scholarly journals pSONIC: Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity

2021 ◽  
Author(s):  
Justin L Conover ◽  
Joel Sharbrough ◽  
Jonathan F Wendel
Keyword(s):  
Related Species ◽  
Tree Topology ◽  
Duplicated Genes ◽  
Rapid Rise ◽  
High Quality ◽  
Separate Species ◽  
Closely Related Species

ABSTRACTWith the rapid rise in availability of high-quality genomes for closely related species, methods for orthology inference that incorporate synteny are increasingly useful. Polyploidy perturbs the 1:1 expected frequencies of orthologs between two species, complicating the identification of orthologs. Here we present a method of ortholog inference, Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity (pSONIC). We demonstrate the utility of pSONIC using four species in the cotton tribe (Gossypieae), including one allopolyploid, and place between 75-90% of genes from each species into nearly 32,000 orthologous groups, 97% of which consist of at most singletons or tandemly duplicated genes -- 58.8% more than comparable methods that do not incorporate synteny. We show that 99% of singleton gene groups follow the expected tree topology, and that our ploidy-aware algorithm recovers 97.5% identical groups when compared to splitting the allopolyploid into its two respective subgenomes, treating each as separate “species”.

scholarly journals pSONIC: Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity

2021 ◽  
Author(s):  
Justin L Conover ◽  
Joel Sharbrough ◽  
Jonathan F Wendel
Keyword(s):  
Related Species ◽  
Tree Topology ◽  
Duplicated Genes ◽  
Rapid Rise ◽  
High Quality ◽  
Separate Species ◽  
Closely Related Species

Abstract With the rapid rise in availability of high-quality genomes for closely related species, methods for orthology inference that incorporate synteny are increasingly useful. Polyploidy perturbs the 1:1 expected frequencies of orthologs between two species, complicating the identification of orthologs. Here we present a method of ortholog inference, Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity (pSONIC). We demonstrate the utility of pSONIC using four species in the cotton tribe (Gossypieae), including one allopolyploid, and place between 75-90% of genes from each species into nearly 32,000 orthologous groups, 97% of which consist of at most singletons or tandemly duplicated genes – 58.8% more than comparable methods that do not incorporate synteny. We show that 99% of singleton gene groups follow the expected tree topology, and that our ploidy-aware algorithm recovers 97.5% identical groups when compared to splitting the allopolyploid into its two respective subgenomes, treating each as separate “species”.

scholarly journals Genes and smells

2011 ◽  
Vol 33 (6) ◽  
pp. 10-13 ◽  
Author(s):  
Andreas Keller
Keyword(s):  
Genetic Variability ◽  
Related Species ◽  
Odorant Receptor ◽  
Gene Duplications ◽  
Duplicated Genes ◽  
Vertebrate Species ◽  
Closely Related Species ◽  
Human Genomes ◽  
Or Genes

The recently sequenced genomes of several vertebrate species revealed large differences between the odorant receptor (OR) repertoires of even closely related species. These differences are a consequence of frequent gene duplications and subsequent mutations of duplicated genes. The same mechanisms are at work within a species, and different human genomes therefore show an unparalleled variability in the number and sequence of OR genes. Recent research has started to explore the consequences of this genetic variability for how we perceive odours.

A new species of the genus Phytoecia Dejean, 1835 (Coleoptera: Cerambycidae) from Greece

Zootaxa ◽  
2017 ◽  
Vol 4268 (1) ◽  
pp. 141-146
Author(s):  
WOJCIECH T. SZCZEPAŃSKI ◽  
LECH KARPIŃSKI
Keyword(s):  
New Species ◽  
Related Species ◽  
Distribution Range ◽  
Separate Species ◽  
Closely Related Species ◽  
Structural Differences ◽  
Continental Part ◽  
A New Species ◽  
Of Greece

Phytoecia (Pilemia) kruszelnickii sp. nov. from Greece is described. Distinguishing characters from closely related species are given and discussed. Moreover, Phytoecia (Pilemia) moreana Breuning 1943 stat. nov. is distinguished as a separate species based on morphological and structural differences. According to the results of our research, P. kruszelnickii is distributed exclusively within the continental part of Greece (Thessaly region) and P. moreana only occurs in the Peloponnese peninsula. However, the taxonomic division and distribution range of Phytoecia (Pilemia) hirsutula (Frölich, 1793) require further research.

scholarly journals Degree of Functional Divergence in Duplicates Is Associated with Distinct Roles in Plant Evolution

2020 ◽  
Author(s):  
Akihiro Ezoe ◽  
Kazumasa Shirai ◽  
Kousuke Hanada
Keyword(s):  
Gene Duplication ◽  
Related Species ◽  
Plant Evolution ◽  
Whole Genome ◽  
Duplicated Genes ◽  
Closely Related Species ◽  
Whole Genome Duplications ◽  
New Genes ◽  
Genome Duplications ◽  
Tandem Duplications

