scholarly journals Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication

2020 ◽  
Vol 52 (12) ◽  
pp. 1423-1432 ◽  
Author(s):  
Xuepeng Sun ◽  
Chen Jiao ◽  
Heidi Schwaninger ◽  
C. Thomas Chao ◽  
Yumin Ma ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Hybrid Origin ◽  
Selective Sweeps ◽  
Specific Expression ◽  
Genetic History ◽  
New Genes ◽  
History Of ◽  
Allele Specific ◽  
Genome Assemblies ◽  
Wild Progenitors

AbstractDomestication of the apple was mainly driven by interspecific hybridization. In the present study, we report the haplotype-resolved genomes of the cultivated apple (Malus domestica cv. Gala) and its two major wild progenitors, M. sieversii and M. sylvestris. Substantial variations are identified between the two haplotypes of each genome. Inference of genome ancestry identifies ~23% of the Gala genome as of hybrid origin. Deep sequencing of 91 accessions identifies selective sweeps in cultivated apples that originated from either of the two progenitors and are associated with important domestication traits. Construction and analyses of apple pan-genomes uncover thousands of new genes, with hundreds of them being selected from one of the progenitors and largely fixed in cultivated apples, revealing that introgression of new genes/alleles is a hallmark of apple domestication through hybridization. Finally, transcriptome profiles of Gala fruits at 13 developmental stages unravel ~19% of genes displaying allele-specific expression, including many associated with fruit quality.

scholarly journals Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars

BMC Biology ◽  
2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Joel-E. Kuon ◽  
Weihong Qi ◽  
Pascal Schläpfer ◽  
Matthias Hirsch-Hoffmann ◽  
Philipp Rogalla von Bieberstein ◽  
...  
Keyword(s):  
De Novo ◽  
Haplotype Diversity ◽  
Mosaic Disease ◽  
Cassava Mosaic Disease ◽  
Specific Expression ◽  
Tropical Regions ◽  
Genome Maps ◽  
Gene Sets ◽  
Allele Specific ◽  
Genome Assemblies

Abstract Background Cassava is an important food crop in tropical and sub-tropical regions worldwide. In Africa, cassava production is widely affected by cassava mosaic disease (CMD), which is caused by the African cassava mosaic geminivirus that is transmitted by whiteflies. Cassava breeders often use a single locus, CMD2, for introducing CMD resistance into susceptible cultivars. The CMD2 locus has been genetically mapped to a 10-Mbp region, but its organization and genes as well as their functions are unknown. Results We report haplotype-resolved de novo assemblies and annotations of the genomes for the African cassava cultivar TME (tropical Manihot esculenta), which is the origin of CMD2, and the CMD-susceptible cultivar 60444. The assemblies provide phased haplotype information for over 80% of the genomes. Haplotype comparison identified novel features previously hidden in collapsed and fragmented cassava genomes, including thousands of allelic variants, inter-haplotype diversity in coding regions, and patterns of diversification through allele-specific expression. Reconstruction of the CMD2 locus revealed a highly complex region with nearly identical gene sets but limited microsynteny between the two cultivars. Conclusions The genome maps of the CMD2 locus in both 60444 and TME3, together with the newly annotated genes, will help the identification of the causal genetic basis of CMD2 resistance to geminiviruses. Our de novo cassava genome assemblies will also facilitate genetic mapping approaches to narrow the large CMD2 region to a few candidate genes for better informed strategies to develop robust geminivirus resistance in susceptible cassava cultivars.

scholarly journals Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis

2021 ◽  
Author(s):  
Xingtan Zhang ◽  
Shuai Chen ◽  
Longqing Shi ◽  
Daping Gong ◽  
Shengcheng Zhang ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Evolutionary History ◽  
Green Revolution ◽  
Genomic Analysis ◽  
Tea Plant ◽  
Specific Expression ◽  
History Of ◽  
Allele Specific ◽  
Tea Cultivar

AbstractTea is an important global beverage crop and is largely clonally propagated. Despite previous studies on the species, its genetic and evolutionary history deserves further research. Here, we present a haplotype-resolved assembly of an Oolong tea cultivar, Tieguanyin. Analysis of allele-specific expression suggests a potential mechanism in response to mutation load during long-term clonal propagation. Population genomic analysis using 190 Camellia accessions uncovered independent evolutionary histories and parallel domestication in two widely cultivated varieties, var. sinensis and var. assamica. It also revealed extensive intra- and interspecific introgressions contributing to genetic diversity in modern cultivars. Strong signatures of selection were associated with biosynthetic and metabolic pathways that contribute to flavor characteristics as well as genes likely involved in the Green Revolution in the tea industry. Our results offer genetic and molecular insights into the evolutionary history of Camellia sinensis and provide genomic resources to further facilitate gene editing to enhance desirable traits in tea crops.

