The complete chloroplast DNA sequence of Trapa maximowiczii Korsh. (Trapaceae), and comparative analysis with other Myrtales species

Xue, Zhi-Qing; Xue, Jianhua; Victorovna, Kryukova Maria; Ma, Keping

doi:10.1016/j.aquabot.2017.09.003

Cited by 17 publications

(20 citation statements)

References 55 publications

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“…Interestingly, in the current study, the intron of rpl2 was detected in all families in Saxifragales, except for 13 species from the examined 8 genera representing the major lineages of Saxifragaceae, as shown in Table S1, which indicates an early loss of this intron within this lineage. Besides Saxifragaceae, nine other independent losses of rpl2 intron were reported in dicotyledons [62,63,64,65,66,67,68,69,70,71,72,73,74,75]. The two most probable mechanisms of loss of the rpl2 intron are homologous recombination and gene conversion [64,76,77].…”

Section: Resultsmentioning

confidence: 99%

Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales

Ding

Zhu

Dong

et al. 2019

Plants

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The genus Sedum, with about 470 recognized species, is classified in the family Crassulaceae of the order Saxifragales. Phylogenetic relationships within the Saxifragales are still unresolved and controversial. In this study, the plastome of S. plumbizincicola was firstly presented, with a focus on the structural analysis of rrn operon and phylogenetic implications within the order Saxifragaceae. The assembled complete plastome of S. plumbizincicola is 149,397 bp in size, with a typical circular, double-stranded, and quadripartite structure of angiosperms. It contains 133 genes, including 85 protein-coding genes (PCGs), 36 tRNA genes, 8 rRNA genes, and four pseudogenes (one ycf1, one rps19, and two ycf15). The predicted secondary structure of S. plumbizincicola 16S rRNA includes three main domains organized in 74 helices. Further, our results confirm that 4.5S rRNA of higher plants is associated with fragmentation of 23S rRNA progenitor. Notably, we also found the sequence of putative rrn5 promoter has some evolutionary implications within the order Saxifragales. Moreover, our phylogenetic analyses suggested that S. plumbizincicola had a closer relationship with S. sarmentosum than S. oryzifolium, and supported the taxonomic revision of Phedimus. Our findings of the present study will be useful for further investigation of the evolution of plastid rRNA operon and phylogenetic relationships within Saxifragales.

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Section: Resultsmentioning

confidence: 99%

Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales

Ding

Zhu

Dong

et al. 2019

Plants

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“…Based on the comparison of the cp genomes among six important sugarcane hybrids, including NCo310, SP80-3280, Q155, RB867515, Q165 and RB72454, and two ancestor species S. officinarum (Badila) and S. spontaneum (Yunnan 83-184), highly conserved genome structures were observed, which are similar to other plant species in different genera [2,3,29,47] or in different families [7,11,27,48,49], while the length is divergent among different accessions. Based on the previous reports [6,27,28,29], GenBank information (Accessions:NC_035224.1; LS975131.1; LN849912.1; LN849914.1; LN896359.1) and two species sequenced in this study, the complete cp genome sequences from 141,151 bp to 141,348 bp among these 11 accessions including the above six sugarcane hybrids and five sugarcane ancestor accessions (Table 6).…”

Section: Discussionmentioning

confidence: 99%

Comparative Analysis of two Sugarcane Ancestors Saccharum officinarum and S. spontaneum based on Complete Chloroplast Genome Sequences and Photosynthetic Ability in Cold Stress

Gao

et al. 2019

IJMS

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Polyploid Saccharum with complex genomes hindered the progress of sugarcane improvement, while their chloroplast genomes are much smaller and simpler. Chloroplast (cp), the vital organelle, is the site of plant photosynthesis, which also evolves other functions, such as tolerance to environmental stresses. In this study, the cp genome of two sugarcane ancestors Saccharum officinarum and S. spontaneum were sequenced, and genome comparative analysis between these two species was carried out, together with the photosynthetic ability. The length is 141,187 bp for S. officinarum and that is 7 bp longer than S. spontaneum, with the same GC content (38.44%) and annotated gene number (134), 13 with introns among them. There is a typical tetrad structure, including LSC, SSC, IRb and IRa. Of them, LSC and IRa/IRb are 18 bp longer and 6 bp shorter than those in S. spontaneum (83,047 bp and 22,795 bp), respectively, while the size of SSC is same (12,544 bp). Five genes exhibit contraction and expansion at the IR junctions, but only one gene ndhF with 29 bp expansion at the border of IRb/SSC. Nucleotide diversity (Pi) based on sliding window analysis showed that the single copy and noncoding regions were more divergent than IR- and coding regions, and the variant hotspots trnG-trnM, psbM-petN, trnR-rps14, ndhC-trnV and petA-psbJ in the LSC and trnL-ccsA in the SSC regions were detected, and petA-psbJ with the highest divergent value of 0.01500. Genetic distances of 65 protein genes vary from 0.00000 to 0.00288 between two species, and the selective pressure on them indicated that only petB was subjected to positive selection, while more genes including rpoC2, rps3, ccsA, ndhA, ndhA, psbI, atpH and psaC were subjected to purifying or very strong purifying selection. There are larger number of codons in S. spontaneum than that in S. officinarum, while both species have obvious codon preference and the codons with highest-(AUG) and lowest frequency (AUA) are same. Whilst, the most abundant amino acid is leucine in both S. officinarum and S. spontaneum, with number of 2175 (10.88% of total) and 2228 (10.90% of total) codons, respectively, and the lowest number is cysteine, with only 221 (1.105%) and 224 (1.096%), respectively. Protein collinearity analysis showed the high collinearity though several divergences were present in cp genomes, and identification of simple sequence repeats (SSRs) were included in this study. In addition, in order to compare cold tolerance and explore the expanding function of this environmental stress, the chlorophyll relative content (SPAD) and chlorophyll fluorescence Fv/Fm were measured. The significantly higher SPAD were observed in S. spontaneum than those in S. officinarum, no matter what the control conditions, exposure to low temperature or during recovery, and so was for Fv/Fm under exposure to low temperature, together with higher level of SPAD in S. spontaneum in each measurement. Aforementioned results suggest much stronger photosynthetic ability and cold tolerance in S. spontaneum. Our findings build a foundation to investigate the biological mechanism of two sugarcane ancestor chloroplasts and retrieve reliable molecular resources for phylogenetic and evolutionary studies, and will be conducive to genetic improvement of photosynthetic ability and cold resistance in modern sugarcane.

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“… 2017 ), with T. maximowiczii (NC_037023) (Xue et al. 2017 ) as the reference. The resultant genome was annotated in Geneious R11 ( http://www.geneious.com ) by comparing to T. maximowiczii .…”

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confidence: 99%

The complete chloroplast genome sequence of Trapa bicornis Osbeck (Lythraceae)

Sun

Yin

Xue

et al. 2020

Mitochondrial DNA Part B

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The complete chloroplast DNA sequence of Trapa maximowiczii Korsh. (Trapaceae), and comparative analysis with other Myrtales species

Cited by 17 publications

References 55 publications

Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales

Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales

Comparative Analysis of two Sugarcane Ancestors Saccharum officinarum and S. spontaneum based on Complete Chloroplast Genome Sequences and Photosynthetic Ability in Cold Stress

The complete chloroplast genome sequence of Trapa bicornis Osbeck (Lythraceae)

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