Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution

Zhang, Shuo; Wang, Jie; Shen, Hongmei; Ai, Bin; Gao, Wei; Zhang, Cui‐Jun; Fei, Qili; Yuan, Daojun; Wu, Zhiqiang; Tembrock, Luke R.; Li, Sen; Gu, Cuihua; Liao, Xuezhu

doi:10.1038/s41598-021-88160-4

Cited by 19 publications

(15 citation statements)

References 83 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…WGS, followed by the use of assembly tools, has resulted in an effective manner to obtain chloroplast genomes for different families of angiosperms [ 13 , 31 , 32 , 33 ], as well as of different Magnoliaceae species [ 40 , 41 , 42 , 44 ]. In this study, the plastomes of 15 Neotropical Magnolia species were assembled through the use of short Illumina reads and the GetOrganelle assembler.…”

Section: Discussionmentioning

confidence: 99%

“…In most plants, this strategy generally results in a much higher proportion of plastome reads compared to other regions of the genome because of the high molarity of these organelles in each cell. This strategy was effective in several plant groups [ 5 , 15 , 28 , 29 , 30 ] and has been applied in studies that use chloroplast genomes to solve evolutionary questions in different angiosperm clades [ 13 , 31 , 32 , 33 ]. Most attention has focused on sequencing crop genomes, and there is little information on wild groups.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion

Guzmán-Díaz

Núñez

Veltjen

et al. 2022

Plants

View full text Add to dashboard Cite

Chloroplast genomes are considered to be highly conserved. Nevertheless, differences in their sequences are an important source of phylogenetically informative data. Chloroplast genomes are increasingly applied in evolutionary studies of angiosperms, including Magnoliaceae. Recent studies have focused on resolving the previously debated classification of the family using a phylogenomic approach and chloroplast genome data. However, most Neotropical clades and recently described species have not yet been included in molecular studies. We performed sequencing, assembly, and annotation of 15 chloroplast genomes from Neotropical Magnoliaceae species. We compared the newly assembled chloroplast genomes with 22 chloroplast genomes from across the family, including representatives from each genus and section. Family-wide, the chloroplast genomes presented a length of about 160 kb. The gene content in all species was constant, with 145 genes. The intergenic regions showed a higher level of nucleotide diversity than the coding regions. Differences were higher among genera than within genera. The phylogenetic analysis in Magnolia showed two main clades and corroborated that the current infrageneric classification does not represent natural groups. Although chloroplast genomes are highly conserved in Magnoliaceae, the high level of diversity of the intergenic regions still resulted in an important source of phylogenetically informative data, even for closely related taxa.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion

Guzmán-Díaz

Núñez

Veltjen

et al. 2022

Plants

View full text Add to dashboard Cite

show abstract

“…), a genus in the family Salicaceae, is widely distributed in most of the Northern Hemisphere due to its rapid growth, stress resistance, and economic importance [ 1 ]. This genus has traditionally been divided into six sections based on leaf, flower, and other characteristics, but five major subclades have been recovered based on recent genetic studies [ 2 , 3 ]. Populus simonii × P. nigra (abbreviated in the text as P. xiaohei ) is an artificial hybrid crossed with P. simonii Carr ( Tacamahaca ) as the maternal plant and P. nigra L. ( Aigeiros ) as the paternal plant [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

Molecular Karyotyping on Populus simonii × P. nigra and the Derived Doubled Haploid

