Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications

Raman, Gurusamy; Park, Kyu Tae; Kim, Joohwan; Park, Seon-Joo

doi:10.1186/s12864-020-07219-0

Cited by 27 publications

(17 citation statements)

References 69 publications

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“…In the case of positive selected sites, Magnoliaceae species showed 13 genes with sites under selection; most of these are related to the photosynthetic process ( atpB , ndhD , ndhF , pbf1 , psaA , psaB , and rbcL ). Other studies have argued that positive selection in those genes could be related to differences in the photosynthetic pathways or in the habitat of each species [ 97 , 98 ].…”

Section: Discussionmentioning

confidence: 99%

Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion

Guzmán-Díaz

Núñez

Veltjen

et al. 2022

Plants

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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.

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Section: Discussionmentioning

confidence: 99%

Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion

Guzmán-Díaz

Núñez

Veltjen

et al. 2022

Plants

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“…The ndhC-trnV(UAC)-trnM(CAU) region is composed of two intergenic spaces (ndhC-trnV(UAC) and trnV(UAC)-trnM(CAU)) and an intron (trnV) with an average length of 1416 bp; this region is the most variableamong the four Crataegus plastomes (Figure 5). ndhC-trnV, trnV, and trnV-trnM were suggested by the authors of [28,60] to be high-variability markers that can be used for DNA barcoding and molecular phylogenetic studies. The trnR-atpA is part of the trnG-atpA intergenic marker, which is split into two intergenic regions: trnG-trnR and trnR-atpA.…”

Section: Potential Highly Variable Chloroplast Barcodesmentioning

confidence: 99%

New Insight into the Phylogeny and Taxonomy of Cultivated and Related Species of Crataegus in China, Based on Complete Chloroplast Genome Sequencing

Wang

et al. 2021

Horticulturae

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Hawthorns (Crataegus L.) are one of the most important processing and table fruits in China, due to their medicinal properties and health benefits. However, the interspecific relationships and evolution history of cultivated Crataegus in China remain unclear. Our previously published data showed C. bretschneideri may be derived from the hybridization of C. pinnatifida with C. maximowiczii, and that introgression occurs between C. hupehensis, C. pinnatifida, and C. pinnatifida var. major. In the present study, chloroplast sequences were used to further elucidate the phylogenetic relationships of cultivated Crataegus native to China. The chloroplast genomes of three cultivated species and one related species of Crataegus were sequenced for comparative and phylogenetic analyses. The four chloroplast genomes of Crataegus exhibited typical quadripartite structures and ranged from 159,607 bp (C. bretschneideri) to 159,875 bp (C. maximowiczii) in length. The plastomes of the four species contained 113 genes consisting of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Six hypervariable regions (ndhC-trnV(UAC)-trnM(CAU), ndhA, atpH-atpI, ndhF, trnR(UCU)-atpA, and ndhF-rpl32), 196 repeats, and a total of 386 simple sequence repeats were detected as potential variability makers for species identification and population genetic studies. In the phylogenomic analyses, we also compared the entire chloroplast genomes of three published Crataegus species: C. hupehensis (MW201730.1), C. pinnatifida (MN102356.1), and C. marshallii (MK920293.1). Our phylogenetic analyses grouped the seven Crataegus taxa into two main clusters. One cluster included C. bretschneideri, C. maximowiczii, and C. marshallii, whereas the other included C. hupehensis, C. pinnatifida, and C. pinnatifida var. major. Taken together, our findings indicate that C. maximowiczii is the maternal origin of C. bretschneideri. This work provides further evidence of introgression between C. hupehensis, C. pinnatifida, and C. pinnatifida var. major, and suggests that C. pinnatifida var. major might have been artificially selected and domesticated from hybrid populations, rather than evolved from C. pinnatifida.

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“…Compared with the nuclear genome, the chloroplast genome (CPG) has a small size, low nucleotide substitution rate, single-parental inheritance, and haploid nature, which make it a good option for the analyses of nucleotide diversity and reconstructing phylogenies of closely related species, especially among polyploid taxa [ 13 – 15 ]. Although the structure of the CPG is generally conserved consisting of a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeat regions (IR) [ 16 ], some structural rearrangements have been discovered, including the loss of genes or introns, as well as IR expansions and contractions [ 17 , 18 ]. The comparative and phylogenetic analyses of CPGs have proved an ideal tool for species identification [ 19 ], detecting structural variation [ 20 ], assessing nucleotide diversity [ 21 ], resolving phylogenetic relationships [ 22 ], and reconstructing the evolutionary history [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species

Xie

Zhang

et al. 2022

BMC Genomics

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Background The subgenus Gynopodium belonging to genus Magnolia have high ornamental, economic, and ecological value. Subgenus Gynopodium contains eight species, but six of these species are threatened. No studies to date have characterized the characteristics of the chloroplast genomes (CPGs) within subgenus Gynopodium species. In this study, we compared the structure of CPGs, identified the mutational hotspots and resolved the phylogenetic relationship of subgenus Gynopodium. Results The CPGs of six subgenus Gynopodium species ranged in size from 160,027 bp to 160,114 bp. A total of 131 genes were identified, including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. We detected neither major expansions or contractions in the inverted repeat region, nor rearrangements or insertions in the CPGs of six subgenus Gynopodium species. A total of 300 large repeat sequences (forward, reverse, and palindrome repeats), 847 simple sequence repeats, and five highly variable regions were identified. One gene (ycf1) and four intergenic regions (psbA-trnH-GUG, petA-psbJ, rpl32-trnL-UAG, and ccsA-ndhD) were identified as mutational hotspots by their high nucleotide diversity (Pi) values (≥ 0.004), which were useful for species discrimination. Maximum likelihood and Bayesian inference trees were concordant and indicated that Magnoliaceae consisted of two genera Liriodendron and Magnolia. Six species of subgenus Gynopodium clustered as a monophyletic clade, forming a sister clade with subgenus Yulania (BS = 100%, PP = 1.00). Due to the non-monophyly of subgenus Magnolia, subgenus Gynopodium should be treated as a section of Magnolia. Within section Gynopodium, M. sinica diverged first (posterior probability = 1, bootstrap = 100), followed by M. nitida, M. kachirachirai and M. lotungensis. M. omeiensis was sister to M. yunnanensis (posterior probability = 0.97, bootstrap = 50). Conclusion The CPGs and characteristics information provided by our study could be useful in species identification, conservation genetics and resolving phylogenetic relationships of Magnoliaceae species.

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Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications

Cited by 27 publications

References 69 publications

Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion

Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion

New Insight into the Phylogeny and Taxonomy of Cultivated and Related Species of Crataegus in China, Based on Complete Chloroplast Genome Sequencing

Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species

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