scholarly journals Chloroplast Genomes and Comparative Analyses among Thirteen Taxa within Myrsinaceae s.str. Clade (Myrsinoideae, Primulaceae)

2019 ◽  
Vol 20 (18) ◽  
pp. 4534 ◽  
Author(s):  
Xiaokai Yan ◽  
Tongjian Liu ◽  
Xun Yuan ◽  
Yuan Xu ◽  
Haifei Yan ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Gene Evolution ◽  
Phylogenetic Reconstruction ◽  
Single Copy ◽  
Synonymous Substitution ◽  
Chloroplast Genomes ◽  
Ssr Loci ◽  
Synonymous Substitution Rates ◽  
Large Single Copy Region ◽  
Simple Sequence

The Myrsinaceae s.str. clade is a tropical woody representative in Myrsinoideae of Primulaceae and has ca. 1300 species. The generic limits and alignments of this clade are unclear due to the limited number of genetic markers and/or taxon samplings in previous studies. Here, the chloroplast (cp) genomes of 13 taxa within the Myrsinaceae s.str. clade are sequenced and characterized. These cp genomes are typical quadripartite circle molecules and are highly conserved in size and gene content. Three pseudogenes are identified, of which ycf15 is totally absent from five taxa. Noncoding and large single copy region (LSC) exhibit higher levels of nucleotide diversity (Pi) than other regions. A total of ten hotspot fragments and 796 chloroplast simple sequence repeats (SSR) loci are found across all cp genomes. The results of phylogenetic analysis support the notion that the monophyletic Myrsinaceae s.str. clade has two subclades. Non-synonymous substitution rates (dN) are higher in housekeeping (HK) genes than photosynthetic (PS) genes, but both groups have a nearly identical synonymous substitution rate (dS). The results indicate that the PS genes are under stronger functional constraints compared with the HK genes. Overall, the study provides hypervariable molecular markers for phylogenetic reconstruction and contributes to a better understanding of plastid gene evolution in Myrsinaceae s.str. clade.

scholarly journals Complete Chloroplast Genome Sequences of Clematis: IR Expansion and Relative Rates of Synonymous Substitutions

2018 ◽  
Author(s):  
Kyoung Su Choi ◽  
Keum Seon Jeong ◽  
Young-Ho Ha ◽  
Kyung Choi
Keyword(s):  
Chloroplast Genome ◽  
Tandem Repeats ◽  
Single Copy ◽  
Synonymous Substitution ◽  
Substitution Rates ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Repeat Structure ◽  
Chloroplast Genomes ◽  
Synonymous Substitution Rates

Genus Clematis is one of the largest within Ranunculaceae. Here we report the chloroplast genome of two Clematis species, C. brachyura and C. trichotoma endemic to Korea. The chloroplast genome lengths of C. brachyura and C. trichotoma are 159,532 bp and 159,170 bp, respectively. Gene contents in the complete chloroplast genomes of these two Clematis species are identical to that of most Ranunculaceae and other angiosperms. However, our data results demonstrated that genus Clematis has inversion and rearrangement events concerning gene rps4 gene, rps16 to trnH region, and trnL to ndhC region, and IR regions expansion. Comparison of IR regions among Ranunculaceae species revealed that Clematis species contained six protein coding genes (infA, rps8, rpl14, rpl16, rps3, and rpl22) usually found in the long single copy (LSC) region of other species. Phylogenetic analysis demonstrated that genus Clematis is closely related to genus Ranunculus. Differences in repeat structure, substitution rates, and IR expansion in genera Clematis and Ranunculus, explained their relationship. Clematis species showed slightly higher tandem repeats content than Ranunculus species. The six protein-coding genes showed lower synonymous substitution rates in the IR of Clematis species than in the LSC of Ranunculus species. Overall, the chloroplast genomes and results presented here provide important information on the evolution of Ranunculaceae.

