scholarly journals Pan-genome analyses of peach and its wild relatives provide insights into the genetics of disease resistance and species adaptation

2020 ◽  
Author(s):  
Ke Cao ◽  
Zhen Peng ◽  
Xing Zhao ◽  
Yong Li ◽  
Kuozhan Liu ◽  
...  
Keyword(s):  
High Altitude ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Genomic Analysis ◽  
Gene Families ◽  
Wild Relatives ◽  
Comparative Genomic ◽  
High Altitude Adaptation ◽  
Pan Genome ◽  
Altitude Adaptation

AbstractAs a foundation to understand the molecular mechanisms of peach evolution and high-altitude adaptation, we performed de novo genome assembling of four wild relatives of P. persica, P. mira, P. kansuensis, P. davidiana and P. ferganensis. Through comparative genomic analysis, abundant genetic variations were identified in four wild species when compared to P. persica. Among them, a deletion, located at the promoter of Prupe.2G053600 in P. kansuensis, was validated to regulate the resistance to nematode. Next, a pan-genome was constructed which comprised 15,216 core gene families among four wild peaches and P. perisca. We identified the expanded and contracted gene families in different species and investigated their roles during peach evolution. Our results indicated that P. mira was the primitive ancestor of cultivated peach, and peach evolution was non-linear and a cross event might have occurred between P. mira and P. dulcis during the process. Combined with the selective sweeps identified using accessions of P. mira originating from different altitude regions, we proposed that nitrogen recovery was essential for high-altitude adaptation of P. mira through increasing its resistance to low temperature. The pan-genome constructed in our study provides a valuable resource for developing elite cultivars, studying the peach evolution, and characterizing the high-altitude adaptation in perennial crops.

scholarly journals Genomic analysis of snub-nosed monkeys (Rhinopithecus) identifies genes and processes related to high-altitude adaptation

2016 ◽  
Vol 48 (8) ◽  
pp. 947-952 ◽  
Author(s):  
Li Yu ◽  
Guo-Dong Wang ◽  
Jue Ruan ◽  
Yong-Bin Chen ◽  
Cui-Ping Yang ◽  
...  
Keyword(s):  
High Altitude ◽  
Genomic Analysis ◽  
High Altitude Adaptation ◽  
Altitude Adaptation

scholarly journals Genomic analysis reveals variant association with high altitude adaptation in native chickens

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hamed Kharrati-Koopaee ◽  
Esmaeil Ebrahimie ◽  
Mohammad Dadpasand ◽  
Ali Niazi ◽  
Ali Esmailizadeh
Keyword(s):  
High Altitude ◽  
Genomic Analysis ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
Native Chickens

scholarly journals The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Xian-Gui Yi ◽  
Xia-Qing Yu ◽  
Jie Chen ◽  
Min Zhang ◽  
Shao-Wei Liu ◽  
...  
Keyword(s):  
Plant Disease Resistance ◽  
De Novo ◽  
Genomic Analysis ◽  
Gene Families ◽  
Single Copy ◽  
Comparative Genomic ◽  
Sequencing Technologies ◽  
History Of ◽  
Flowering Cherry ◽  
Plant Disease Resistance Genes

Abstract Cerasus serrulata is a flowering cherry germplasm resource for ornamental purposes. In this work, we present a de novo chromosome-scale genome assembly of C. serrulata by the use of Nanopore and Hi-C sequencing technologies. The assembled C. serrulata genome is 265.40 Mb across 304 contigs and 67 scaffolds, with a contig N50 of 1.56 Mb and a scaffold N50 of 31.12 Mb. It contains 29,094 coding genes, 27,611 (94.90%) of which are annotated in at least one functional database. Synteny analysis indicated that C. serrulata and C. avium have 333 syntenic blocks composed of 14,072 genes. Blocks on chromosome 01 of C. serrulata are distributed on all chromosomes of C. avium, implying that chromosome 01 is the most ancient or active of the chromosomes. The comparative genomic analysis confirmed that C. serrulata has 740 expanded gene families, 1031 contracted gene families, and 228 rapidly evolving gene families. By the use of 656 single-copy orthologs, a phylogenetic tree composed of 10 species was constructed. The present C. serrulata species diverged from Prunus yedoensis ~17.34 million years ago (Mya), while the divergence of C. serrulata and C. avium was estimated to have occurred ∼21.44 Mya. In addition, a total of 148 MADS-box family gene members were identified in C. serrulata, accompanying the loss of the AGL32 subfamily and the expansion of the SVP subfamily. The MYB and WRKY gene families comprising 372 and 66 genes could be divided into seven and eight subfamilies in C. serrulata, respectively, based on clustering analysis. Nine hundred forty-one plant disease-resistance genes (R-genes) were detected by searching C. serrulata within the PRGdb. This research provides high-quality genomic information about C. serrulata as well as insights into the evolutionary history of Cerasus species.

