scholarly journals Transcriptome Analysis of Young Ovaries Reveals Candidate Genes Involved in Gamete Formation in Lantana camara

Plants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 263 ◽  
Author(s):  
Ze Peng ◽  
Krishna Bhattarai ◽  
Saroj Parajuli ◽  
Zhe Cao ◽  
Zhanao Deng
Keyword(s):  
Candidate Genes ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Gene Families ◽  
Unreduced Gametes ◽  
Lantana Camara ◽  
Unreduced Gamete ◽  
Genomic Resources ◽  
Gamete Formation ◽  
Gamete Production

Lantana (Lantana camara L., Verbenaceae) is an important ornamental crop, yet can be a highly invasive species. The formation of unreduced female gametes (UFGs) is a major factor contributing to its invasiveness and has severely hindered the development of sterile cultivars. To enrich the genomic resources and gain insight into the genetic mechanisms of UFG formation in lantana, we investigated the transcriptomes of young ovaries of two lantana genotypes, GDGHOP-36 (GGO), producing 100% UFGs, and a cultivar Landmark White Lantana (LWL), not producing UFGs. The de novo transcriptome assembly resulted in a total of 90,641 unique transcript sequences with an N50 of 1692 bp, among which, 29,383 sequences contained full-length coding sequences (CDS). There were 214 transcripts associated with the biological processes of gamete production and 10 gene families orthologous to genes known to control unreduced gamete production in Arabidopsis. We identified 925 transcription factor (TF)-encoding sequences, 91 nucleotide-binding site (NBS)-containing genes, and gene families related to drought/salt tolerance and allelopathy. These genomic resources and candidate genes involved in gamete formation will be valuable for developing new tools to control the invasiveness in L. camara, protect native lantana species, and understand the formation of unreduced gametes in plants.

scholarly journals A Review of Unreduced Gametes and Neopolyploids in Alfalfa: How to Fill the Gap between Well-Established Meiotic Mutants and Next-Generation Genomic Resources

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 999
Author(s):  
Fabio Palumbo ◽  
Elisa Pasquali ◽  
Emidio Albertini ◽  
Gianni Barcaccia
Keyword(s):  
Reverse Genetics ◽  
Gene Diversity ◽  
Unreduced Gametes ◽  
Unreduced Gamete ◽  
Next Generation ◽  
Gene Characterization ◽  
Meiotic Mutants ◽  
Genomic Resources ◽  
Gamete Formation ◽  
2N Gamete

The gene flow mediated by unreduced gametes between diploid and tetraploid plants of the Medicago sativa–coerulea–falcata complex is pivotal for alfalfa breeding. Sexually tetraploidized hybrids could represent the best way to exploit progressive heterosis simultaneously derived from gene diversity, heterozygosity, and polyploidy. Moreover, unreduced gametes combined with parthenogenesis (i.e., apomixis) would enable the cloning of plants through seeds, providing a unique opportunity for the selection of superior genotypes with permanently fixed heterosis. This reproductive strategy has never been detected in the genus Medicago, but features of apomixis, such as restitutional apomeiosis and haploid parthenogenesis, have been reported. By means of an original case study, we demonstrated that sexually tetraploidized plants maintain apomeiosis, but this trait is developmentally independent from parthenogenesis. Alfalfa meiotic mutants producing unreduced egg cells revealed a null or very low capacity for parthenogenesis. The overall achievements reached so far are reviewed and discussed along with the efforts and strategies made for exploiting reproductive mutants that express apomictic elements in alfalfa breeding programs. Although several studies have investigated the cytological mechanisms responsible for 2n gamete formation and the inheritance of this trait, only a very small number of molecular markers and candidate genes putatively linked to unreduced gamete formation have been identified. Furthermore, this scenario has remained almost unchanged over the last two decades. Here, we propose a reverse genetics approach, by exploiting the genomic and transcriptomic resources available in alfalfa. Through a comparison with 9 proteins belonging to Arabidopsis thaliana known for their involvement in 2n gamete production, we identified 47 orthologous genes and evaluated their expression in several tissues, paving the way for novel candidate gene characterization studies. An overall view on strategies suitable to fill the gap between well-established meiotic mutants and next-generation genomic resources is presented and discussed.

Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus)

2015 ◽  
Vol 23 ◽  
pp. 87-97 ◽  
Author(s):  
Nguyen Minh Thanh ◽  
Hyungtaek Jung ◽  
Russell E. Lyons ◽  
Isaac Njaci ◽  
Byoung-Ha Yoon ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Pangasianodon Hypophthalmus ◽  
Genomic Resources ◽  
Striped Catfish

scholarly journals De novo transcriptome analysis of Lantana camara L. revealed candidate genes involved in phenylpropanoid biosynthesis pathway

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Muzammil Shah ◽  
Hesham F. Alharby ◽  
Khalid Rehman Hakeem ◽  
Niaz Ali ◽  
Inayat Ur Rahman ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Transcriptome Analysis ◽  
De Novo ◽  
Lantana Camara ◽  
Biosynthesis Pathway ◽  
De Novo Transcriptome ◽  
Phenylpropanoid Biosynthesis

scholarly journals Genomics-based discrimination of 2n gamete formation mechanisms in polyploids: a case study in nonaploid Diospyros kaki ‘Akiou’

2021 ◽  
Author(s):  
Peng Sun ◽  
Soichiro Nishiyama ◽  
Hideaki Asakuma ◽  
Roeland E Voorrips ◽  
Jianmin Fu ◽  
...  
Keyword(s):  
2N Gametes ◽  
Unreduced Gametes ◽  
Formation Mechanisms ◽  
Common Source ◽  
Diospyros Kaki ◽  
Normal Female ◽  
Gamete Formation ◽  
Allele Dosage ◽  
2N Gamete ◽  
Gamete Production

Abstract Unreduced gametes (2n gametes), possessing double the haploid genome, whatever ploidy that happens to be, are a common source of ploidy variation in plant populations. First and second division restitution (FDR and SDR) are the dominant mechanisms of 2n gamete production; all else being equal, FDR gametes have a higher degree of heterozygosity, thus they are advantageous in breeding. The discrimination of these mechanisms from the consequence of hybridization is challenging, especially in higher polyploids, and usually requires information on centromere location. In this study, we propose a genotyping-based strategy to uncover the mechanisms of 2n gamete formation in progeny that has a higher ploidy than its parents. Simulation of 2n gamete production revealed that FDR and SDR pathways can be discriminated based on allele transmission patterns alone without information on centromere location. We applied this strategy to study the formation mechanism of a nonaploid Diospyros kaki ‘Akiou’, which was bred via hybridization between D. kaki hexaploid cultivars. The result demonstrated that ‘Akiou’ was derived from the fertilization of a normal female gamete by a 2n male gamete, and that this 2n gamete was produced through FDR. Consequently, the distinct duplex transmission pattern in the FDR gamete enabled us to infer the genomic characteristics of polyploid persimmon. The method could be tested only for the plant being polypoid, which allows for the ability to discriminate causes of 2n gamete formation using allele dosage in progeny, and will be useful in future studies of polyploid genomics.

scholarly journals Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus

2021 ◽  
Vol 22 (16) ◽  
pp. 8835
Author(s):  
Megha Rai ◽  
Amit Rai ◽  
Tetsuya Mori ◽  
Ryo Nakabayashi ◽  
Manami Yamamoto ◽  
...  
Keyword(s):  
Candidate Genes ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Biological Properties ◽  
Bioactive Metabolites ◽  
Tissue Specific ◽  
Specialized Metabolites ◽  
Manual Curation ◽  
Specific Accumulation ◽  
Mallotus Japonicus

Mallotus japonicus is a valuable traditional medicinal plant in East Asia for applications as a gastrointestinal drug. However, the molecular components involved in the biosynthesis of bioactive metabolites have not yet been explored, primarily due to a lack of omics resources. In this study, we established metabolome and transcriptome resources for M. japonicus to capture the diverse metabolite constituents and active transcripts involved in its biosynthesis and regulation. A combination of untargeted metabolite profiling with data-dependent metabolite fragmentation and metabolite annotation through manual curation and feature-based molecular networking established an overall metabospace of M. japonicus represented by 2129 metabolite features. M. japonicus de novo transcriptome assembly showed 96.9% transcriptome completeness, representing 226,250 active transcripts across seven tissues. We identified specialized metabolites biosynthesis in a tissue-specific manner, with a strong correlation between transcripts expression and metabolite accumulations in M. japonicus. The correlation- and network-based integration of metabolome and transcriptome datasets identified candidate genes involved in the biosynthesis of key specialized metabolites of M. japonicus. We further used phylogenetic analysis to identify 13 C-glycosyltransferases and 11 methyltransferases coding candidate genes involved in the biosynthesis of medicinally important bergenin. This study provides comprehensive, high-quality multi-omics resources to further investigate biological properties of specialized metabolites biosynthesis in M. japonicus.