scholarly journals Comparing Patterns of Nucleotide Substitution Rates Among Chloroplast Loci Using the Relative Ratio Test

Genetics ◽  
1997 ◽  
Vol 146 (1) ◽  
pp. 393-399 ◽  
Author(s):  
Spencer V Muse ◽  
Brandon S Gaut
Keyword(s):  
Nucleotide Substitution ◽  
Nonsynonymous Substitution ◽  
Synonymous Substitution ◽  
Joint Analysis ◽  
Ratio Test ◽  
Substitution Rates ◽  
Chloroplast Genomes ◽  
Synonymous Substitution Rates ◽  
Nucleotide Substitution Rates ◽  
Evolutionary Lineages

Even when several genetic loci are used in molecular evolutionary studies, each locus is typically analyzed independently of the others. This type of approach makes it difficult to study mechanisms and processes that affect multiple genes. In this work we develop a statistical approach for the joint analysis of two or more loci. The tests we propose examine whether or not nucleotide substitution rates across evolutionary lineages have the same relative proportions at two loci. Theses procedures are applied to 33 genes from the chloroplast genomes of rice, tobacco, pine, and liverwort. With the exception of five clearly distinct loci, we find that synonymous substitution rates tend to change proportionally across genes. We interpret these results to be consistent with a “lineage effect” acting on the entire chloroplast genome. In contrast, nonsynonymous rates do not change proportionally across genes, suggesting that locus-specific evolutionary effects dominate patterns of nonsynonymous substitution.

scholarly journals Development of Chloroplast Genomic Resources in Chinese Yam (Dioscorea polystachya)

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Junling Cao ◽  
Dan Jiang ◽  
Zhenyu Zhao ◽  
Subo Yuan ◽  
Yujun Zhang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Single Copy ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Complete Chloroplast Genome ◽  
Genomic Resources ◽  
Chinese Yam ◽  
Chloroplast Genomes ◽  
Chloroplast Genome Sequence ◽  
Simple Sequence

Chinese yam has been used both as a food and in traditional herbal medicine. Developing more effective genetic markers in this species is necessary to assess its genetic diversity and perform cultivar identification. In this study, new chloroplast genomic resources were developed using whole chloroplast genomes from six genotypes originating from different geographical locations. The Dioscorea polystachya chloroplast genome is a circular molecule consisting of two single-copy regions separated by a pair of inverted repeats. Comparative analyses of six D. polystachya chloroplast genomes revealed 141 single nucleotide polymorphisms (SNPs). Seventy simple sequence repeats (SSRs) were found in the six genotypes, including 24 polymorphic SSRs. Forty-three common indels and five small inversions were detected. Phylogenetic analysis based on the complete chloroplast genome provided the best resolution among the genotypes. Our evaluation of chloroplast genome resources among these genotypes led us to consider the complete chloroplast genome sequence of D. polystachya as a source of reliable and valuable molecular markers for revealing biogeographical structure and the extent of genetic variation in wild populations and for identifying different cultivars.

scholarly journals Stable and widespread structural heteroplasmy in chloroplast genomes revealed by a new long-read quantification method

2019 ◽  
Author(s):  
Weiwen Wang ◽  
Robert Lanfear
Keyword(s):  
Chloroplast Genome ◽  
Single Copy ◽  
Land Plant ◽  
Inverted Repeats ◽  
Equal Frequency ◽  
Large Single Copy ◽  
Chloroplast Genomes ◽  
Long Read ◽  
Small Single Copy ◽  
Large Single Copy Region

