Comparative analyses of six complete chloroplast genomes from the genus Cupressus and Juniperus (Cupressaceae)

Chen, Can; Xia, Xi; Peng, Jingyu; Wang, Dawei

doi:10.1016/j.gene.2022.146696

Cited by 6 publications

(15 citation statements)

References 44 publications

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“…Despite the strong similarity of these seven pt genomes, several highly divergent regions, including accD , clpP-infA , matK , matK-ndhA , ycf1 , ycf2 , and ycf3 , were identified. In particular, the specific regions of accD and ycf2 were characterized by high levels of nucleotide diversity ( Fig 2 ), confirming the results reported in other studies of Juniperus species [ 54 , 72 ]. Therefore, the highlighted sequence regions of accD and ycf2 could be used as candidate molecular markers for DNA barcoding and phylogenetic analyses.…”

Section: Discussionsupporting

confidence: 89%

“…Similar to in other studies [ 44 – 47 ], the rps12 and ycf3 genes included two intronic regions, trnI-CAU , and trnQ-UUG were duplicated in the Juniperus pt genomes. The sequenced genomes in this study were characterized by a lack of inverted repeats, like in other species from the Cupressaceae family [ 45 – 47 , 54 ]. This contrasts with the majority of angiosperm chloroplast genomes that are characterized by two inverted repeats, which divide the genome into large and small single-copy regions [ 69 ].…”

Section: Discussionmentioning

confidence: 99%

“…pingii , and J . procumbens [ 44 , 45 , 48 , 54 ]. Despite the strong similarity of these seven pt genomes, several highly divergent regions, including accD , clpP-infA , matK , matK-ndhA , ycf1 , ycf2 , and ycf3 , were identified.…”

Section: Discussionmentioning

confidence: 99%

“…Despite its slower evolution and lack of recombination, it has variable regions, which can potentially resolve the phylogenetic relationships at the family or the genus level [ 80 ]. Unfortunately, previous studies in Juniperus used sequences of short DNA regions in nuclear and plastid genomes, which may have potentially affected the precision of the taxonomic relationships [ 18 , 54 ]. Therefore, we reconstructed a phylogenetic tree using the concatenated sequences of 82 protein-coding genes from 26 samples of different Juniperus species, including seven species from Kazakhstan and an outgroup ( Fig 3 ).…”

Section: Discussionmentioning

confidence: 99%

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Comparative analysis of chloroplast genomes of seven Juniperus species from Kazakhstan

Almerekova,

Yermagambetova,

Jumanov

et al. 2024

PLoS ONE

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Juniperus species are shrubs or trees in the family Cupressaceae that play an important role in forest ecosystems. In this study, we report the complete sequences of the plastid (pt) genomes of five Juniperus species collected in Kazakhstan (J. communis, J. sibirica, J. pseudosabina, J. semiglobosa, and J. davurica). The sequences of the pt genomes of the five species were annotated in addition to two full pt genome sequences from J. sabina and J. seravschanica, which we have previously reported. The pt genome sequences of these seven species were compared to the pt genomes of Juniperus species available in the public NCBI database. The total length of the pt genomes of Juniperus species, including previously published pt genome data, ranged from 127,469 bp (J. semiglobosa) to 128,097 bp (J. communis). Each Juniperus plastome consisted of 119 genes, including 82 protein-coding genes, 33 transfer RNA and 4 ribosomal RNA genes. Among the identified genes, 16 contained one or two introns, and 2 tRNA genes were duplicated. A comparative assessment of pt genome sequences suggested the identification of 1145 simple sequence repeat markers. A phylogenetic tree of 26 Juniperus species based on the 82 protein-coding genes separated the Juniperus samples into two major clades, corresponding to the Juniperus and Sabina sections. The analysis of pt genome sequences indicated that accD and ycf2 were the two most polymorphic genes. The phylogenetic evaluation of 26 Juniperus species using these two genes confirmed that they can be efficiently used as DNA barcodes for phylogenetic analyses in the genus. The sequenced plastomes of these Juniperus species have provided a large amount of genetic data that will be valuable for future genomic studies of this genus.

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Section: Discussionsupporting

confidence: 89%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Comparative analysis of chloroplast genomes of seven Juniperus species from Kazakhstan

Almerekova,

Yermagambetova,

Jumanov

et al. 2024

PLoS ONE

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“…For example, deletion of one IR region in cpDNA was found in gymnosperms and legumes. 21,22 Gene deletion or pseudogenization was more common in heterotrophic species such as parasite and mycoheterotrophic plants. 23,24 Additionally, sequence data of cpDNA were applied to reconstruct the phylogeny of land plants.…”

Section: Introductionmentioning

confidence: 99%

New Insights Into The Evolution of Chloroplast Genomes in Ochna Species (Ochnaceae, Malpighiales)

Nhat Nam,

Hoang Danh,

Minh Thiet

et al. 2023

Evol Bioinform Online

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Ochnaceae DC. includes more than 600 species that exhibit potential values for environmental ecology, ornamental, pharmaceutical, and timber industries. Although studies on phylogeny and phytochemicals have been intensively conducted, chloroplast genome data of Ochnaceae species have not been fully explored. In this study, the next-generation sequencing method was used to sequence the chloroplast genomes of Ochna integerrima and Ochna serrulata which were 157 329 and 157 835 bp in length, respectively. These chloroplast genomes had a quadripartite structure and contained 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. Comparative analysis revealed 8 hypervariable regions, including trnK_UUU-trnQ_UUG, rpoB-psbM, trnS_GGA-rps4, accD-psaI, rpl33-rps18, rpl14-rpl16, ndhF-trnL_UAG, and rps15-ycf1 among 6 Ochnaceae taxa. Additionally, there were shared and unique repeats among 6 examined chloroplast genomes. The notable changes were the loss of rpl32 in Ochna species and the deletion of rps16 exon 2 in O. integerrima compared to other taxa. This study is the first comprehensive comparative genomic analysis of complete chloroplast genomes of Ochna species and related taxa in Ochnaceae. Consequently, the current study provides initial results for further research on genomic evolution, population genetics, and developing molecular markers in Ochnaceae and related taxa.

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Full-length chloroplast genome of Vincetoxicum atratum and phylogeny of the genus Vincetoxicum

Ren,

Jiang,

et al. 2024

Genet Resour Crop Evol

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Comparative analyses of six complete chloroplast genomes from the genus Cupressus and Juniperus (Cupressaceae)

Cited by 6 publications

References 44 publications

Comparative analysis of chloroplast genomes of seven Juniperus species from Kazakhstan

Comparative analysis of chloroplast genomes of seven Juniperus species from Kazakhstan

New Insights Into The Evolution of Chloroplast Genomes in Ochna Species (Ochnaceae, Malpighiales)

Full-length chloroplast genome of Vincetoxicum atratum and phylogeny of the genus Vincetoxicum

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