scholarly journals Reannotation of the cultivated strawberry genome and establishment of a strawberry genome database

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Tianjia Liu ◽  
Muzi Li ◽  
Zhongchi Liu ◽  
Xiaoyan Ai ◽  
Yongping Li
Keyword(s):  
Developmental Stages ◽  
Expression Profiles ◽  
Hybrid Origin ◽  
Rna Seq ◽  
Crop Species ◽  
Genome Database ◽  
Functional Studies ◽  
New Genes ◽  
Alternatively Spliced ◽  
Current Annotation

AbstractCultivated strawberry (Fragaria × ananassa) is an important fruit crop species whose fruits are enjoyed by many worldwide. An octoploid of hybrid origin, the complex genome of this species was recently sequenced, serving as a key reference genome for cultivated strawberry and related species of the Rosaceae family. The current annotation of the F. ananassa genome mainly relies on ab initio predictions and, to a lesser extent, transcriptome data. Here, we present the structure and functional reannotation of the F. ananassa genome based on one PacBio full-length RNA library and ninety-two Illumina RNA-Seq libraries. This improved annotation of the F. ananassa genome, v1.0.a2, comprises a total of 108,447 gene models, with 97.85% complete BUSCOs. The models of 19,174 genes were modified, 360 new genes were identified, and 11,044 genes were found to have alternatively spliced isoforms. Additionally, we constructed a strawberry genome database (SGD) for strawberry gene homolog searching and annotation downloading. Finally, the transcriptome of the receptacles and achenes of F. ananassa at four developmental stages were reanalyzed and qualified, and the expression profiles of all the genes in this annotation are also provided. Together, this study provides an updated annotation of the F. ananassa genome, which will facilitate genomic analyses across the Rosaceae family and gene functional studies in cultivated strawberry.

scholarly journals The haplotype-resolved chromosome pairs and transcriptome of a heterozygous diploid African cassava cultivar

2021 ◽  
Author(s):  
Weihong Qi ◽  
Yi-Wen Lim ◽  
Andrea Patrignani ◽  
Pascal Schlaepfer ◽  
Anna Bratus-Neuenschwander ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Cost Effective ◽  
Structural Variations ◽  
Specific Expression ◽  
Tropical Regions ◽  
Reference Quality ◽  
Allele Specific ◽  
High Gene ◽  
Genome Assemblies ◽  
Genome Comparisons

Background: Cassava (Manihot esculenta) is an important clonally propagated food crop in tropical and sub-tropical regions worldwide. Genetic gain by molecular breeding is limited because cassava has a highly heterozygous, repetitive and difficult to assemble genome. Findings: Here we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, in combination with the assembler hifiasm, produced genome assemblies at near complete haplotype resolution with higher continuity and accuracy compared to conventional long sequencing reads. We present two chromosome scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. Genome comparisons revealed extensive chromosome re-arrangements and abundant intra-genomic and inter-genomic divergent sequences despite high gene synteny, with most large structural variations being LTR-retrotransposon related. Allele-specific expression analysis of different tissues based on the haplotype-resolved transcriptome identified both stable and inconsistent alleles with imbalanced expression patterns, while most alleles expressed coordinately. Among tissue-specific differentially expressed transcripts, coordinately and biasedly regulated transcripts were functionally enriched for different biological processes. We use the reference-quality assemblies to build a cassava pan-genome and demonstrate its importance in representing the genetic diversity of cassava for downstream reference-guided omics analysis and breeding. Conclusions: The haplotype-resolved genome allows the first systematic view of the heterozygous diploid genome organization in cassava. The completely phased and annotated chromosome pairs will be a valuable resource for cassava breeding and research. Our study may also provide insights into developing cost-effective and efficient strategies for resolving complex genomes with high resolution, accuracy and continuity.

scholarly journals Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

2019 ◽  
Author(s):  
Wai Yee Low ◽  
Rick Tearle ◽  
Ruijie Liu ◽  
Sergey Koren ◽  
Arang Rhie ◽  
...  
Keyword(s):  
Copy Number Variants ◽  
Fatty Acid Desaturase ◽  
Gene Families ◽  
Specific Reference ◽  
Single Individual ◽  
Extra Copy ◽  
Specific Expression ◽  
Genome Wide ◽  
Allele Specific ◽  
Genome Assemblies

