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 Comparative and Phylogenetic Analysis of the Complete Chloroplast Genome of Santalum (Santalaceae)

Forests ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1303
Author(s):  
Xiaojin Liu ◽  
Daping Xu ◽  
Zhou Hong ◽  
Ningnan Zhang ◽  
Zhiyi Cui
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Evolutionary Dynamics ◽  
Divergence Time ◽  
Purifying Selection ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genomes ◽  
Branch Model ◽  
Extant Species ◽  
Ndh Genes

Santalum (Santalaceae, sandalwood) is a hemiparasitic genus that includes approximately 15 extant species. It is known for its aromatic heartwood oil, which is used in incense and perfume. Demand for sandalwood-based products has led to drastic over-harvesting, and wild Santalum populations are now threatened. Knowledge of phylogenetic relationships will be critical for the conservation and proper management of this genus. Here, we sequenced the chloroplast genome of 11 Santalum species. The data were then used to investigate chloroplast genome evolutionary dynamics and relationships and divergence time within Santalum and related species. The Santalum chloroplast genome contains typical quadripartite structures, ranging from 143,291 to 144,263 bp. The chloroplast genome contains 110 unique genes. The whole set of ndh genes and the infA gene were found to lose their functions. The P-distance among the Santalum species was 0.0003 to 0.00828. Three mutation hotspot regions, 14 small inversions, and 460 indels events were discovered in the Santalum chloroplast genome. Branch-model-based selection analyses showed that the Santalum species were under widespread purifying selection. Our phylogenomic assessment provides an improved resolution to the phylogenetic relationships of Santalum compared to the past analyses. Our divergence time analysis showed that the crown age of Santalum was 8.46 Mya (million years ago), the first divergence occurred around 6.97 Mya, and diversification was completed approximately 1 Mya. By sequencing the 11 Santalum species chloroplast genomes, we identified the variations in the Santalum chloroplast genomes. Using the chloroplast genome sequences, phylogeny and divergence time analyses discovered that the Santalum species were likely to originate due to radiation evolution, and most speciation events occurred less than 1 Mya.

scholarly journals Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia

2021 ◽  
Author(s):  
LI li ◽  
Yunfei Hu ◽  
Min He ◽  
Bo Zhang ◽  
Wei Wu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Camellia Sinensis ◽  
Evolutionary Dynamics ◽  
Divergence Time ◽  
Tea Plant ◽  
Genome Comparison ◽  
Induced Mutations ◽  
Polyploid Evolution ◽  
Chloroplast Genomes ◽  
Indian Tea

Abstract Background: Chloroplast genome resources can provide useful information for the evolution of plant species. Tea plant (Camellia sinensis) is among the most economically valuable member of Camellia. Here, we determined the chloroplast genome of the first natural triploid Chinary type tea (‘Wuyi narcissus’ cultivar of Camellia sinensis var. sinensis, CWN) and conducted the genome comparison with the diploid Chinary type tea (Camellia sinensis var. sinensis, CSS) and two types of diploid Assamica type teas (Camellia sinensis var. assamica: Chinese Assamica type tea, CSA and Indian Assamica type tea, CIA). Further, the evolutionary mechanism of the chloroplast genome of Camellia sinensis and the relationships of Camellia species based on chloroplast genome were discussed.Results: Comparative analysis showed the evolutionary dynamics of chloroplast genome of Camellia sinensis were the repeats and insertion-deletions (indels), and distribution of the repeats, indels and substitutions were significantly correlated. Chinese tea and Indian tea had significant differences in the structural characteristic and the codon usage of the chloroplast genome. Analysis of sequence characterized amplified region (SCAR) using sequences of the intergenic spacers (trnE/trnT) showed none of 292 different Camellia sinensis cultivars had similar sequence characteristic to triploid CWN, but the other four Camellia species did. Estimations of the divergence time showed that CIA diverged from the common ancestor of two Assamica type teas about 6.2 Mya (CI: 4.4-8.1 Mya). CSS and CSA diverged to each other about 0.8 Mya (CI: 0.4-1.5 Mya). Moreover, phylogenetic clustering was not exactly consistent with the current taxonomy of Camellia.Conclusions: The repeat-induced and indel-induced mutations were two important dynamics contributed to the diversification of the chloroplast genome in Camellia sinensis, which were not mutually exclusive. Chinese tea and Indian tea might have undergone different selection pressures. Chloroplast transfer occurred during the polyploid evolution in Camellia sinensis. In addition, our results supported the three different domestication origins of Chinary type tea, Chinese Assamica type tea and Indian Assamica type tea. And, the current classification of some Camellia species might need to be further discussed.

