scholarly journals Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

2017 ◽  
Vol 49 (6) ◽  
pp. 904-912 ◽  
Author(s):  
Jarkko Salojärvi ◽  
Olli-Pekka Smolander ◽  
Kaisa Nieminen ◽  
Sitaram Rajaraman ◽  
Omid Safronov ◽  
...  
Keyword(s):  
Response Regulator ◽  
Nuclear Genome ◽  
Light Response ◽  
Silver Birch ◽  
Adaptive Landscape ◽  
Effective Population ◽  
Individual Gene ◽  
Wood Development ◽  
Environmental Responses ◽  
Cytokinin Response

Abstract Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.

scholarly journals Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1511-1518 ◽  
Author(s):  
Ning Yu ◽  
Michael I Jensen-Seaman ◽  
Leona Chemnick ◽  
Judith R Kidd ◽  
Amos S Deinard ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Demographic History ◽  
Nuclear Genome ◽  
Limited Data ◽  
Effective Population ◽  
East Central ◽  
Dna Diversity ◽  
History Of ◽  
Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

Genome-wide expression profiling of ARABIDOPSIS RESPONSE REGULATOR 7(ARR7) overexpression in cytokinin response

2006 ◽  
Vol 277 (2) ◽  
pp. 115-137 ◽  
Author(s):  
Dong Ju Lee ◽  
Jin-Young Park ◽  
Su-Jin Ku ◽  
Young-Min Ha ◽  
Sunmi Kim ◽  
...  
Keyword(s):  
Expression Profiling ◽  
Response Regulator ◽  
Genome Wide ◽  
Cytokinin Response ◽  
Genome Wide Expression

scholarly journals The Type-B Cytokinin Response Regulator ARR1 Inhibits Shoot Regeneration in an ARR12-Dependent Manner in Arabidopsis

2020 ◽  
Vol 32 (7) ◽  
pp. 2271-2291 ◽  
Author(s):  
Zhenhua Liu ◽  
Xuehuan Dai ◽  
Juan Li ◽  
Na Liu ◽  
Xiangzheng Liu ◽  
...  
Keyword(s):  
Shoot Regeneration ◽  
Response Regulator ◽  
Dependent Manner ◽  
Type B ◽  
Cytokinin Response

scholarly journals A Y-Encoded Suppressor of Feminization Arose via Lineage-Specific Duplication of a Cytokinin Response Regulator in Kiwifruit

2018 ◽  
Vol 30 (4) ◽  
pp. 780-795 ◽  
Author(s):  
Takashi Akagi ◽  
Isabelle M. Henry ◽  
Haruka Ohtani ◽  
Takuya Morimoto ◽  
Kenji Beppu ◽  
...  
Keyword(s):  
Response Regulator ◽  
Cytokinin Response

scholarly journals Author Correction: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

2019 ◽  
Vol 51 (7) ◽  
pp. 1187-1189
Author(s):  
Jarkko Salojärvi ◽  
Olli-Pekka Smolander ◽  
Kaisa Nieminen ◽  
Sitaram Rajaraman ◽  
Omid Safronov ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Silver Birch ◽  
Adaptive Landscape ◽  
Population Genomic ◽  
Genomic Analyses

Involvement of cytokinin response regulator RhRR1 in the control of flowering

2019 ◽  
Vol 41 (7) ◽  
Author(s):  
Lin Wu ◽  
Ming Feng ◽  
Yangchao Jia ◽  
Honglei Li ◽  
Yiqing Liu ◽  
...  
Keyword(s):  
Response Regulator ◽  
Cytokinin Response

scholarly journals “Ghost Introgression” As a Cause of Deep Mitochondrial Divergence in a Bird Species Complex

2019 ◽  
Vol 36 (11) ◽  
pp. 2375-2386 ◽  
Author(s):  
Dezhi Zhang ◽  
Linfang Tang ◽  
Yalin Cheng ◽  
Yan Hao ◽  
Ying Xiong ◽  
...  
Keyword(s):  
Bird Species ◽  
Nuclear Genome ◽  
Distinct Species ◽  
Comparative Genomic ◽  
Genetic Introgression ◽  
Effective Population ◽  
Westward Expansion ◽  
Whole Genomes ◽  
Linked Selection ◽  
Two Populations

Abstract In the absence of nuclear-genomic differentiation between two populations, deep mitochondrial divergence (DMD) is a form of mito-nuclear discordance. Such instances of DMD are rare and might variably be explained by unusual cases of female-linked selection, by male-biased dispersal, by “speciation reversal” or by mitochondrial capture through genetic introgression. Here, we analyze DMD in an Asian Phylloscopus leaf warbler (Aves: Phylloscopidae) complex. Bioacoustic, morphological, and genomic data demonstrate close similarity between the taxa affinis and occisinensis, even though DMD previously led to their classification as two distinct species. Using population genomic and comparative genomic methods on 45 whole genomes, including historical reconstructions of effective population size, genomic peaks of differentiation and genomic linkage, we infer that the form affinis is likely the product of a westward expansion in which it replaced a now-extinct congener that was the donor of its mtDNA and small portions of its nuclear genome. This study provides strong evidence of “ghost introgression” as the cause of DMD, and we suggest that “ghost introgression” may be a widely overlooked phenomenon in nature.

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