scholarly journals Chloroplast Genomes for Five Skeletonema Species: Comparative and Phylogenetic Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Shuya Liu ◽  
Qing Xu ◽  
Kuiyan Liu ◽  
Yongfang Zhao ◽  
Nansheng Chen
Keyword(s):  
Molecular Evolution ◽  
Critical Role ◽  
Nuclear Genome ◽  
Sequence Divergence ◽  
Purifying Selection ◽  
Species Selection ◽  
Chloroplast Genomes ◽  
High Sequence Divergence ◽  
High Conservation ◽  
Genomic Regions

Skeletonema species are cosmopolitan coastal diatoms that exhibit important roles in ecological system. The chloroplast genomes (cpDNAs) have been proven to be important in the study of molecular evolution and genetic diversity. However, cpDNA of only a single Skeletonema species (S. pseudocostatum) has been constructed, hindering in-depth investigation on Skeletonema species. In this study, complete cpDNAs of five Skeletonema species were constructed with cpDNAs of four species S. marinoi, S. tropicum, S. costatum, and S. grevillea constructed for the first time. These cpDNAs had similar sizes and same numbers of genes. These cpDNAs were highly syntenic with no substantial expansions, contractions, or inversions. Interestingly, two copies of petF, which encodes ferredoxin with critical role in iron dependency, were found in all five Skeletonema species, with one copy in the cpDNA and another copy in the nuclear genome of each species. Selection analysis revealed that all PCGs of cpDNAs were undergoing purifying selection. Despite the high conservation of these cpDNAs, nine genomic regions with high sequence divergence were identified, which illustrated substantial variations that could be used as markers for phylogenetic inference and for tracking Skeletonema species in the field. Additionally, the numbers of simple sequence repeats varied among different cpDNAs, which were useful for detecting genetic polymorphisms. The divergence times estimated using PCGs of cpDNAs revealed that most of these species were established within ∼33 Mya, consistent with that estimated using mtDNAs. Overall, the current study deepened our understanding about the molecular evolution of Skeletonema cpDNAs.

scholarly journals Sexually dimorphic gene expression and transcriptome evolution provides mixed evidence for a fast-Z effect in Heliconius

2018 ◽  
Author(s):  
A Pinharanda ◽  
M Rousselle ◽  
SH Martin ◽  
JJ Hanly ◽  
JW Davey ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Evolution ◽  
Adaptive Evolution ◽  
Sex Chromosomes ◽  
Expression Profiles ◽  
Sequence Divergence ◽  
Gene Expression Profiles ◽  
Purifying Selection ◽  
Specific Gene ◽  
Sex Determination System

AbstractSex chromosomes have different evolutionary properties as compared to the autosomes due to their hemizygous nature. In particular, recessive mutations are more readily exposed to selection, which can lead to faster rates of molecular evolution. Here, we report patterns of gene expression and molecular evolution in the sex chromosomes of a group of tropical butterflies. We first improved the completeness of the Heliconius melpomene reference annotation, a neotropical butterfly with a ZW sex determination system. Then we sequenced RNA from male and female whole abdomens and female ovary and gut tissue to identify sex and tissue specific gene expression profiles in H. melpomene. Using these expression profiles we compare sequence divergence and polymorphism, the strength of positive and negative selection and rates of adaptive evolution for Z and autosomal genes between two species of Heliconius butterflies, H. melpomene and H. erato.We show that the rate of adaptive substitutions is higher for Z as compared to autosomal genes, but contrary to expectation it is also higher for male as compared to female biased genes. There is therefore mixed evidence that hemizygosity influences the rate of adaptive substitutions. Additionally, we find no significant increase in the rate of adaptive evolution or purifying selection on genes expressed in ovary tissue, a heterogametic specific tissue. Together our results provide limited support for fast-Z evolution. This contributes to a growing body of literature from other ZW systems that also provide mixed evidence for a fast-Z effect.

scholarly journals Comparison of Chloroplast genomes of Gynura species:Sequence Variation, Genome Rearrangement and Divergence studies

2019 ◽  
Author(s):  
Tianyu Han(Former Corresponding Author) ◽  
Mimi Li ◽  
Jiawei Li ◽  
Han Lv ◽  
Bingru Ren ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Rearrangement ◽  
Agronomic Traits ◽  
Divergence Time ◽  
Sequence Divergence ◽  
Purifying Selection ◽  
Chloroplast Genomes ◽  
Small Change ◽  
Artemisia Pollen ◽  
Relationship Of