scholarly journals Eusociality Shapes Convergent Patterns of Molecular Evolution across Mitochondrial Genomes of Snapping Shrimps

2020 ◽  
Author(s):  
Solomon T C Chak ◽  
Juan Antonio Baeza ◽  
Phillip Barden
Keyword(s):  
Molecular Evolution ◽  
Genome Evolution ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Mitochondrial Genomes ◽  
Comparative Genomic ◽  
Effective Population ◽  
Protein Coding ◽  
Marine Realm ◽  
Snapping Shrimps

Abstract Eusociality is a highly conspicuous and ecologically impactful behavioral syndrome that has evolved independently across multiple animal lineages. So far, comparative genomic analyses of advanced sociality have been mostly limited to insects. Here, we study the only clade of animals known to exhibit eusociality in the marine realm—lineages of socially diverse snapping shrimps in the genus Synalpheus. To investigate the molecular impact of sociality, we assembled the mitochondrial genomes of eight Synalpheus species that represent three independent origins of eusociality and analyzed patterns of molecular evolution in protein-coding genes. Synonymous substitution rates are lower and potential signals of relaxed purifying selection are higher in eusocial relative to noneusocial taxa. Our results suggest that mitochondrial genome evolution was shaped by eusociality-linked traits—extended generation times and reduced effective population sizes that are hallmarks of advanced animal societies. This is the first direct evidence of eusociality impacting genome evolution in marine taxa. Our results also strongly support the idea that eusociality can shape genome evolution through profound changes in life history and demography.

scholarly journals Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on Chloroplast genomes

2020 ◽  
Author(s):  
Benwen Liu ◽  
Yu Xin Hu ◽  
Zheng Yu Hu ◽  
Guo Xiang Liu ◽  
Huan Zhu
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Rdna Sequences ◽  
Chloroplast Genomes ◽  
Basal Clade

Abstract Background Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. Most studies have primarily focused on intergeneric phylogenetic relationships within this order and the phylogenetic relationships with four other Chlorophycean orders (Chaetophorales, Chaetopeltidales and Oedogoniales, and Volvocales). This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales. The taxonomic scheme of Chaetophorales has been inferred primarily through phylogenetic analysis based on rDNA sequences and phylogenetic relationships among families in order Chaetophorales remain unclear. Results In present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales, Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships. Conclusions In conclusion, chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and Chaetopeltidales.

scholarly journals Chloroplast phylogenomics and the dynamic evolution of Santalum (Santalaceae)

2021 ◽  
Author(s):  
Xiaojin Liu ◽  
Daping Xu ◽  
Zhou Hong ◽  
Ningnan Zhang ◽  
Zhiyi Cui
Keyword(s):  
Chloroplast Genome ◽  
Evolutionary Dynamics ◽  
Divergence Time ◽  
Major Type ◽  
Time Analysis ◽  
Chloroplast Genomes ◽  
Extant Species ◽  
History Of ◽  
Insight Into ◽  
Simple Sequence