scholarly journals The chromosomal-level genome assembly and comprehensive transcriptomes of Chinese razor clam (Sinonovacula constricta) with deep-burrowing life style and broad-range salinity adaptation

2019 ◽  
Author(s):  
Yinghui Dong ◽  
Qifan Zeng ◽  
Jianfeng Ren ◽  
Hanhan Yao ◽  
Wenbin Ruan ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Developmental Stages ◽  
De Novo ◽  
Gene Families ◽  
Sequencing Data ◽  
High Quality ◽  
Protein Coding ◽  
Sinonovacula Constricta ◽  
Razor Clam ◽  
Genomic Resources

AbstractBackgroundThe Chinese razor clam, Sinonovacula constricta, is one of the commercially important marine bivalves with deep-burrowing lifestyle and remarkable adaptability of broad-range salinity. Despite its economic impact and representative of the less-understood deep-burrowing bivalve lifestyle, there are few genomic resources for exploring its unique biology and adaptive evolution. Herein, we reported a high-quality chromosomal-level reference genome of S. constricta, the first genome of the family Solenidae, along with a large amount of short-read/full-length transcriptomic data of whole-ontogeny developmental stages, all major adult tissues, and gill tissues under salinity challenge.FindingsA total of 101.79 Gb and 129.73 Gb sequencing data were obtained with the PacBio and Illumina platforms, which represented approximately 186.63X genome coverage. In addition, a total of 160.90 Gb and 24.55 Gb clean data were also obtained with the Illumina and PacBio platforms for transcriptomic investigation. A de novo genome assembly of 1,340.13 Mb was generated, with a contig N50 of 689.18 kb. Hi-C scaffolding resulted in 19 chromosomes with a scaffold N50 of 57.99 Mb. The repeat sequences account for 50.71% of the assembled genome. A total of 26,273 protein-coding genes were predicted and 99.5% of them were annotated. Phylogenetic analysis revealed that S. constricta diverged from the lineage of Pteriomorphia at approximately 494 million years ago. Notably, cytoskeletal protein tubulin and motor protein dynein gene families are rapidly expanded in the S. constricta genome and are highly expressed in the mantle and gill, implicating potential genomic bases for the well-developed ciliary system in the S. constricta.ConclusionsThe high-quality genome assembly and comprehensive transcriptomes generated in this work not only provides highly valuable genomic resources for future studies of S. constricta, but also lays a solid foundation for further investigation into the adaptive mechanisms of benthic burrowing mollusks.

scholarly journals De Novo Transcriptome Assembly of Isatis indigotica at Reproductive Stages and Identification of Candidate Genes Associated with Flowering Pathways

2018 ◽  
Vol 143 (1) ◽  
pp. 56-66
Author(s):  
Yu Bai ◽  
Ying Zhou ◽  
Xiaoqing Tang ◽  
Yu Wang ◽  
Fangquan Wang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Orthologous Group ◽  
Rna Seq ◽  
Isatis Indigotica ◽  
Regulatory Pathways ◽  
Kegg Pathways ◽  
Bolting And Flowering

The appropriate timing of bolting and flowering is one of the keys to the reproductive success of Isatis indigotica. Several flowering regulatory pathways have been reported in plant species, but we know little about flowering regulatory in I. indigotica. In the present study, we performed RNA-seq and annotated I. indigotica transcriptome using RNA from five tissues (leaves, roots, flowers, fruit, and stems). Illumina sequencing generated 149,907,857 high-quality clean reads and 124,508 unigenes were assembled from the sequenced reads. Of these unigenes, 88,064 were functionally annotated by BLAST searches against the public protein databases. Functional classification and annotation assigned 55,991 and 23,072 unigenes to 52 gene ontology (GO) terms and 25 clusters of orthologous group (COG) categories, respectively. A total of 19,927 unigenes were assigned to 124 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 80 candidate genes related to plant circadian rhythm were identified. We also identified a number of differentially expressed genes (DEG) and 91 potential bolting and flowering-related genes from the RNA-seq data. This study is the first to identify bolting and flowering-related genes based on transcriptome sequencing and assembly in I. indigotica. The results provide foundations for the exploration of flowering pathways in I. indigotica and investigations of the molecular mechanisms of bolting and flowering in Brassicaceae plants.

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