scholarly journals Gene Duplication and Gain in the Trematode Atriophallophorus Winterbourni Contributes to Adaptation to Parasitism

2021 ◽  
Author(s):  
Natalia Zajac ◽  
Stefan Zoller ◽  
Katri Seppälä ◽  
David Moi ◽  
Christophe Dessimoz ◽  
...  
Keyword(s):  
De Novo ◽  
Genomic Analysis ◽  
Enrichment Analysis ◽  
Gene Families ◽  
Comparative Genomic ◽  
Genomic Changes ◽  
Go Enrichment ◽  
Duplication Events ◽  
Parasitic Lifestyle ◽  
Host Parasite

Abstract Gene duplications and novel genes have been shown to play a major role in helminth adaptation to a parasitic lifestyle because they provide the novelty necessary for adaptation to a changing environment, such as living in multiple hosts. Here we present the de novo sequenced and annotated genome of the parasitic trematode Atriophallophorus winterbourni and its comparative genomic analysis to other major parasitic trematodes. First, we reconstructed the species phylogeny, and dated the split of A. winterbourni from the Opisthorchiata suborder to approximately 237.4 MYA (± 120.4 MY). We then addressed the question of which expanded gene families and gained genes are potentially involved in adaptation to parasitism. To do this, we used Hierarchical Orthologous Groups to reconstruct three ancestral genomes on the phylogeny leading to A. winterbourni and performed a GO enrichment analysis of the gene composition of each ancestral genome, allowing us to characterize the subsequent genomic changes. Out of the 11,499 genes in the A. winterbourni genome, as much as 24% have arisen through duplication events since the speciation of A. winterbourni from the Opisthorchiata, and as much as 31.9% appear to be novel, i.e. newly acquired. We found 13 gene families in A. winterbourni to have had more than 10 genes arising through these recent duplications; all of which have functions potentially relating to host behavioural manipulation, host tissue penetration, and hiding from host immunity through antigen presentation. We identified several families with genes evolving under positive selection. Our results provide a valuable resource for future studies on the genomic basis of adaptation to parasitism and point to specific candidate genes putatively involved in antagonistic host-parasite adaptation.

scholarly journals Genomic Analysis of High-Altitude Adaptation

2011 ◽  
Vol 10 (2) ◽  
pp. 59-61 ◽  
Author(s):  
Megan J. Wilson ◽  
Colleen Glyde Julian ◽  
Robert C. Roach
Keyword(s):  
High Altitude ◽  
Genomic Analysis ◽  
High Altitude Adaptation ◽  
Altitude Adaptation

scholarly journals De Novo Transcriptomic and Metabolomic Analyses Reveal the Ecological Adaptation of High-Altitude Bombus pyrosoma

Insects ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 631
Author(s):  
Yanjie Liu ◽  
Huiyue Zhao ◽  
Qihua Luo ◽  
Yadong Yang ◽  
Guangshuo Zhang ◽  
...  
Keyword(s):  
High Altitude ◽  
Signaling Pathways ◽  
De Novo ◽  
Tibet Plateau ◽  
Joint Analysis ◽  
Cold Temperatures ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
Low Altitude ◽  
Upregulated Genes