Abstract Gene duplication is a major mechanism to create new genes. After gene duplication, some duplicated genes undergo functionalization, whereas others largely maintain redundant functions. Duplicated genes comprise various degrees of functional diversification in plants. However, the evolutionary fate of high and low diversified duplicates is unclear at genomic scale. To infer high and low diversified duplicates in Arabidopsis thaliana genome, we generated a prediction method for predicting whether a pair of duplicate genes was subjected to high or low diversification based on the phenotypes of knock-out mutants. Among 4,017 pairs of recently duplicated A. thaliana genes, 1,052 and 600 are high and low diversified duplicate pairs, respectively. The predictions were validated based on the phenotypes of generated knock-down transgenic plants. We determined that the high diversified duplicates resulting from tandem duplications tend to have lineage-specific functions, whereas the low diversified duplicates produced by whole-genome duplications are related to essential signaling pathways. To assess the evolutionary impact of high and low diversified duplicates in closely related species, we compared the retention rates and selection pressures on the orthologs of A. thaliana duplicates in two closely related species. Interestingly, high diversified duplicates resulting from tandem duplications tend to be retained in multiple lineages under positive selection. Low diversified duplicates by whole-genome duplications tend to be retained in multiple lineages under purifying selection. Taken together, the functional diversities determined by different duplication mechanisms had distinct effects on plant evolution.

Using DNA data to determine the taxonomic status of Ammopiptanthus kamelinii in Kyrgyzstan (Thermopsideae, Leguminosae)

Phytotaxa ◽  
2018 ◽  
Vol 360 (2) ◽  
pp. 103
Author(s):  
WEI SHI ◽  
ZHIHAO SU ◽  
BORONG PAN ◽  
SHIXIN WU
Keyword(s):  
Plant Height ◽  
Related Species ◽  
Taxonomic Status ◽  
Genetic Data ◽  
Separate Species ◽  
Closely Related Species ◽  
Phenotypic Characters ◽  
Significant Difference ◽  
Cpdna Markers ◽  
Complex Relationships

The taxonomic status of Ammopiptanthus kamelinii has been unresolved because of numerous characters that make it similar to another closely related species, A. nanus. In this study, we set out to resolve the complex relationships among A. kamelinii using samples from three populations, with a total of 38 individuals. Phenotypic indices (plant height, canopy, and leaf characters) and DNA data (ITS 1–4 nrDNA markers, as well as trnH-psbA, trnL-trnF, and trnS-trnG cpDNA markers) were used to understand the controversial taxonomic status of A. kamelinii. The phenotypic characters of A. kamelinii did not show a significant difference from A. nanus, and the nrDNA data did not reflect any variability from A. nanus, but all the individuals of A. kamelinii in Kyrgyzstan showed two new haplotypes in the cpDNA. When the genetic data were combined, specimens of A. kamelinii clustered together with A. nanus; therefore, we have confirmed that A. kamelinii cannot be recognized as a separate species of A. nanus and should be merged with the latter species. The description of A. nanus is revised here.

Microsatellite Marker: Importance and Implications of Cross-genome Analysis for Finger Millet (Eleusine coracana (L.) Gaertn)

2020 ◽  
Vol 9 (3) ◽  
pp. 160-170
Author(s):  
Thumadath P.A. Krishna ◽  
Maharajan Theivanayagam ◽  
Gurusunathan V. Roch ◽  
Veeramuthu Duraipandiyan ◽  
Savarimuthu Ignacimuthu
Keyword(s):  
Molecular Marker ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Genome Analysis ◽  
Related Species ◽  
Finger Millet ◽  
Crop Improvement ◽  
Human Beings ◽  
Closely Related Species ◽  
Genome Amplification

Finger millet is a superior staple food for human beings. Microsatellite or Simple Sequence Repeat (SSR) marker is a powerful tool for genetic mapping, diversity analysis and plant breeding. In finger millet, microsatellites show a higher level of polymorphism than other molecular marker systems. The identification and development of microsatellite markers are extremely expensive and time-consuming. Only less than 50% of SSR markers have been developed from microsatellite sequences for finger millet. Therefore, it is important to transfer SSR markers developed for related species/genus to finger millet. Cross-genome transferability is the easiest and cheapest method to develop SSR markers. Many comparative mapping studies using microsatellite markers clearly revealed the presence of synteny within the genomes of closely related species/ genus. Sufficient homology exists among several crop plant genomes in the sequences flanking the SSR loci. Thus, the SSR markers are beneficial to amplify the target regions in the finger millet genome. Many SSR markers were used for the analysis of cross-genome amplification in various plants such as Setaria italica, Pennisetum glaucum, Oryza sativa, Triticum aestivum, Zea mays and Hordeum vulgare. However, there is very little information available about cross-genome amplification of these markers in finger millet. The only limited report is available for the utilization of cross-genome amplified microsatellite markers in genetic analysis, gene mapping and other applications in finger millet. This review highlights the importance and implication of microsatellite markers such as genomic SSR (gSSR) and Expressed Sequence Tag (EST)-SSR in cross-genome analysis in finger millet. Nowadays, crop improvement has been one of the major priority areas of research in agriculture. The genome assisted breeding and genetic engineering plays a very crucial role in enhancing crop productivity. The rapid advance in molecular marker technology is helpful for crop improvement. Therefore, this review will be very helpful to the researchers for understanding the importance and implication of SSR markers in closely related species.

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