Abstract Background Some Gynura species were reported to be natural anti-diabetic plants. The chloroplast genomes of four Gynura species were sequenced for hybridizations to improve agronomic traits. There are only 4 genera of tribe Senecioneae have published chloroplast genome in Genbank up to now. The internal relationships of the genus Gynura and the relationship of the genus Gynura with other genera in tribe Senecioneae need further researches. Results The chloroplast genome of 4 Gynura species were sequenced, assembled and annotated. Comparing with other 12 Senecioneae species, the chloroplast genome features were detailedly analyzed. Subsequently, the differences of the microsatellites and repeats type in the tribe were found. By comparison, the IR expansion and contraction is conserved in the genera Gynura, Dendrosenecio and Ligularia. The region from 25,000 to 50,000 bp is relatively not conservative but the 7 ndh genes in this region are under purifying selection with small change in amino acids. The phylogenetic tree shows two major clades, same as the sequence divergence in region 25,000 to 50,000 bp. Based on the oldest Artemisia pollen fossil, the divergence time were estimated. Conclusions Sequencing of chloroplast genome of the 4 Gynura species help us to develop abundant genetic resources. The phylogenetic relationships and divergence time among 4 Gynura and 16 Senecioneae species were sorted out by comparing the chloroplast genomes. The phylogenetic relationship of the genera Gynura and Ligularia is different with former work and further morphology and genome-wide analysis are needed to clarify the genera relationship.

scholarly journals Comparative Chloroplast genomes of Gynura species:Sequence Variation, Genome Rearrangement and Divergence studies

2019 ◽  
Author(s):  
Tianyu Han ◽  
Mimi Li ◽  
Jiawei Li ◽  
Han Lv ◽  
Bingru Ren ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Rearrangement ◽  
Agronomic Traits ◽  
Divergence Time ◽  
Sequence Divergence ◽  
Purifying Selection ◽  
Chloroplast Genomes ◽  
Small Change ◽  
Artemisia Pollen ◽  
Relationship Of

Abstract Background Some Gynura species were reported to be natural anti-diabetic plants. The chloroplast genomes of four Gynura species were sequenced for hybridizations to improve agronomic traits. There are only 4 genera of tribe Senecioneae have published chloroplast genome in Genbank up to now. The internal relationships of the genus Gynura and the relationship of the genus Gynura with other genera in tribe Senecioneae need further researches. Results The chloroplast genome of 4 Gynura species were sequenced, assembled and annotated. Comparing with other 12 Senecioneae species, the chloroplast genome features were detailedly analyzed. Subsequently, the differences of the microsatellites and repeats type in the tribe were found. By comparison, the IR expansion and contraction is conserved in the genera Gynura, Dendrosenecio and Ligularia. The region from 25,000 to 50,000 bp is relatively not conservative but the 7 ndh genes in this region are under purifying selection with small change in amino acids. The phylogenetic tree shows two major clades, same as the sequence divergence in region 25,000 to 50,000 bp. Based on the oldest Artemisia pollen fossil, the divergence time were estimated. Conclusions Sequencing of chloroplast genome of the 4 Gynura species help us to develop abundant genetic resources. The phylogenetic relationships and divergence time among 4 Gynura and 16 Senecioneae species were sorted out by comparing the chloroplast genomes. The phylogenetic relationship of the genera Gynura and Ligularia is different with former work and further morphology and genome-wide analysis are needed to clarify the genera relationship.

scholarly journals Fragmentation in mitochondrial genomes in relation to elevated sequence divergence and extreme rearrangements

BMC Biology ◽  
2022 ◽  
Vol 20 (1) ◽  
Author(s):  
Shiqian Feng ◽  
Andrea Pozzi ◽  
Vaclav Stejskal ◽  
George Opit ◽  
Qianqian Yang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Sequence Divergence ◽  
Purifying Selection ◽  
Protein Coding ◽  
High Conservation ◽  
Genome Fragmentation ◽  
Mt Genome ◽  
Very High ◽  
Gene Order Rearrangement

