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Divergence time

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Chloroplast phylogenomics and divergence times of Lagerstroemia (Lythraceae)

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Divergence time of Lagerstroemia. The fossil record of the Lagerstroemia consists of leaf impressions, wood, and pollen [18]. According to the fossil record, the oldest confirmed evidence of the Lager- stroemia is a leaf impression of L. Those records indicated the origin time of Lagerstroemia was earlier than 56 Ma.. There were a number of putative fossil Lagerstroemia leaves and wood in the middle Miocene [18].

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

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The traditional view on diver- gence time of the genus Gynura is in the Old World after the Atlantic opening. The divergence time of Gynura spe- cies was approximately 0.3 mya, and the result showed that the divergence time of the genus Gynura was much earlier than that of the traditional view.

New insights into the evolution and functional divergence of the CIPK gene family in Saccharum

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By estimat- ing the divergence time of these 16 pairs of duplicated genes with an average duplication time of approximately 35.66 Mya, we hypothesize that these duplication events occurred after the divergence of the monocots and eudicots (165 Mya) [63]. In addition, the divergence time of the BrCIPK paralogs was be- tween 1.4457 and 28.1533 Mya, with an average du- plication time of approximately 12.4194 Mya [65]..

Effects of parental genetic divergence on gene expression patterns in interspecific hybrids of Camellia

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That means the relative frequency of cis- and trans-regulatory changes in hybrids may be related to the divergence time between the parental species. However, the results were completely different for that the propor- tions of genes with significant evidence of cis- and trans- regulatory divergence in the intra-sectional cross (C.. chekiangoleosa) were 8.09 and 13.34%, respectively, whereas in the inter-sectional cross of C..

Identification, evolution and expression analyses of whole genome-wide TLP gene family in Brassica napus

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In addition, the divergence time and selection types of orthologous TLP gene pairs were calculated according to the nonsynonymous substitutions (Ka) and synonymous (Ks). 1, indi- cating purifying selection on these orthologous TLP gene pairs. Furthermore, we estimated the divergence time of orthologous TLP gene pairs according to syn- onymous substitution rate (Table S3). The results indi- cated that the divergence time was million years ago (Mya) for 28 orthologous TLP gene pairs be- tween B.

Genome-wide analyses of the relict gull (Larus relictus): Insights and evolutionary implications

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The genus Larus was split with Rissa tridactyla at approximately 20.51 Mya, which was close to that divergence time of the genus between Larus and Rissa. from other species were estimated at approximately 69.81 Mya, which is in agreement with the divergence time of the Charadriiformes as a whole (79–102 Mya) [27]..

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

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Estimations of the divergence time showed that CIA diverged from the common ancestor of two Assamica type teas about 6.2 Mya (CI Mya). 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. Full list of author information is available at the end of the article Li et al.

The draft genome of horseshoe crab Tachypleus tridentatus reveals its evolutionary scenario and well-developed innate immunity

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On the time axis, the green bar shows the divergence time for split of the scorpion from horseshoe crabs. the brown bar shows the inner split time of the three spiders. the blue bar shows the origin of the the last common ancestor of Asian horseshoe crabs (including T. Analysis of the Hox gene family showed that the T. We further examined the positions of the identified Hox genes in the two genomes and found two clusters of adjacently distributed Hox1 and Hox4 in the T.

Comparative genomics of four strains of the edible brown alga, Cladosiphon okamuranus

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The branch length or divergence time between the S-strain. Four strains of Cladosiphon okamuranus are classified as the order Chordariales. and the K/C/O-strains is longer than that between the K-strain and the C/O-strains. This suggests that the S-strain is the likely ancestor of the four strains, and that the K-strain probably blanched out first from the K/C/O-strains ancestor. Conservation of genome architecture among the four strains. 3b-f) suggested that the four strains of C.

Genome-wide identification and expression analysis of the B-box transcription factor gene family in grapevine (Vitis vinifera L.)

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The divergence time of the segmental duplication event was calcu- lated as between ~ 77 and 110 million years ago (Mya) in grapevine alone (Additional file 6: Table S2), and between ~ 102 and 349 Mya, with an average of 178.8 Mya, in grapevine and Arabidopsis (Additional file 7: Table S3)..

The structure, functional evolution, and evolutionary trajectories of the H+ -PPase gene family in plants

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Divergence time indicates the estimated divergence time of the genus that each species belongs to according to data obtained from the online database Timetree (http://www.timetree.org. This seed alignment was used as a background to explore the genetic position of the plant H + -PPases.. Identification of H + -PPase gene family members. Because the protein domain of the H. These results were used for down- stream analysis of the H + -PPase gene family..

Evolution of cis- and trans-regulatory divergence in the chicken genome between two contrasting breeds analyzed using three tissue types at one-day-old

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Previous studies on regulatory divergence genes did not select identical time points from the embryo to adult. therefore, different results would be obtained from the regulatory divergence genes across different development stages.. First, the SNP list we used to identify the parental origin was fil- tered strictly from the re-sequencing data of the four parents.

Genetic divergence analysis in advanced breeding lines of groundnut (Arachis hypogaea L.)

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Genetic Divergence Analysis in Advanced Breeding Lines of Groundnut (Arachis hypogaea L.).

Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa)

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The heritable transcriptional divergence may be due to genetic variants that influence gene expression and are divergent between Indica and Japonica.

Genetic boundaries delineate the potential human pathogen Salmonella bongori into discrete lineages: Divergence and speciation

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Later, Subgroup V regained the scientific name of Salmonella bongori based on its greater genetic divergence from all other subgroups [25]. bongori, but the precise phylogenetic rela- tionships of the bacteria among the serotypes and the phyletic status within each of the serotypes remain largely unclear..

Contrasting genetic variation and positive selection followed the divergence of NBSencoding genes in Asian and European pears

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For instance, only 6 and 5 NBS-encoding genes show high divergence (F ST value >.

Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria

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Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria. Full list of author information is available at the end of the article. The haploid genome of the reference isolate IPO323 comprises thirteen core and eight accessory chromosomes [23].

Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): Insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales

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In this study, we elucidated the complete chloroplast genome of S. persica cp genome cp genome annotation. persica cp genome divergence with related eleven species where S. persica phylogenetic analysis and cp genome divergence. Chloroplast genome divergence among S. org/10.1186/s x..

Comparative population genomics reveals genetic divergence and selection in lotus, Nelumbo nucifera

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The observed differences in mapping rates were caused by the divergence between the sequenced geno- types and the reference genome of the sacred lotus var- iety ‘China Antique’.. and average, 0.17%) for rhizome lotus. Most of the wild sacred lotus accessions showed low heterozy- gosity (Het rate.

The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data

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Depending on the used data and underlying assumption about biological clocks, estimates of divergence between Bos taurus and Bos indicus vary from approximately 200, 000 to 300,000 years BP to 575,000 to. a East African crossbreds. The PCA and F ST results showed a clear divergence between Bos indicus , African Bos taurus , and European Bos taurus reference breeds, which is in agreement with several previous studies [4, 26–32].