scholarly journals Insights into phylogeny, age and evolution of Allium (Amaryllidaceae) based on the whole plastome sequences

2020 ◽  
Vol 125 (7) ◽  
pp. 1039-1055 ◽  
Author(s):  
Deng-Feng Xie ◽  
Jin-Bo Tan ◽  
Yan Yu ◽  
Lin-Jian Gui ◽  
Dan-Mei Su ◽  
...  
Keyword(s):  
Divergence Time ◽  
Species Relationships ◽  
Allium Species ◽  
The Third ◽  
Evolutionary Lineage ◽  
Chloroplast Genomes ◽  
Medicinal Value ◽  
Relationship Of ◽  
Ks Values ◽  
Evolutionary Lineages

Abstract Background and Aims The genus Allium L., one of the largest monocotyledonous genera and one that includes many economically important crops with nutritional and medicinal value, has been the focus of classification or phylogeny studies for centuries. Recent studies suggested that the genus can be divided into 15 subgenera and 72 sections, which were further classified into three evolutionary lineages. However, the phylogenetic relationships reconstructed by one or two loci showed weaker support, especially for the third evolutionary lineage, which might not show the species relationships very clearly and could hinder further adaptive and evolutionary study. Methods In this study, a total of 39 complete chloroplast genomes of Allium (covering 12 Allium subgenera) were collected, and combining these with 125 species of plastomes from 19 other families of monocots, we reconstructed the phylogeny of the genus Allium, estimated the origin and divergence time of the three evolutionary lineages and investigated the adaptive evolution in this genus and related families. Results Our phylogenetic analysis confirmed the monophyly and three evolutionary lineages of Allium, while new species relationships were detected within the third evolutionary lineage. The divergence time of the three evolutionary lineages was estimated to be in the early Eocene to the middle Miocene, and numerous positive selected genes (PSGs) and PSGs with high average Ka/Ks values were found in Allium species. Conclusions Our results detected a well-supported phylogenetic relationship of Allium. The PSGs and PSGs with high Ka/Ks values, as well as diversified morphologies, complicated chromosome characteristics and unique reproductive modes may play important roles in the adaptation and evolution of Allium species. This is the first study that conducted phylogenetic and evolutionary analyses on the genus Allium combined with the plastome and morphological and cytological data. We hope that this study can contribute to further analysis of Allium for other researchers.

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 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 Comparison of chloroplast genomes of Gynura species: sequence variation, genome rearrangement and divergence studies

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Tianyu Han ◽  
Mimi Li ◽  
Jiawei Li ◽  
Han Lv ◽  
Bingru Ren ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Genome Rearrangement ◽  
Divergence Time ◽  
Purifying Selection ◽  
Genome Sequences ◽  
Chloroplast Genomes ◽  
Genome Features ◽  
Relationship Of

Abstract Background Some Gynura species have been reported to be natural anti-diabetic plants. Improvement of their traits towards application relies on hybridization. Clearly, phylogenetic relationships could optimize compatible hybridizations. For flowerings plants, chloroplast genomes have been used to solve many phylogenetic relationships. To date, the chloroplast genome sequences of 4 genera of the tribe Senecioneae have been uploaded to GenBank. The internal relationships within the genus Gynura and the relationship of the genus Gynura with other genera in the tribe Senecioneae need further research. Results The chloroplast genomes of 4 Gynura species were sequenced, assembled and annotated. In comparison with those of 12 other Senecioneae species, the Gynura chloroplast genome features were analysed in detail. Subsequently, differences in the microsatellite and repeat types in the tribe were found. From the comparison, it was found that IR expansion and contraction are conserved in the genera Gynura, Dendrosenecio and Ligularia. Compared to other regions on the chloroplast genome, the region from 25,000 to 50,000 bp was not conserved. Seven ndh genes in this region are under purifying selection, with small changes in amino acids. The whole chloroplast genome sequences of 16 Senecioneae species were used to build a phylogenetic tree. Based on the oldest Artemisia pollen fossil, the divergence time was estimated. Conclusions Sequencing the chloroplast genomes of 4 Gynura species helps us to solve many problems. The phylogenetic relationships and divergence time among 4 Gynura and 16 Senecioneae species were evaluated by comparing their chloroplast genomes. The phylogenetic relationship of the genera Gynura and Ligularia was different from that observed previous work. In a previous phylogenetic tree, the genus Ligularia belonged to the Tussilagininae subtribe, which was in a lineage that diverged earlier than other genera. Further morphology and genome-wide analyses are needed to clarify the genus relationships.

scholarly journals Out of the Qinghai-Tibetan Plateau (QTP) and rapid radiation across Eurasia for Allium section Daghestanica (Amaryllidaceae)

AoB Plants ◽  
2021 ◽  
Author(s):  
Min-Jie Li ◽  
Huan-Xi Yu ◽  
Xian-Lin Guo ◽  
Xing-Jin He
Keyword(s):  
Evolutionary History ◽  
Divergence Time ◽  
Time Estimation ◽  
Adjacent Region ◽  
Rapid Radiation ◽  
Divergence Time Estimation ◽  
Species Diversification ◽  
The Third ◽  
Evolutionary Line ◽  
History Of

Abstract The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of the modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidate the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the QTP and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4–3 Mya. Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.

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 Airline Financial Distress and Customer Satisfaction

2011 ◽  
Vol 48 (1) ◽  
Author(s):  
Dina Ribbink ◽  
Christian Hofer ◽  
Martin Dresner
Keyword(s):  
Customer Service ◽  
Airline Industry ◽  
Financial Distress ◽  
Service Levels ◽  
The Third ◽  
Time Performance ◽  
Using Data ◽  
Relationship Of ◽  
The Impact ◽  
The Relationship

An investigation is conducted on the effect of financial distress on customer service levels in the U.S. airline industry. Using data from the first quarter of 1998 to the third quarter of 2006, we employ a seemingly unrelated regressions (SUR) model to analyze the impact of financial distress on three measures of customer service. We find that higher financial distress is associated with better on-time performance of airlines and fewer lost bags. The relationship of airline financial distress to the number of bumped customers, however, is insignificant.

scholarly journals Observations on the age and growth of Varicorhinus damascinus (Val.) in Tigris river at Salahuldin province – Iraq

2008 ◽  
Vol 5 (2) ◽  
pp. 243-248
Author(s):  
Baghdad Science Journal
Keyword(s):  
Regression Coefficient ◽  
Age Groups ◽  
Age And Growth ◽  
Gill Nets ◽  
The Third ◽  
Weight Relationship ◽  
Tigris River ◽  
Straight Line ◽  
Males And Females ◽  
Relationship Of

Age and growth of Varicorhinus damascinus (Val.) in Tigris river at Salahuldin province have been investigated. Monthly samples were taken during the period from September 1999 to August 2000, using small-meshed gill nets. The age data showed that there were six age groups and the dominant age groups were (III – IV) for both sexes. The results of the present study revealed that the increment in length of V. damascinus at the sites of study showed a tendency to decrease with the increase in age, after the third year of life in both sexes. The length-weight relationship of males and females were calculated and demonstrated in a straight line logarithmic formula, as follows: Log W = 1.5404 + 2.6885 log L for males r = 0.95 (P > 0.05) Log W = 1.6723 + 2.7877 log L for females r = 0.77 (P > 0.05) The values of the regression coefficient (b) indicated that the growth of both sexes of V. damascinus was allometric..

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