Abstract Background A single circular mitochondrial (mt) genome is a common feature across most metazoans. The mt-genome includes protein-coding genes involved in oxidative phosphorylation, as well as RNAs necessary for translation of mt-RNAs, whose order and number are highly conserved across animal clades, with few known exceptions of alternative mt-gene order or mt-genome architectures. One such exception consists of the fragmented mitochondrial genome, a type of genome architecture where mt-genes are split across two or more mt-chromosomes. However, the origins of mt-genome fragmentation and its effects on mt-genome evolution are unknown. Here, we investigate these origin and potential mechanisms underlying mt-genome fragmentation, focusing on a genus of booklice, Liposcelis, which exhibits elevated sequence divergence, frequent rearrangement of mt-gene order, and fragmentation of the mt genome, and compare them to other Metazoan clades. Results We found this genus Liposcelis exhibits very low conservation of mt-gene order across species, relative to other metazoans. Levels of gene order rearrangement were, however, unrelated to whether or not mt-genomes were fragmented or intact, suggesting mitochondrial genome fragmentation is not affecting mt-gene order directly. We further investigated possible mechanisms underpinning these patterns and revealed very high conservation of non-coding sequences at the edges of multiple recombination regions across populations of one particular Liposcelis species, supportive of a hypothesis that mt-fragmentation arises from recombination errors between mt-genome copies. We propose these errors may arise as a consequence of a heightened mutation rate in clades exhibiting mt-fragmentation. Consistent with this, we observed a striking pattern across three Metazoan phyla (Arthropoda, Nematoda, Cnidaria) characterised by members exhibiting high levels of mt-gene order rearrangement and cases of mt-fragmentation, whereby the mt-genomes of species more closely related to species with fragmented mt-genomes diverge more rapidly despite experiencing strong purifying selection. Conclusions We showed that contrary to expectations, mt-genome fragmentation is not correlated with the increase in mt-genome rearrangements. Furthermore, we present evidence that fragmentation of the mt-genome may be part of a general relaxation of a natural selection on the mt-genome, thus providing new insights into the origins of mt-genome fragmentation and evolution.

scholarly journals Comparison of Chloroplast genomes of Gynura species:Sequence Variation, Genome Rearrangement and Divergence studies

2019 ◽  
Author(s):  
Tianyu Han ◽  
Mimi Li ◽  
Jiawei Li ◽  
Han Lv ◽  
Bingru Ren ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Rearrangement ◽  
Agronomic Traits ◽  
Divergence Time ◽  
Sequence Divergence ◽  
Purifying Selection ◽  
Chloroplast Genomes ◽  
Small Change ◽  
Artemisia Pollen ◽  
Relationship Of

Abstract Background Some Gynura species were reported to be natural anti-diabetic plants. The chloroplast genomes of four Gynura species were sequenced for hybridizations to improve agronomic traits. There are only 4 genera of tribe Senecioneae have published chloroplast genome in Genbank up to now. The internal relationships of the genus Gynura and the relationship of the genus Gynura with other genera in tribe Senecioneae need further researches. Results The chloroplast genome of 4 Gynura species were sequenced, assembled and annotated. Comparing with other 12 Senecioneae species, the chloroplast genome features were detailedly analyzed. Subsequently, the differences of the microsatellites and repeats type in the tribe were found. By comparison, the IR expansion and contraction is conserved in the genera Gynura, Dendrosenecio and Ligularia. The region from 25,000 to 50,000 bp is relatively not conservative but the 7 ndh genes in this region are under purifying selection with small change in amino acids. The phylogenetic tree shows two major clades, same as the sequence divergence in region 25,000 to 50,000 bp. Based on the oldest Artemisia pollen fossil, the divergence time were estimated. Conclusions Sequencing of chloroplast genome of the 4 Gynura species help us to develop abundant genetic resources. The phylogenetic relationships and divergence time among 4 Gynura and 16 Senecioneae species were sorted out by comparing the chloroplast genomes. The phylogenetic relationship of the genera Gynura and Ligularia is different with former work and further morphology and genome-wide analysis are needed to clarify the genera relationship.

scholarly journals Molecular Evolution of CatSper in Mammals and Function of Sperm Hyperactivation in Gray Short-Tailed Opossum

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1047
Author(s):  
Jae Yeon Hwang ◽  
Jamie Maziarz ◽  
Günter P. Wagner ◽  
Jean-Ju Chung
Keyword(s):  
Molecular Evolution ◽  
Reproductive Tract ◽  
Sequence Divergence ◽  
Monodelphis Domestica ◽  
Female Reproductive Tract ◽  
Molecular Characteristics ◽  
High Sequence Divergence ◽  
And Function ◽  
Motility Change ◽  
First Time

