Comparative analysis of chloroplast genomes of five Robinia species: Genome comparative and evolution analysis

Yu, Xiaoyue; Zuo, Lihui; Lu, Dongping; Lu, Bin; Wang, Jinmao

doi:10.1016/j.gene.2018.12.023

Cited by 44 publications

(33 citation statements)

References 22 publications

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“…Despite the IR regions of cp genome were recognized as highly conserved, structural variation in the IR/SC boundary regions was very common. The contraction and expansion of the IR regions could give rise to size difference among cp genomes [55,56]. Comparisons of the IR/SC junctions among five Juglandaceae cp genomes (C. illinoinensis, C. kweichowensis, A. sinensis, J. regia, and P. strobilacea) were presented in Figure 4.…”

Section: Ir Contraction and Expansionmentioning

confidence: 99%

The Chloroplast Genome of Carya illinoinensis: Genome Structure, Adaptive Evolution, and Phylogenetic Analysis

Lou

Chen

et al. 2020

Forests

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Research Highlights: For the first time, the complete chloroplast (cp) genome of Carya illinoinensis cv. ‘Pawnee’ was de novo assembled. Comprehensive analysis the cp genome of C. illinoinensis revealed potential cpDNA markers for intraspecies identification, genes involved in adaptation, and its phylogenetic position. Background and Objectives: C. illinoinensis is an economically important nut tree in the family Juglandaceae. Cp-derived markers are helpful for genetic research, but they still need to be developed in C. illinoinensis. Additionally, the adaptation and phylogenetic relationships of C. illinoinensis have not been revealed based on the complete cp genome. Materials and Methods: Chloroplast genomic DNA of C. illinoinensis cv. ‘Pawnee’ was extracted and subjected to Illumina sequencing. Results: The cp genome is 160,819 bp in size, exhibiting a typical quadripartite structure with a large single copy (LSC) of 90,022 bp, a small single copy (SSC) of 18,791 bp, and a pair of inverted repeats (IRA and IRB) regions of 26,003 bp each. The genome was predicted to encode 112 unique genes, including 79 protein-coding genes, 29 tRNAs, and four rRNAs, with 19 duplicates in the IR regions. In total, 213 SSRs and 44 long repeats were identified in the cp genome. A comparison of two different C. illinoinensis genotypes, ‘Pawnee’ and 87MX3-2.11, obtained 143 SNPs and 74 indels. The highly variable regions such as atpF, clpP, and ndhA genes, and matK-rps16, trnS-trnG, and trnT-psbD intergenic spacers might be helpful for future intraspecific identification. Positive selection was acting on the ccsA and rps12 cp genes based on the Ka/Ks ratios. Phylogenetic analysis indicated that C. illinoinensis forms a sister clade to Asian Carya species, represented by C. kweichowensis and Annamocarya sinensis. Conclusions: The genome information in our study will have significance for further research on the intraspecies identification and genetic improvement of C. illinoinensis.

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Section: Ir Contraction and Expansionmentioning

confidence: 99%

The Chloroplast Genome of Carya illinoinensis: Genome Structure, Adaptive Evolution, and Phylogenetic Analysis

Lou

Chen

et al. 2020

Forests

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Section: Comparative Genomics Among De Novo Assembled Chloroplast Genmentioning

confidence: 99%

“…The amino acid frequency analyses revealed high encoding of leucine, whereas the rarest encoding was recorded for cysteine ( Figure S1). The RNA editing analyses revealed the presence of [62][63][64][65][66][67][68][69][70][71][72][73][74] RNA editing sites in 19-21 genes (Table S4). The RNA editing sites were found in the same genes with a few exceptions: RNA editing sites were detected in psaB genes of only Z. zamiifolia, whereas the RNA editing site was not found in rpl20 of S. bogneri and rps8 of L.…”

Section: Analyses Of Codon Usage Amino Acid Frequency and Rna Editingmentioning

confidence: 99%

“…We also found three genes under positive selection in the chloroplast genome of S. bogneri, including ycf2, clpP, and rpl36, which might be due to the different types of stresses faced by these species in their respective ecological niches. These genes were also found to be under positive selection in various other species [11,16,55,66,67].This study presents a comparison of the complete chloroplast genomes of four species representing three subfamilies of Araceae including Orontioideae, Lasioideae and Zamioculcadoideae, and the independent taxon S. bogneri. IR contraction and expansion appears to be homoplasious among these taxa, precluding the use of the IR architecture in phylogenetic analyses.…”

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confidence: 99%

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Comparison among the first representative chloroplast genomes ofOrontium, Lasia, Zamioculcas, andStylochaetonof the plant family Araceae: inverted repeat dynamics are not linked to phylogenetic signaling

