Comparative analysis of microsatellites in chloroplast genomes of lower and higher plants

Abstract Background Gaoben has a long history of application as medicine. There are few records of Liaogaoben in ancient books. The varieties of Ligusticum in practical application are confused. Therefore, it is very important to identify Ligusticum accurately. The phylogenetic position of Ligusticum in Umbelliferae needs to be determined. It is also of great significance to analyze the phylogeny of Ligusticum in Umbelliferae the difference of somatic genome. Methods Chloroplast (cp) genomic DNA was extracted from two species of Ligusticum and sequenced on Hiseq4000 light source. The sequence was assembled into contrags by soapenovo 2.04, aligned with reference genome by blast, and then corrected manually. Genereanation is performed by online dogma tools. The general characteristics of cp genomes of two species were analyzed, and compared with the relative species. The DNA of chloroplasts of higher plants is double stranded covalently closed loop molecule, and its length varies with species. According to the assembly genome sequence of the sequenced samples, combined with the prediction results of the coding genes, the genome of the samples was displayed in circles. After alignment, the evolutionary tree was constructed based on the single nucleotide polymorphism (SNP) of cp genome in 31 species by ML method. Results The whole chloroplast genome of Gaoben and Liaogaoben is 148,515 bp and 148,493 bp, both of which contain IR (IRa and IRb) LSC and SSC. 127 genes have been annotated, including 83 protein coding genes, 8 tRNA and 36 rRNA of all species, and 28 coding genes in IR region. There are six genes in the ATPase subunit of photosynthesis gene group, and there are obvious differences in the types of introns in NADH dehydrogenase subunit between them. In the comparative analysis of Pi value, two significant gene variation points are petG gene and psaL-ycf4 gene. The phylogenetic tree of the whole cp genome of SNP Umbelliferae was constructed, including 28 Umbelliferae and 3 Ligusticum. Conclusions In this study, the cp genomic characteristics of Ligusticum sinense and L. jeholense were identified, which provided a theoretical basis and documentation for the identification and phylogenetic analysis of Ligusticum.

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Characteration and comparative analysis of the whole chloroplast genomes of five common millet (Panicum miliaceum)

Mitochondrial DNA Part B ◽

10.1080/23802359.2020.1866452 ◽

2021 ◽

Vol 6 (3) ◽

pp. 738-744

Author(s):

Xiaoning Cao ◽

Sichen Liu ◽

Zhixin Mu ◽

Zhijun Qiao

Keyword(s):

Comparative Analysis ◽

Panicum Miliaceum ◽

Chloroplast Genomes

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Comparative analysis of chloroplast genomes of cultivars and wild species of sweetpotato (Ipomoea batatas [L.] Lam)

BMC Genomics ◽

10.1186/s12864-021-07544-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Shizhuo Xiao ◽

Pan Xu ◽

Yitong Deng ◽

Xibin Dai ◽

Lukuan Zhao ◽

...

Keyword(s):

Comparative Analysis ◽

Genetic Structure ◽

Chloroplast Genome ◽

Wild Species ◽

Ipomoea Batatas ◽

Nuclear Genome ◽

Ipomoea Trifida ◽

Chloroplast Markers ◽

Chloroplast Genomes ◽

Chloroplast Dna Markers

Abstract Background Sweetpotato (Ipomoea batatas [L.] Lam.) is an important food crop. However, the genetic information of the nuclear genome of this species is difficult to determine accurately because of its large genome and complex genetic background. This drawback has limited studies on the origin, evolution, genetic diversity and other relevant studies on sweetpotato. Results The chloroplast genomes of 107 sweetpotato cultivars were sequenced, assembled and annotated. The resulting chloroplast genomes were comparatively analysed with the published chloroplast genomes of wild species of sweetpotato. High similarity and certain specificity were found among the chloroplast genomes of Ipomoea spp. Phylogenetic analysis could clearly distinguish wild species from cultivars. Ipomoea trifida and Ipomoea tabascana showed the closest relationship with the cultivars, and different haplotypes of ycf1 could be used to distinguish the cultivars from their wild relatives. The genetic structure was analyzed using variations in the chloroplast genome. Compared with traditional nuclear markers, the chloroplast markers designed based on the InDels on the chloroplast genome showed significant advantages. Conclusions Comparative analysis of chloroplast genomes of 107 cultivars and several wild species of sweetpotato was performed to help analyze the evolution, genetic structure and the development of chloroplast DNA markers of sweetpotato.

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Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes

Scientific Reports ◽

10.1038/s41598-021-84705-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Bobby Lim-Ho Kong ◽

Hyun-Seung Park ◽

Tai-Wai David Lau ◽

Zhixiu Lin ◽

Tae-Jin Yang ◽

...

Keyword(s):

Hong Kong ◽

Comparative Analysis ◽

Phylogenetic Relationships ◽

Species Level ◽

The Other ◽

Trna Genes ◽

Protein Coding ◽

Chloroplast Genomes ◽

Plant Group ◽

Ilex Rotunda

AbstractIlex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genomes of all 19 Ilex types that are native to Hong Kong. The genomes are conserved in structure, gene content and arrangement. The chloroplast genomes range in size from 157,119 bp in Ilex graciliflora to 158,020 bp in Ilex kwangtungensis. All these genomes contain 125 genes, of which 88 are protein-coding and 37 are tRNA genes. Four highly varied sequences (rps16-trnQ, rpl32-trnL, ndhD-psaC and ycf1) were found. The number of repeats in the Ilex genomes is mostly conserved, but the number of repeating motifs varies. The phylogenetic relationship among the 19 Ilex genomes, together with eight other available genomes in other studies, was investigated. Most of the species could be correctly assigned to the section or even series level, consistent with previous taxonomy, except Ilex rotunda var. microcarpa, Ilex asprella var. tapuensis and Ilex chapaensis. These species were reclassified; I. rotunda was placed in the section Micrococca, while the other two were grouped with the section Pseudoaquifolium. These studies provide a better understanding of Ilex phylogeny and refine its classification.

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