Males have evolved species-specifical sperm morphology and swimming patterns to adapt to different fertilization environments. In eutherians, only a small fraction of the sperm overcome the diverse obstacles in the female reproductive tract and successfully migrate to the fertilizing site. Sperm arriving at the fertilizing site show hyperactivated motility, a unique motility pattern displaying asymmetric beating of sperm flagella with increased amplitude. This motility change is triggered by Ca2+ influx through the sperm-specific ion channel, CatSper. However, the current understanding of the CatSper function and its molecular regulation is limited in eutherians. Here, we report molecular evolution and conservation of the CatSper channel in the genome throughout eutherians and marsupials. Sequence analyses reveal that CatSper proteins are slowly evolved in marsupials. Using an American marsupial, gray short-tailed opossum (Monodelphis domestica), we demonstrate the expression of CatSper in testes and its function in hyperactivation and unpairing of sperm. We demonstrate that a conserved IQ-like motif in CatSperζ is required for CatSperζ interaction with the pH-tuned Ca2+ sensor, EFCAB9, for regulating CatSper activity. Recombinant opossum EFCAB9 can interact with mouse CatSperζ despite high sequence divergence of CatSperζ among CatSper subunits in therians. Our finding suggests that molecular characteristics and functions of CatSper are evolutionarily conserved in gray short-tailed opossum, unraveling the significance of sperm hyperactivation and fertilization in marsupials for the first time.

scholarly journals Evolutionary Dynamics of Chloroplast Genomes in Low Light: A Case Study of the Endolithic Green Alga Ostreobium quekettii

2016 ◽  
Vol 8 (9) ◽  
pp. 2939-2951 ◽  
Author(s):  
Vanessa R. Marcelino ◽  
Ma Chiela M. Cremen ◽  
Chistopher J. Jackson ◽  
Anthony A. W. Larkum ◽  
Heroen Verbruggen
Keyword(s):  
Molecular Evolution ◽  
Chloroplast Genome ◽  
Evolutionary Dynamics ◽  
Resource Constraints ◽  
Energy Levels ◽  
Purifying Selection ◽  
Light Limitation ◽  
Comparative Genomic ◽  
Low Light ◽  
Chloroplast Genomes

Abstract Some photosynthetic organisms live in extremely low light environments. Light limitation is associated with selective forces as well as reduced exposure to mutagens, and over evolutionary timescales it can leave a footprint on species’ genomes. Here, we present the chloroplast genomes of four green algae (Bryopsidales, Ulvophyceae), including the endolithic (limestone-boring) alga Ostreobium quekettii, which is a low light specialist. We use phylogenetic models and comparative genomic tools to investigate whether the chloroplast genome of Ostreobium corresponds to our expectations of how low light would affect genome evolution. Ostreobium has the smallest and most gene-dense chloroplast genome among Ulvophyceae reported to date, matching our expectation that light limitation would impose resource constraints reflected in the chloroplast genome architecture. Rates of molecular evolution are significantly slower along the phylogenetic branch leading to Ostreobium, in agreement with the expected effects of low light and energy levels on molecular evolution. We expected the ability of Ostreobium to perform photosynthesis in very low light to be associated with positive selection in genes related to the photosynthetic machinery, but instead, we observed that these genes may be under stronger purifying selection. Besides shedding light on the genome dynamics associated with a low light lifestyle, this study helps to resolve the role of environmental factors in shaping the diversity of genome architectures observed in nature.

scholarly journals Evolutionary dynamics of chloroplast genomes in low light: a case study of the endolithic green algaOstreobium quekettii

2016 ◽  
Author(s):  
Vanessa R. Marcelino ◽  
Ma Chiela M. Cremen ◽  
Christopher J. Jackson ◽  
Anthony W.D. Larkum ◽  
Heroen Verbruggen
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Chloroplast Genome ◽  
Evolutionary Dynamics ◽  
Purifying Selection ◽  
Light Sensitivity ◽  
Light Limitation ◽  
Comparative Genomic ◽  
Low Light ◽  
Chloroplast Genomes