Bombus pyrosoma is one of the most abundant bumblebee species in China, with a distribution range of very varied geomorphology and vegetation, which makes it an ideal pollinator species for research into high-altitude adaptation. Here, we sequenced and assembled transcriptomes of B. pyrosoma from the low-altitude North China Plain and the high-altitude Tibet Plateau. Subsequent comparative analysis of de novo transcriptomes from the high- and low-altitude groups identified 675 common upregulated genes (DEGs) in the high-altitude B. pyrosoma. These genes were enriched in metabolic pathways and corresponded to enzyme activities involved in energy metabolism. Furthermore, according to joint analysis with comparative metabolomics, we suggest that the metabolism of coenzyme A (CoA) and the metabolism and transport of energy resources contribute to the adaptation of high-altitude B. pyrosoma. Meanwhile, we found many common upregulated genes enriched in the Toll and immune deficiency (Imd)signaling pathways that act as important immune defenses in insects, and hypoxia and cold temperatures could induce the upregulation of immune genes in insects. Therefore, we suppose that the Toll and Imd signaling pathways also participated in the high-altitude adaptation of B. pyrosoma. Like other organisms, we suggest that the high-altitude adaptation of B. pyrosoma is controlled by diverse mechanisms.

scholarly journals Genomic analysis identified a potential novel molecular mechanism for high-altitude adaptation in sheep at the Himalayas

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Neena Amatya Gorkhali ◽  
Kunzhe Dong ◽  
Min Yang ◽  
Shen Song ◽  
Adiljian Kader ◽  
...  
Keyword(s):  
High Altitude ◽  
Molecular Mechanism ◽  
Genomic Analysis ◽  
High Altitude Adaptation ◽  
Altitude Adaptation

scholarly journals High-altitude adaptation and incipient speciation in geladas

2021 ◽  
Author(s):  
Kenneth L Chiou ◽  
Mareike C Janiak ◽  
India Schneider-Crease ◽  
Sharmi Sen ◽  
Ferehiwot Ayele ◽  
...  
Keyword(s):  
High Altitude ◽  
Gene Families ◽  
Extreme Conditions ◽  
Morphometric Data ◽  
Incipient Speciation ◽  
Protein Coding ◽  
Coding Sequences ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
Insight Into

Survival at high altitude requires adapting to extreme conditions such as environmental hypoxia. To understand high-altitude adaptations in a primate, we assembled the genome of the gelada (Theropithecus gelada), an endemic Ethiopian monkey, and complemented it with population resequencing, hematological, and morphometric data. Unexpectedly, we identified a novel karyotype that may contribute to reproductive isolation between gelada populations. We also identified genomic elements including protein-coding sequences and gene families that exhibit accelerated changes in geladas and may contribute to high-altitude adaptation. Our findings lend insight into mechanisms of speciation and adaptation while providing promising avenues for functional hypoxia research.

scholarly journals Genome of octoploid plant maca (Lepidium meyenii) illuminates genomic basis for high altitude adaptation in the central Andes

2015 ◽  
Author(s):  
Jun Sheng ◽  
Wei Chen ◽  
Yang Dong ◽  
Liangsheng Zhang ◽  
Jing Zhang ◽  
...  
Keyword(s):  
High Altitude ◽  
Leaf Shape ◽  
Gene Families ◽  
Central Andes ◽  
Economic Plant ◽  
Abiotic Stress Response ◽  
High Altitude Adaptation ◽  
Lepidium Meyenii ◽  
Genome Duplications ◽  
Altitude Adaptation

Maca (Lepidium meyenii Walp, 2n = 8x = 64) of Brassicaceae family is an Andean economic plant cultivated on the 4000-4500 meters central sierra in Peru. Considering the rapid uplift of central Andes occurred 5 to 10 million years ago (Mya), an evolutionary question arises on how plants like maca acquire high altitude adaptation within short geological period. Here, we report the high-quality genome assembly of maca, in which two close-spaced maca-specific whole genome duplications (WGDs, ~ 6.7 Mya) were identified. Comparative genomics between maca and close-related Brassicaceae species revealed expansions of maca genes and gene families involved in abiotic stress response, hormone signaling pathway and secondary metabolite biosynthesis via WGDs. Retention and subsequent evolution of many duplicated genes may account for the morphological and physiological changes (i.e. small leaf shape and loss of vernalization) in maca for high altitude environment. Additionally, some duplicated maca genes under positive selection were identified with functions in morphological adaptation (i.e. MYB59) and development (i.e. GDPD5 and HDA9). Collectively, the octoploid maca genome sheds light on the important roles of WGDs in plant high altitude adaptation in the Andes.

Sign in / Sign up

Export Citation Format

Share Document