scholarly journals The Evolutionary History of Human and Chimpanzee Y-Chromosome Gene Loss

2006 ◽  
Vol 24 (3) ◽  
pp. 853-859 ◽  
Author(s):  
G. H. Perry ◽  
R. Y. Tito ◽  
B. C. Verrelli
Keyword(s):  
Y Chromosome ◽  
Evolutionary History ◽  
Gene Loss ◽  
Chromosome Gene ◽  
History Of

scholarly journals Insights on the process of reciprocal gene loss in the duplicate DPL genes of rice

2019 ◽  
Author(s):  
Xun Xu ◽  
Song Ge ◽  
Fu-min Zhang
Keyword(s):  
Evolutionary History ◽  
Gene Loss ◽  
Diploid Species ◽  
Recent Common Ancestor ◽  
Duplicate Genes ◽  
Evolutionary Divergence ◽  
Dna Transposons ◽  
B Genome ◽  
A Genome ◽  
History Of

Abstract Background: Reciprocal gene loss (RGL) of duplicate genes is an important genetic resource of reproductive isolation, which is essential for speciation. In the past decades, various RGL patterns have been revealed, but RGL process is still poorly understood. The RGL of the duplicate DOPPELGANGER1 (DPL1) and DOPPELGANGER2 (DPL2) gene can lead to BDM-type hybrid incompatibility between two rice subspecies. The evolutionary history of the duplicate genes, including their origin and mechanism of duplication as well as their evolutionary divergence after the duplication, remains unclear. In this study, we investigated the evolutionary history of the duplicate genes for gaining insights into the process of RGL.Results: We reconstructed phylogenetic relationships of DPL copies from all 15 diploid species representing six genome types of rice genus and then found that all the DPL copies from the latest diverged A- and B-genome gather into one monophyletic clade. Southern blot analysis also detected definitely two DPL copies only in A- and B-genome. High conserved collinearity can be observed between A- and B-genomic segments containing DPL1 and DPL2 respectively but not between DPL1 and DPL2 segments. Investigations of transposon elements indicated that DPL duplication is related to DNA transposons. Likelihood-based analyses with branch models showed a relaxation of selective constraint in DPL1 lineage but an enhancement in DPL2 lineage after DPL duplication. Sequence analysis also indicated that quite a few defective DPL1 can be found in 6 wild and cultivated species out of all 8 species of A-genome but only one defective DPL2 occurs in a cultivated rice subspecies. Conclusions: DPL duplication of rice originated in the recent common ancestor of A- and B-genome about 6.76 million years ago and the duplication was possibly caused by DNA transposons. The DPL1 is a redundant copy and has being in the process of pseudogenization, suggesting that artificial selection may play an important role in forming the RGL of DPLs between two rice subspecies during the domestication.

scholarly journals Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yoichiro Nakatani ◽  
Prashant Shingate ◽  
Vydianathan Ravi ◽  
Nisha E. Pillai ◽  
Aravind Prasad ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Gene Loss ◽  
De Novo ◽  
Genome Structure ◽  
Origin And Evolution ◽  
Long Read ◽  
History Of ◽  
And Function ◽  
Genome Assemblies ◽  
Key Questions

AbstractAncient polyploidization events have had a lasting impact on vertebrate genome structure, organization and function. Some key questions regarding the number of ancient polyploidization events and their timing in relation to the cyclostome-gnathostome divergence have remained contentious. Here we generate de novo long-read-based chromosome-scale genome assemblies for the Japanese lamprey and elephant shark. Using these and other representative genomes and developing algorithms for the probabilistic macrosynteny model, we reconstruct high-resolution proto-vertebrate, proto-cyclostome and proto-gnathostome genomes. Our reconstructions resolve key questions regarding the early evolutionary history of vertebrates. First, cyclostomes diverged from the lineage leading to gnathostomes after a shared tetraploidization (1R) but before a gnathostome-specific tetraploidization (2R). Second, the cyclostome lineage experienced an additional hexaploidization. Third, 2R in the gnathostome lineage was an allotetraploidization event, and biased gene loss from one of the subgenomes shaped the gnathostome genome by giving rise to remarkably conserved microchromosomes. Thus, our reconstructions reveal the major evolutionary events and offer new insights into the origin and evolution of vertebrate genomes.

scholarly journals Evolutionary history of novel genes on the tammar wallaby Y chromosome: Implications for sex chromosome evolution

2011 ◽  
Vol 22 (3) ◽  
pp. 498-507 ◽  
Author(s):  
V. J. Murtagh ◽  
D. O'Meally ◽  
N. Sankovic ◽  
M. L. Delbridge ◽  
Y. Kuroki ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Evolutionary History ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Tammar Wallaby ◽  
Sex Chromosome Evolution ◽  
Novel Genes ◽  
History Of

Genomic regression of claw keratin, taste receptor and light-associated genes inform biology and evolutionary origins of snakes

2017 ◽  
Author(s):  
Christopher A. Emerling
Keyword(s):  
Evolutionary History ◽  
Light Adaptation ◽  
Gene Loss ◽  
Taste Receptor ◽  
Taste Buds ◽  
Molecular Dating ◽  
Evolutionary Origins ◽  
Associated Functions ◽  
History Of ◽  
Dim Light

AbstractRegressive evolution of anatomical traits corresponds with the regression of genomic loci underlying such characters. As such, studying patterns of gene loss can be instrumental in addressing questions of gene function, resolving conflicting results from anatomical studies, and understanding the evolutionary history of clades. The origin of snakes coincided with the regression of a number of anatomical traits, including limbs, taste buds and the visual system. By studying the genomes of snakes, I was able to test three hypotheses associated with the regression of these features. The first concerns two keratins that are putatively specific to claws. Both genes that encode these keratins were pseudogenized/deleted in snake genomes, providing additional evidence of claw- specificity. The second hypothesis is whether snakes lack taste buds, an issue complicated by unequivocal, conflicting results in the literature. I found evidence that different snakes have lost one or more taste receptors, but all snakes examined retained at least some capacity for taste. The final hypothesis I addressed is that the earliest snakes were adapted to a dim light niche. I found evidence of deleted and pseudogenized genes with light- associated functions in snakes, demonstrating a pattern of gene loss similar to other historically nocturnal clades. Together these data also provide some bearing on the ecological origins of snakes, including molecular dating estimates that suggest dim light adaptation preceded the loss of limbs.

scholarly journals Sex chromosome-to-autosome transposition events counter Y-chromosome gene loss in mammals

2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Jennifer F Hughes ◽  
Helen Skaletsky ◽  
Natalia Koutseva ◽  
Tatyana Pyntikova ◽  
David C Page
Keyword(s):  
Y Chromosome ◽  
Gene Loss ◽  
Sex Chromosome ◽  
Chromosome Gene
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