AbstractWe present high quality, phased genome assemblies representative of taurine and indicine cattle, subspecies that differ markedly in productivity-related traits and environmental adaptation. We report a new haplotype-aware scaffolding and polishing pipeline using contigs generated by the trio binning method to produce haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle breeds. These assemblies were used to identify structural and copy number variants that differentiate the subspecies and we found variant detection was sensitive to the specific reference genome chosen. Six gene families with immune related functions are expanded in the indicine lineage. Assembly of the genomes of both subspecies from a single individual enabled transcripts to be phased to detect allele-specific expression, and to study genome-wide selective sweeps. An indicus-specific extra copy of fatty acid desaturase is under positive selection and may contribute to indicine adaptation to heat and drought.

scholarly journals Gene age predicts the transcriptional landscape of sexual morphogenesis in multicellular fungi

2021 ◽  
Author(s):  
Zsolt Merenyi ◽  
Mate Viragh ◽  
Emile Gluck-Thaler ◽  
Jason C. Slot ◽  
Brigitta Kiss ◽  
...  
Keyword(s):  
Gene Expression ◽  
Evolutionary Constraint ◽  
Regulatory Evolution ◽  
Specific Expression ◽  
Developmental Gene Expression ◽  
Evolutionary Changes ◽  
History Of ◽  
Allele Specific ◽  
Gene Age

Multicellularity has been one of the most important innovations in the history of life. The role of regulatory evolution in driving transitions to multicellularity is being increasingly recognized; however, patterns and drivers of transcriptome evolution are poorly known in many clades. We here reveal that allele-specific expression, natural antisense transcripts and developmental gene expression, but not RNA editing or a developmental hourglass act in concert to shape the transcriptome of complex multicellular fruiting bodies of fungi. We find that transcriptional patterns of genes are strongly predicted by their evolutionary age. Young genes showed more expression variation both in time and space, possibly because of weaker evolutionary constraint, calling for partially non-adaptive interpretations of evolutionary changes in the transcriptome of multicellular fungi. Gene age also correlated with function, allowing us to separate fruiting body gene expression related to simple sexual development from that potentially underlying complex morphogenesis. Our study highlighted a transcriptional complexity that provides multiple speeds for transcriptome evolution, but also that constraints associated with gene age shape transcriptomic patterns during transitions to complex multicellularity in fungi.

Review of early developmental stages of trilobites and agnostids from the Barrandian area (Czech Republic)

2017 ◽  
Vol 186 (1) ◽  
pp. 103-112
Author(s):  
Lukáš Laibl ◽  
Oldřich Fatka
Keyword(s):  
Czech Republic ◽  
Developmental Stages ◽  
History Of Research ◽  
Early Developmental Stages ◽  
History Of ◽  
Barrandian Area ◽  
Early Developmental

This contribution briefly summarizes the history of research, modes of preservation and stratigraphic distribution of 51 trilobite and five agnostid taxa from the Barrandian area, for which the early developmental stages have been described.

scholarly journals Transcriptome Analysis of Ginkgo biloba L. Leaves across Late Developmental Stages Based on RNA-Seq and Co-Expression Network

Forests ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 315
Author(s):  
Hailin Liu ◽  
Xin Han ◽  
Jue Ruan ◽  
Lian Xu ◽  
Bing He
Keyword(s):  
Ginkgo Biloba ◽  
Leaf Development ◽  
Developmental Stages ◽  
Leaf Growth ◽  
Rna Seq ◽  
Final Size ◽  
Dioecious Species ◽  
Related Factors ◽  
New Genes ◽  
Gene Modules

The final size of plant leaves is strictly controlled by environmental and genetic factors, which coordinate cell expansion and cell cycle activity in space and time; however, the regulatory mechanisms of leaf growth are still poorly understood. Ginkgo biloba is a dioecious species native to China with medicinally and phylogenetically important characteristics, and its fan-shaped leaves are unique in gymnosperms, while the mechanism of G. biloba leaf development remains unclear. In this study we studied the transcriptome of G. biloba leaves at three developmental stages using high-throughput RNA-seq technology. Approximately 4167 differentially expressed genes (DEGs) were obtained, and a total of 12,137 genes were structure optimized together with 732 new genes identified. More than 50 growth-related factors and gene modules were identified based on DEG and Weighted Gene Co-expression Network Analysis. These results could remarkably expand the existing transcriptome resources of G. biloba, and provide references for subsequent analysis of ginkgo leaf development.

scholarly journals Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
M. Joseph Tomlinson ◽  
Shawn W. Polson ◽  
Jing Qiu ◽  
Juniper A. Lake ◽  
William Lee ◽  
...  
Keyword(s):  
Broiler Chickens ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Specific Expression ◽  
Single Nucleotide ◽  
Allele Specific Expression ◽  
Detection Tool ◽  
Commercial Broiler ◽  
Significant Phenomenon ◽  
Allele Specific

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

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