Abdullah

Henriquez

Mehmood

et al. 2020

Preprint

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The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of the first representatives of four genera representing three subfamilies: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using the plastomes. The size of the chloroplast genomes ranged from 163,770-169,982 bp. These genomes comprise 114 unique genes, including 80 protein-coding, 4 rRNA, and 30 tRNA genes. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The junctions JSB (IRb/SSC) and JSA (SSC/IRa) are highly variable, as is oligonucleotide repeats content among the genomes. The patterns of inverted repeats contraction and expansion were shown to be homoplasious and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were shown for several genes in S. bogneri. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae.Many other types of mutational events also take place within chloroplast genomes, including insertion-deletion (indels), substitutions, tandem repeat variations and variations in number and type of oligonucleotide repeats [11,[18][19][20]. The single parent inheritance of the chloroplast genome -paternally in some gymnosperms and maternally in most angiospermsalong with adequate levels of polymorphism make it suitable for studies of evolution, domestication, phylogeography, population genetics, and phylogenetics [7,10,11,[21][22][23][24].Araceae is an ancient and large monocot plant family, comprising 114 genera and 3750 species [25]. This family is subdivided into eight subfamilies: Gymnostachydoideae, Orotioideae, Lemnoideae, Pothoideae, Monsteroideae, Lasioideae, Zamioculcadoideae, and Aroideae [22,26,27]. Advancements in next generation sequencing have made genomic resources available for species of Lemnoideae [28], Monsteroideae [18,29,30], and Aroideae [10,31,32]; chloroplast genomes of Symplocarpus renifolius Schott ex Tzvelev and S. nipponicus Makino of Orotioideae have also been reported [33,34]. Previous studies provide insight into some unique evolutionary events of chloroplast genomes in Araceae, including IR contraction and expansion, gene rearrangement, and positive selection [10,18,28]. Moreover, loss/pseudogenation of some important genes are also reported in the genus Amorphophallus Blume (Aroideae) [17]. Nevertheless, data for the chloroplast genome ≥ 10, dinucleotide ≥ 5, trinucleotide ≥ 4, tetranucleotide, pentanucleotide and hexanucleotide ≥ 3. The forward and reverse oligonucleotide repeats were determined with length ≥ 14 bp with 1 editing site, initially. Later, we removed all repeats that contained mismatches from the analyses and left only those repeat pairs that exhibited 100% similarities, following Abdullah et al. 2020 [50].We determined transition substitutions (Ts), transvers...

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“…Chloroplasts (CPs) are photosynthetic organelles converting light energy from the sun into chemical energy stored in carbohydrates. Therefore, the cp proteome is abundant with enzymatic machineries catalyzing photosynthesis, and proteins responsible for starch synthesis, amino acid synthesis, fatty acid synthesis, phytohormone synthesis, and DNA and RNA synthesis (Yu et al 2019). The multifaceted roles cp played in plant metabolism make it a key organelle for plant productivity and survival.…”

Section: Introductionmentioning

confidence: 99%

The Complete Chloroplast Genome of Tamarix Ramosissima and Comparative Analysis of Tamaricaceae Species 

Wang

Guo

2020

Preprint

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Background: Tamarix ramosissima is a deciduous shrub resided in arid and semi-arid regions. Although of ecological and medicinal values, some Tamarix species are considered invasive as they have dominated the riparian zones of dryland in some parts of the world. Chloroplast (cp) DNA is highly conserved in structure and gene arrangement, making cp genomic data valuable resources for species delimitation and phylogenetics. The cp genome of T. ramosissima was de novo assembled with the aim of providing reference and data resource for further cp-derived marker development and species delimitation of Tamarix.Results: Here, the complete chloroplast (CP) genome of T. ramosissima was sequenced and analyzed, showing a size of 156150 bp and a GC content of 36.5%. The plastome displayed a typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions of 26554 bp, separated by a large single copy (LSC) region of 84795 bp, and a small single copy (SSC) region of 18247 bp. The cp genome encoded 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. A total of 32 repeat sequences and 64 simple sequence repeats (SSR) were identified in the plastome, and an obvious A/T bias was observed in the majority of the SSRs detected. By comparing the T. ramosissima cp genome with those of four other Tamaricaceae species, a number of divergence hotspots were identified among these plastomes. Together with the SSRs and long repeats identified, these divergence hotspots could be developed as potential molecular markers facilitating species discrimination and evolutionary studies. Using plastome sequences, we re-investigated the phylogenetic relationship among 19 species, and T. ramosissima was found to be a sister of Tamarix chinensis.Conclusions: Taken together, our study provides valuable genomic resources to deepen the understanding of the plant photosynthetic mechanism and phylogenomics.

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Comparative analysis of chloroplast genomes of five Robinia species: Genome comparative and evolution analysis

Cited by 44 publications

References 22 publications

The Chloroplast Genome of Carya illinoinensis: Genome Structure, Adaptive Evolution, and Phylogenetic Analysis

The Chloroplast Genome of Carya illinoinensis: Genome Structure, Adaptive Evolution, and Phylogenetic Analysis

Comparison among the first representative chloroplast genomes ofOrontium, Lasia, Zamioculcas, andStylochaetonof the plant family Araceae: inverted repeat dynamics are not linked to phylogenetic signaling

The Complete Chloroplast Genome of Tamarix Ramosissima and Comparative Analysis of Tamaricaceae Species

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Comparative analysis of chloroplast genomes of five Robinia species: Genome comparative and evolution analysis

Cited by 44 publications

References 22 publications

The Chloroplast Genome of Carya illinoinensis: Genome Structure, Adaptive Evolution, and Phylogenetic Analysis

The Chloroplast Genome of Carya illinoinensis: Genome Structure, Adaptive Evolution, and Phylogenetic Analysis

Comparison among the first representative chloroplast genomes ofOrontium, Lasia, Zamioculcas, andStylochaetonof the plant family Araceae: inverted repeat dynamics are not linked to phylogenetic signaling

The Complete Chloroplast Genome of Tamarix Ramosissima and Comparative Analysis of Tamaricaceae Species&nbsp;

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The Complete Chloroplast Genome of Tamarix Ramosissima and Comparative Analysis of Tamaricaceae Species