted repeat regions are conserved than the single copy regions and the noncoding regions show high rate of variation than the coding region. All the genomes have ndhF and ycf1 genes in the border junction of IRb and SSC. Sequence divergence analysis of the protein coding genes showed that seven genes (petB, atpF, psaI, rpl32, rpl16, ycf1, and clpP) are under positive selection. The phylogenetic analysis revealed that Justiceae is sister to Ruellieae. This study reported the first cp genome of the largest genus in Acanthaceae and provided resources for studying genetic diversity of J. flava as well as resolving phylogenetic relationships within the core Acanthaceae.

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