Some photosynthetic organisms live in extremely low light environments. Light limitation is associated with selective forces as well as reduced exposure to mutagens, and over evolutionary timescales it can leave a footprint on species genome. Here we present the chloroplast genomes of four green algae (Bryopsidales, Ulvophyceae), including the endolithic (limestone-boring) alga Ostreobium quekettii, which is a low light specialist. We use phylogenetic models and comparative genomic tools to investigate whether the chloroplast genome of Ostreobium corresponds to our expectations of how low light would affect genome evolution. Ostreobium has the smallest and most gene-dense chloroplast genome among Ulvophyceae reported to date, matching our expectation that light limitation would impose resource constraints. Rates of molecular evolution are significantly slower along the phylogenetic branch leading to Ostreobium, in agreement with the expected effects of low light and energy levels on molecular evolution. Given the exceptional ability of our model organism to photosynthesize under extreme low light conditions, we expected to observe positive selection in genes related to the photosynthetic machinery. However, we observed stronger purifying selection in these genes, which might either reflect a lack of power to detect episodic positive selection followed by purifying selection and/or a strengthening of purifying selection due to the loss of a gene related to light sensitivity. Besides shedding light on the genome dynamics associated with a low light lifestyle, this study helps to resolve the role of environmental factors in shaping the diversity of genome architectures observed in nature.

scholarly journals Contribution of recombination and selection to molecular evolution of Citrus tristeza virus

2009 ◽  
Vol 90 (6) ◽  
pp. 1527-1538 ◽  
Author(s):  
Susana Martín ◽  
Adrián Sambade ◽  
Luis Rubio ◽  
María C. Vives ◽  
Patricia Moya ◽  
...  
Keyword(s):  
Gene Flow ◽  
Molecular Evolution ◽  
Phylogenetic Trees ◽  
Phylogenetic Network ◽  
Purifying Selection ◽  
South American ◽  
Significant Gene ◽  
Selection Gene ◽  
Genomic Regions ◽  
Citrus Tristeza

The genetic variation of Citrus tristeza virus (CTV) was analysed by comparing the predominant sequence variants in seven genomic regions (p33, p65, p61, p18, p13, p20 and p23) of 18 pathogenically distinct isolates from seven different countries. Analyses of the selective constraints acting on each codon suggest that most regions were under purifying selection. Phylogenetic analysis shows diverse patterns of molecular evolution for different genomic regions. A first clade composed of isolates that are genetically close to the reference mild isolates T385 or T30 was inferred from all genomic regions. A second clade, mostly comprising virulent isolates, was defined from regions p33, p65, p13 and p23. For regions p65, p61, p18, p13 and p23, a third clade that mostly included South American isolates could not be related to any reference genotype. Phylogenetic relationships among isolates did not reflect their geographical origin, suggesting significant gene flow between geographically distant areas. Incongruent phylogenetic trees for different genomic regions suggested recombination events, an extreme that was supported by several recombination-detecting methods. A phylogenetic network incorporating the effect of recombination showed an explosive radiation pattern for the evolution of some isolates and also grouped isolates by virulence. Taken together, the above results suggest that negative selection, gene flow, sequence recombination and virulence may be important factors driving CTV evolution.

scholarly journals Structural characterization and duplication modes of pseudogenes in plants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Flavia Mascagni ◽  
Gabriele Usai ◽  
Andrea Cavallini ◽  
Andrea Porceddu
Keyword(s):  
Evolutionary Rate ◽  
Populus Trichocarpa ◽  
Sequence Divergence ◽  
Strand Break ◽  
Whole Genome ◽  
Flanking Sequence ◽  
Plant Genomes ◽  
High Sequence Divergence ◽  
Flanking Regions

AbstractWe identified and characterized the pseudogene complements of five plant species: four dicots (Arabidopsis thaliana, Vitis vinifera, Populus trichocarpa and Phaseolus vulgaris) and one monocot (Oryza sativa). Retroposition was considered of modest importance for pseudogene formation in all investigated species except V. vinifera, which showed an unusually high number of retro-pseudogenes in non coding genic regions. By using a pipeline for the classification of sequence duplicates in plant genomes, we compared the relative importance of whole genome, tandem, proximal, transposed and dispersed duplication modes in the pseudo and functional gene complements. Pseudogenes showed higher tendencies than functional genes to genomic dispersion. Dispersed pseudogenes were prevalently fragmented and showed high sequence divergence at flanking regions. On the contrary, those deriving from whole genome duplication were proportionally less than expected based on observations on functional loci and showed higher levels of flanking sequence conservation than dispersed pseudogenes. Pseudogenes deriving from tandem and proximal duplications were in excess compared to functional loci, probably reflecting the high evolutionary rate associated with these duplication modes in plant genomes. These data are compatible with high rates of sequence turnover at neutral sites and double strand break repairs mediated duplication mechanisms.

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