AbstractThe chloroplast genome usually has a quadripartite structure consisting of a large single copy region and a small single copy region separated by two long inverted repeats. It has been known for some time that a single cell may contain at least two structural haplotypes of this structure, which differ in the relative orientation of the single copy regions. However, the methods required to detect and measure the abundance of the structural haplotypes are labour-intensive, and this phenomenon remains understudied. Here we develop a new method, Cp-hap, to detect all possible structural haplotypes of chloroplast genomes of quadripartite structure using long-read sequencing data. We use this method to conduct a systematic analysis and quantification of chloroplast structural haplotypes in 61 land plant species across 19 orders of Angiosperms, Gymnosperms and Pteridophytes. Our results show that there are two chloroplast structural haplotypes which occur with equal frequency in most land plant individuals. Nevertheless, species whose chloroplast genomes lack inverted repeats or have short inverted repeats have just a single structural haplotype. We also show that the relative abundance of the two structural haplotypes remains constant across multiple samples from a single individual plant, suggesting that the process which maintains equal frequency of the two haplotypes operates rapidly, consistent with the hypothesis that flip-flop recombination mediates chloroplast structural heteroplasmy. Our results suggest that previous claims of differences in chloroplast genome structure between species may need to be revisited.Significance StatementChloroplast genome consists of a large single copy region, a small single copy region, and two inverted repeats. Some decades ago, a discovery showed that there are two types chloroplast genome in some plants, which differ the way that the four regions are put together. However, this phenomenon has been shown in just a small number of species, and many open questions remain. Here, we develop a fast method to measure the chloroplast genome structures, based on long-reads. We show that almost all plants we analysed contain two possible genome structures, while a few plants contain only one structure. Our findings hint at the causes of the phenomenon, and provide a convenient new method with which to make rapid progress.

scholarly journals Biased gene conversion, copy number, and apparent mutation rate differences within chloroplast and bacterial genomes.

Genetics ◽  
1992 ◽  
Vol 130 (3) ◽  
pp. 677-683 ◽  
Author(s):  
C W Birky ◽  
J B Walsh
Keyword(s):  
Copy Number ◽  
Molecular Mechanisms ◽  
Single Copy ◽  
Synonymous Substitution ◽  
Mutation Rates ◽  
Bacterial Genomes ◽  
Gene Copies ◽  
Bacterial Chromosomes ◽  
Synonymous Substitution Rates ◽  
Bacterial Genes

Abstract We investigate the possibility that differences between synonymous substitution rates of organelle and bacterial genes differing only in copy number may be due to conversion bias. We find that the rather large observed difference in the synonymous rates between genes in the single copy and inverted-repeat regions of chloroplasts can be accounted for by a very small bias against new mutants. More generally, differences in the within-organelle fixation probability result in different apparent mutation rates as measured by the expected rate of appearance of cells homoplasmic for new mutants. Thus, differences in intracellular population parameters rather than molecular mechanisms can account for some variation in the apparent mutation rates of organelle genes, and possibly in other systems with variable numbers of gene copies. On the other hand, our analysis suggests that conversion bias is not a likely explanation for relatively low mutation rates observed near the replication origin of bacterial chromosomes.

scholarly journals Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in Pogostemon (Lamiaceae)

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1497
Author(s):  
Cai-Yun Zhang ◽  
Tong-Jian Liu ◽  
Xiao-Lu Mo ◽  
Hui-Run Huang ◽  
Gang Yao ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Gc Content ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Great Economic Importance ◽  
Chloroplast Genomes ◽  
Interspecific Divergence ◽  
Variation Range

