Plastome structure and phylogenetic relationships of Styracaceae (Ericales)

Cai, Xiu-Lian; Landis, Jacob B.; Wang, Hongxin; Wang, Jianhua; Zhu, Zhi‐Xin; Wang, Huafeng

doi:10.1186/s12862-021-01827-4

Cited by 20 publications

(20 citation statements)

References 70 publications

(73 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, rpoC mainly encodes the β subunit of RNA polymerase. In this study, rpoC1 and rpoC2 were under positive selection, which may lead to alterations in cell wall metabolism, possibly as a result of altered transcription (Bisson et al, 2012;Cai et al, 2021). ACCase catalyzes malonyl-CoA formation from acetyl-CoA and bicarbonate in the first committed step of de novo fatty acid synthesis (Rawsthorne, 2002).…”

Section: Adaptive Selectionmentioning

confidence: 85%

Comparative Chloroplast Genomes of Zosteraceae Species Provide Adaptive Evolution Insights Into Seagrass

et al. 2021

View full text Add to dashboard Cite

Seagrasses are marine flowering plants found in tropical and sub-tropical areas that live in coastal regions between the sea and land. All seagrass species evolved from terrestrial monocotyledons, providing the opportunity to study plant adaptation to sea environments. Here, we sequenced the chloroplast genomes (cpGenomes) of three Zostera species, then analyzed and compared their cpGenome structures and sequence variations. We also performed a phylogenetic analysis using published seagrass chloroplasts and calculated the selection pressure of 17 species within seagrasses and nine terrestrial monocotyledons, as well as estimated the number of shared genes of eight seagrasses. The cpGenomes of Zosteraceae species ranged in size from 143,877 bp (Zostera marina) to 152,726 bp (Phyllospadix iwatensis), which were conserved and displayed similar structures and gene orders. Additionally, we found 17 variable hotspot regions as candidate DNA barcodes for Zosteraceae species, which will be helpful for studying the phylogenetic relationships and interspecies differences between seagrass species. Interestingly, nine genes had positive selection sites, including two ATP subunit genes (atpA and atpF), two ribosome subunit genes (rps4 and rpl20), two DNA-dependent RNA polymerase genes (rpoC1 and rpoC2), as well as accD, clpP, and ycf2. These gene regions may have played key roles in the seagrass adaptation to diverse environments. The Branch model analysis showed that seagrasses had a higher rate of evolution than terrestrial monocotyledons, suggesting that seagrasses experienced greater environmental pressure. Moreover, a branch-site model identified positively selected sites (PSSs) in ccsA, suggesting their involvement in the adaptation to sea environments. These findings are valuable for further investigations on Zosteraceae cpGenomes and will serve as an excellent resource for future studies on seagrass adaptation to sea environments.

show abstract

Section: Adaptive Selectionmentioning

confidence: 85%

Comparative Chloroplast Genomes of Zosteraceae Species Provide Adaptive Evolution Insights Into Seagrass

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Of the six subgenus Gynopodium species, the overall GC content of CPGs was approximately 39.3%, which is similar to that of other Magnolia species, such as M. shiluensis [ 32 ] , M. grandiflora [ 35 ] , and M. zenii [ 36 ] but higher than the average GC content (35%) of most angiosperms [ 37 ]. The GC content also varies among different regions of the CPG [ 34 , 38 ]. IR region (43.2%) contains significantly higher GC content than that of the LSC (38%) and SSC regions (34.3%) (Table S 1 ), which can attribute to the high GC content in the ribosomal RNA (rRNA) genes in IR region (Fig.…”

Section: Discussionmentioning

confidence: 99%

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

Xie

Zhang

et al. 2022

BMC Genomics

View full text Add to dashboard Cite

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.

show abstract

“…Ribosomal genes participate in the synthesis of the ribosomal complex, which participates in the proteins required for normal cell function ( Depamphilis and Palmer, 1990 ; Wang et al, 2019 ). The photosynthetic genes and NADH dehydrogenase genes participate in the synthesis of photosynthetic system II and chloroplast NADH dehydrogenase complex, which are involved in photosynthesis ( Sazanov et al, 1998 ; Cai et al, 2021 ). It is speculated that these genes related to photosynthesis, such as psbF , psbL , psbD , ndhA , and ndhF , may be the result of chloroplast genes transferred to mitochondria in R. × pulchrum .…”

Section: Discussionmentioning

confidence: 99%

“…(B) PCR products detection. (The P1∼P6 sites located in 21,232,56,637,63,979,115,230,125,853,and 145,493 Cai et al, 2021). It is speculated that these genes related to photosynthesis, such as psbF, psbL, psbD, ndhA, and ndhF, may be the result of chloroplast genes transferred to mitochondria in R. × pulchrum.…”

Section: Gene Transfer Between Mitochondrial and Chloroplast Genomesmentioning

confidence: 99%

Characterization, comparative phylogenetic, and gene transfer analyses of organelle genomes of Rhododendron × pulchrum

Jia

Li²,

Cheng

et al. 2022

Front. Plant Sci.

View full text Add to dashboard Cite

Rhododendron × pulchrum, an important horticultural species, is widely distributed in Europe, Asia, and North America. To analyze the phylogenetic and organelle genome information of R. × pulchrum and its related species, the organelle genome of R. × pulchrum was sequenced and assembled. The complete mitochondrial genome showed lineage DNA molecules, which were 816,410 bp long and contained 64 genes, namely 24 transfer RNA (tRNA) genes, 3 ribosomal RNA (rRNA) genes, and 37 protein-coding genes. The chloroplast genome of R. × pulchrum was reassembled and re-annotated; the results were different from those of previous studies. There were 42 and 46 simple sequence repeats (SSR) identified from the mitochondrial and chloroplast genomes of R. × pulchrum, respectively. Five genes (nad1, nad2, nad4, nad7, and rps3) were potentially useful molecular markers. The R. × pulchrum mitochondrial genome collinear alignment among five species of the Ericaceae showed that the mitochondrial genomes of these related species have a high degree of homology with R. × pulchrum in this gene region, and the most conservative genes were trnC-GCA, trnD-GUC, trnM-CAU, trnN-GUU, trnY-GUA, atp4, nad4, nad2, nad5, ccmC, and rrn26. The phylogenetic trees of mitochondrial genome showed that R. simsii was a sister to R. × pulchrum. The results verified that there was gene rearrangement between R. × pulchrum and R. simsii mitochondrial genomes. The codon usage bias of 10 Ericaceae mitochondrial genes and 7 Rhododendron chloroplast genes were influenced by mutation, while other genes codon usages had undergone selection. The study identified 13 homologous fragments containing gene sequences between the chloroplast and mitochondrial genomes of R. × pulchrum. Overall, our results illustrate the organelle genome information could explain the phylogenetics of plants and could be used to develop molecular markers and genetic evolution. Our study will facilitate the study of population genetics and evolution in Rhododendron and other genera in Ericaceae.

show abstract

Plastome structure and phylogenetic relationships of Styracaceae (Ericales)

Cited by 20 publications

References 70 publications

Comparative Chloroplast Genomes of Zosteraceae Species Provide Adaptive Evolution Insights Into Seagrass

Comparative Chloroplast Genomes of Zosteraceae Species Provide Adaptive Evolution Insights Into Seagrass

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

Characterization, comparative phylogenetic, and gene transfer analyses of organelle genomes of Rhododendron × pulchrum

Contact Info

Product

Resources

About