Liu

Wang

Tao

et al. 2021

IJMS

View full text Add to dashboard Cite

The molecular karyotype could represent the basic genetic make-up in a cell nucleus of an organism or species. A doubled haploid (DH) is a genotype formed from the chromosome doubling of haploid cells. In the present study, molecular karyotype analysis of the poplar hybrid Populus simonii × P. nigra (P. xiaohei) and the derived doubled haploids was carried out with labeled telomeres, rDNA, and two newly repetitive sequences as probes by fluorescence in situ hybridization (FISH). The tandem repeats, pPC349_XHY and pPD284_XHY, with high-sequence homology were used, and the results showed that they presented the colocalized distribution signal in chromosomes. For P. xiaohei, pPD284_XHY produced hybridizations in chromosomes 1, 5, 8, and 9 in the hybrid. The combination of pPD284_XHY, 45S rDNA, and 5S rDNA distinctly distinguished six pairs of chromosomes, and the three pairs of chromosomes showed a significant difference in the hybridization between homologous chromosomes. The repeat probes used produced similar FISH hybridizations in the DH; nevertheless, pPD284_XHY generated an additional hybridization site in the telomere region of chromosome 14. Moreover, two pairs of chromosomes showed differential hybridization distributions between homologous chromosomes. Comparisons of the distinguished chromosomes between hybrid and DH poplar showed that three pairs of chromosomes in the DH presented hybridization patterns that varied from those of the hybrid. The No. 8 chromosome in DH and one of the homologous chromosomes in P. xiaohei shared highly similar FISH patterns, which suggested the possibility of intact or mostly partial transfer of the chromosome between the hybrid and DH. Our study will contribute to understanding the genetic mechanism of chromosomal variation in P. xiaohei and derived DH plants.

show abstract

“…6 B). These results indicate that these regions evolve rapidly in the genus Viola , as well as in other related Malpighiales species [ 73 ].…”

Section: Resultsmentioning

confidence: 99%

An integrated study of Violae Herba (Viola philippica) and five adulterants by morphology, chemical compositions and chloroplast genomes: insights into its certified plant origin

Qiao

Wang

et al. 2022

Chin Med

View full text Add to dashboard Cite

Background Viola philippica Cav. is the only original plant for Violae Herba, as described in the Chinese Pharmacopoeia. The quality of this crude drug is affected by several adulterants from congeneric Viola species, and the authentic plant origin of Violae Herba is still controversial. Genome-based identification offers abundant genetic information and potential molecular markers that can be used for the authentication of closely related species. This study aims to investigate the certified origin of Violae Herba and to develop more effective markers for these easily confused species at the genetic level. Methods We compared the morphology and chemical composition of 18 batches of commercial samples and six widespread medicinal Viola plants used as Violae Herba or its substitutes by TLC and HPLC-Triple-TOF–MS/MS analyses. The complete chloroplast genomes of these species were sequenced and analyzed, including the general features, repeat sequences, mutational hotspots and phylogeny. The complete chloroplast genomes used as superbarcodes and some specific barcodes screened from mutational hotspots were tested for their ability to distinguish Viola species. Results A comparative study showed that Violae Herba is a multi-origin traditional Chinese medicine. Commercial decoction pieces and the standard reference drug were mainly derived from V. prionantha, clashing with the record in the Chinese Pharmacopoeia. Chloroplast genome analyses of V. philippica and five adulterants indicated that sequence divergence was relatively low within Viola species. By tree-based approaches, the complete chloroplast genomes showed a better discrimination ability and phylogenetic resolution for each Viola species. These results indicate that the whole chloroplast genomes can be used as superbarcodes to differentiate Viola medicinal plants. More specific DNA barcodes could be further developed from the Viola chloroplast genomes for more efficient and rapid identification of commercial Violae Herba and its adulterants. Conclusions This study has implications for chloroplast genome-based phylogenetic analysis and the authentication of multiple Viola species used as Violae Herba. The legal origin recorded in the Chinese Pharmacopoeia should be further revised to V. prionantha, in line with the commercial Violae Herba in the TCM markets.

show abstract

Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution

Cited by 19 publications

References 83 publications

Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion

Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion

Molecular Karyotyping on Populus simonii × P. nigra and the Derived Doubled Haploid

An integrated study of Violae Herba (Viola philippica) and five adulterants by morphology, chemical compositions and chloroplast genomes: insights into its certified plant origin

Contact Info

Product

Resources

About