Pogostemon Desf., the largest genus of the tribe Pogostemoneae (Lamiaceae), consists of ca. 80 species distributed mainly from South and Southeast Asia to China. The genus contains many patchouli plants, which are of great economic importance but taxonomically difficult. Therefore, it is necessary to characterize more chloroplast (cp) genomes for infrageneric phylogeny analyses and species identification of Pogostemon, especially for patchouli plants. In this study, we newly generated four cp genomes for three patchouli plants (i.e., Pogostemon plectranthoides Desf., P. septentrionalis C. Y. Wu et Y. C. Huang, and two cultivars of P. cablin (Blanoco) Benth.). Comparison of all samples (including online available cp genomes of P. yatabeanus (Makino) Press and P. stellatus (Lour.) Kuntze) suggested that Pogostemon cp genomes are highly conserved in terms of genome size and gene content, with a typical quadripartite circle structure. Interspecific divergence of cp genomes has been maintained at a relatively low level, though seven divergence hotspot regions were identified by stepwise window analysis. The nucleotide diversity (Pi) value was correlated significantly with gap proportion (indels), but significantly negative with GC content. Our phylogenetic analyses based on 80 protein-coding genes yielded high-resolution backbone topologies for the Lamiaceae and Pogostemon. For the overall mean substitution rates, the synonymous (dS) and nonsynonymous (dN) substitution rate values of protein-coding genes varied approximately threefold, while the dN values among different functional gene groups showed a wider variation range. Overall, the cp genomes of Pogostemon will be useful for phylogenetic reconstruction, species delimitation and identification in the future.

scholarly journals Complete Chloroplast Genomes and Comparative Analyses of L. chinensis, L. anhuiensis, and L. aurea (Amaryllidaceae)

2020 ◽  
Vol 21 (16) ◽  
pp. 5729
Author(s):  
Fengjiao Zhang ◽  
Tao Wang ◽  
Xiaochun Shu ◽  
Ning Wang ◽  
Weibing Zhuang ◽  
...  
Keyword(s):  
Native Species ◽  
Ornamental Plants ◽  
Gc Content ◽  
Single Copy ◽  
Protein Coding ◽  
Germplasm Identification ◽  
Gene Expansion ◽  
Phylogeny Analysis ◽  
Chloroplast Genomes ◽  
Simple Sequence

The genus Lycoris (about 20 species) includes important medicinal and ornamental plants. Due to the similar morphological features and insufficient genomic resources, germplasm identification and molecular phylogeny analysis are very limited. Here, we sequenced the complete chloroplast genomes of L. chinensis, L. anhuiensis, and L. aurea; they have very similar morphological traits that make it difficult to identify. The full length of their cp genomes was nearly 158k bp with the same guanine-cytosine content of 37.8%. A total of 137 genes were annotated, including 87 protein-coding genes, 42 tRNAs, and eight rRNAs. A comparative analysis revealed the conservation in sequence size, GC content, and gene content. Some variations were observed in repeat structures, gene expansion on the IR-SC (Inverted Repeat-Single-Copy) boundary regions. Together with the cpSSR (chloroplast simple sequence repeats), these genetic variations are useful to develop molecular markers for germplasm identification. Phylogenetic analysis showed that seven Lycoris species were clustered into a monophyletic group, and closed to Narcissus in Amaryllidaceae. L. chinensis, L. anhuiensis, and L. longituba were clustered together, suggesting that they were very likely to be derived from one species, and had the same ancestor with L. squamigera. Our results provided information on the study of genetic diversity, origins or relatedness of native species, and the identification of cultivars.

scholarly journals Genealogical Evidence for Positive Selection in the nef Gene of HIV-1

Genetics ◽  
1999 ◽  
Vol 153 (3) ◽  
pp. 1077-1089
Author(s):  
Paolo M de A. Zanotto ◽  
Esper G Kallas ◽  
Robson F de Souza ◽  
Edward C Holmes
Keyword(s):  
Positive Selection ◽  
Gene Evolution ◽  
Synonymous Substitution ◽  
Good Evidence ◽  
Likelihood Method ◽  
Variable Intensity ◽  
Subtype B ◽  
Synonymous Substitution Rates ◽  
Hiv 1 ◽  
Positively Selected Sites