Abstract Background Santalum (Santalaceae, sandalwood) is a hemiparasitic genus including approximately 15 extant species. It is known for its aromatic heartwood oil, which is used in incense and perfume. Demand for sandalwood-based products has led to drastic over-harvesting, and wild Santalum populations are now threatened. Knowledge of the phylogenetic relationships and genetic diversity will be critical for the conservation and proper management of this genus. Here, we sequenced the chloroplast genome of 11 Santalum species. The data were then used to investigate the chloroplast genome evolutionary dynamics and relationships and divergence time within Santalum and related species. Results The Santalum chloroplast genome contains the typical quadripartite structures, ranging from 143,291 to 144,263 bp. The chloroplast genome contains 124 genes. The whole set of ndh genes and the infA gene were found to lose their function. Between 17 and 31 SSRs were found in the Santalum chloroplast genome, and mononucleotide simple sequence repeats (SSRs) were the major type. The P-distance among the Santalum species was 0.0003 to 0.00828. Three mutation hotspot regions, 14 small inversions, and 460 indels events were discovered in the Santalum chloroplast genome. Our phylogenomic assessment provides improved resolution compared to past analyses. Our divergence time analysis shows that the crown age of Santalum was 8.46 Mya, the first divergence occurred around 6.97 Mya, and diversification was complete within approximately 1 Mya. Conclusions By sequencing the 12 chloroplast genomes of Santalum, we gain insight into the evolution of its chloroplast genomes. The chloroplast genome sequences had sufficient polymorphic information to elucidate the evolutionary history of Santalum.

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: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Li Li ◽  
Yunfei Hu ◽  
Min He ◽  
Bo Zhang ◽  
Wei Wu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Camellia Sinensis ◽  
Evolutionary Dynamics ◽  
Divergence Time ◽  
Tea Plant ◽  
Genome Comparison ◽  
Induced Mutations ◽  
Polyploid Evolution ◽  
Chloroplast Genomes ◽  
Indian Tea

Abstract Background Chloroplast genome resources can provide useful information for the evolution of plant species. Tea plant (Camellia sinensis) is among the most economically valuable member of Camellia. Here, we determined the chloroplast genome of the first natural triploid Chinary type tea (‘Wuyi narcissus’ cultivar of Camellia sinensis var. sinensis, CWN) and conducted the genome comparison with the diploid Chinary type tea (Camellia sinensis var. sinensis, CSS) and two types of diploid Assamica type teas (Camellia sinensis var. assamica: Chinese Assamica type tea, CSA and Indian Assamica type tea, CIA). Further, the evolutionary mechanism of the chloroplast genome of Camellia sinensis and the relationships of Camellia species based on chloroplast genome were discussed. Results Comparative analysis showed the evolutionary dynamics of chloroplast genome of Camellia sinensis were the repeats and insertion-deletions (indels), and distribution of the repeats, indels and substitutions were significantly correlated. Chinese tea and Indian tea had significant differences in the structural characteristic and the codon usage of the chloroplast genome. Analysis of sequence characterized amplified region (SCAR) using sequences of the intergenic spacers (trnE/trnT) showed none of 292 different Camellia sinensis cultivars had similar sequence characteristic to triploid CWN, but the other four Camellia species did. Estimations of the divergence time showed that CIA diverged from the common ancestor of two Assamica type teas about 6.2 Mya (CI: 4.4–8.1 Mya). CSS and CSA diverged to each other about 0.8 Mya (CI: 0.4–1.5 Mya). Moreover, phylogenetic clustering was not exactly consistent with the current taxonomy of Camellia. Conclusions The repeat-induced and indel-induced mutations were two important dynamics contributed to the diversification of the chloroplast genome in Camellia sinensis, which were not mutually exclusive. Chinese tea and Indian tea might have undergone different selection pressures. Chloroplast transfer occurred during the polyploid evolution in Camellia sinensis. In addition, our results supported the three different domestication origins of Chinary type tea, Chinese Assamica type tea and Indian Assamica type tea. And, the current classification of some Camellia species might need to be further discussed.

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 Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on Chloroplast genomes

2020 ◽  
Author(s):  
Benwen Liu(Former Corresponding Author) ◽  
Yu Xin Hu ◽  
Zheng Yu Hu ◽  
Guo Xiang Liu ◽  
Huan Zhu(New Corresponding Author)
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Rdna Sequences ◽  
Chloroplast Genomes ◽  
Basal Clade

Abstract Background: Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. The phylogenetic relationships of Chaetophorales have been inferred primarily through phylogenetic analysis based on rDNA sequences. Most studies have primarily focused on intergeneric phylogenetic relationships within this order and the phylogenetic relationships with four other Chlorophycean orders (Chaetophorales, Chaetopeltidales and Oedogoniales, and Volvocales). The phylogenetic relationships among families in order Chaetophorales remain unclear. This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales . Results: In the present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales. Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships. Conclusions: chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and Chaetopeltidales.

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