Abstract The pattern and process of evolution in the nef gene of HIV-1 was analyzed within and among patients. Using a maximum likelihood method that allows for variable intensity of selection pressure among codons, strong positive selection was detected in a hemophiliac patient over 30 mo of infection. By reconstructing the process of allele substitution in this patient using parsimony, the synapomorphic amino acid changes separating each time point were found to have high probabilities of being under positive selection, with selective coefficients of at least 3.6%. Positive selection was also detected among 39 nef sequences from HIV-1 subtype B. In contrast, multiple pairwise comparisons of nonsynonymous and synonymous substitution rates provided no good evidence for positive selection and sliding window analyses failed to detect most positively selected sites. These findings demonstrate that positive selection is an important determinant of nef gene evolution and that genealogy-based methods outperform pairwise methods in the detection of adaptive evolution. Mapping the locations of positively selected sites may also be of use in identifying targets of the immune response and hence aid vaccine design.

scholarly journals Chloroplast microsatellites in barley: the reduction of variability spectrum in cultivated forms

2006 ◽  
Vol 4 (1) ◽  
pp. 17-21 ◽  
Author(s):  
Natalia V Lukhanina ◽  
Marina G Sinyavskaya ◽  
Inessa M Goloenko ◽  
Oleg G Davydenko
Keyword(s):  
Simple Sequence Repeat ◽  
Rare Variants ◽  
Chloroplast Microsatellites ◽  
Repeat Polymorphism ◽  
Hordeum Vulgare L ◽  
Chloroplast Genomes ◽  
Intergenic Regions ◽  
Ssr Loci ◽  
Cultivated Barley ◽  
Simple Sequence

The chloroplast genomes of 67 accessions of Hordeum vulgare L were surveyed for simple sequence repeat polymorphism. Seven SSR loci were investigated, trnL/trnF and psbI-trnS intergenic regions, as well as two regions 3' trnS genes were polymorphic. The rare variants of these loci were revealed and five rare accessions were found. Our results show an extremely low level of cpDNA polymorphism of cultivated barley.

scholarly journals Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences from Aldama (Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10886
Author(s):  
Benoit Loeuille ◽  
Verônica Thode ◽  
Carolina Siniscalchi ◽  
Sonia Andrade ◽  
Magdalena Rossi ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Sequence Divergence ◽  
Single Copy ◽  
Gene Content ◽  
Tithonia Diversifolia ◽  
Large Single Copy ◽  
Genome Sequences ◽  
Chloroplast Genomes ◽  
Mexican Species ◽  
Similar Gene

Aldama (Heliantheae, Asteraceae) is a diverse genus in the sunflower family. To date, nearly 200 Asteraceae chloroplast genomes have been sequenced, but the plastomes of Aldama remain undescribed. Plastomes in Asteraceae usually show little sequence divergence, consequently, our hypothesis is that species of Aldama will be overall conserved. In this study, we newly sequenced 36 plastomes of Aldama and of five species belonging to other Heliantheae genera selected as outgroups (i.e., Dimerostemma asperatum, Helianthus tuberosus, Iostephane heterophylla, Pappobolus lanatus var. lanatus, and Tithonia diversifolia). We analyzed the structure and gene content of the assembled plastomes and performed comparative analyses within Aldama and with other closely related genera. As expected, Aldama plastomes are very conserved, with the overall gene content and orientation being similar in all studied species. The length of the plastome is also consistent and the junction between regions usually contain the same genes and have similar lengths. A large ∼20 kb and a small ∼3 kb inversion were detected in the Large Single Copy (LSC) regions of all assembled plastomes, similarly to other Asteraceae species. The nucleotide diversity is very low, with only 1,509 variable sites in 127,466 bp (i.e., 1.18% of the sites in the alignment of 36 Aldama plastomes, with one of the IRs removed, is variable). Only one gene, rbcL, shows signatures of positive selection. The plastomes of the selected outgroups feature a similar gene content and structure compared to Aldama and also present the two inversions in the LSC region. Deletions of different lengths were observed in the gene ycf2. Multiple SSRs were identified for the sequenced Aldama and outgroups. The phylogenetic analysis shows that Aldama is not monophyletic due to the position of the Mexican species A. dentata. All Brazilian species form a strongly supported clade. Our results bring new understandings into the evolution and diversity of plastomes at the species level.

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