Pack-MULEs: Recycling and reshaping genes through GC-biased acquisition

Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice

Transcription factors (TFs) form the major class of regulatory genes and play key roles in multiple plant stress responses. In most eukaryotic plants, transcription factor (TF) families (WRKY, MADS-box and MYB) activate unique cellular-level abiotic and biotic stress-responsive strategies, which are considered as key determinants for defense and developmental processes. Arabidopsis and rice are two important representative model systems for dicot and monocot plants, respectively. A comprehensive comparative study on 101 OsWRKY, 34 OsMADS box and 122 OsMYB genes (rice genome) and, 71 AtWRKY, 66 AtMADS box and 144 AtMYB genes (Arabidopsis genome) showed various relationships among TFs across species. The phylogenetic analysis clustered WRKY, MADS-box and MYB TF family members into 10, 7 and 14 clades, respectively. All clades in WRKY and MYB TF families and almost half of the total number of clades in the MADS-box TF family are shared between both species. Chromosomal and gene structure analysis showed that the Arabidopsis-rice orthologous TF gene pairs were unevenly localized within their chromosomes whilst the distribution of exon–intron gene structure and motif conservation indicated plausible functional similarity in both species. The abiotic and biotic stress-responsive cis-regulatory element type and distribution patterns in the promoter regions of Arabidopsis and rice WRKY, MADS-box and MYB orthologous gene pairs provide better knowledge on their role as conserved regulators in both species. Co-expression network analysis showed the correlation between WRKY, MADs-box and MYB genes in each independent rice and Arabidopsis network indicating their role in stress responsiveness and developmental processes.

In silico analysis of promoter region and regulatory elements of glucan endo-1,3-beta-glucosidase encoding genes in Solanum tuberosum: cultivar DM 1-3 516 R44

Background

Potato (Solanum tuberosum L.) is one of the most important food crops in the world. Pathogens remain as one of the major constraints limiting potato productivity. Thus, understanding of gene regulation mechanism of pathogenesis-related genes such as glucan endo-1,3-beta-glucosidase is a foundation for genetic engineering of potato for disease resistance and reduces the use of fungicides. In the present study, 19 genes were selected and attempts were made through in silico methods to identify and characterize the promoter regions, regulatory elements, and CpG islands of glucan endo-1,3-beta-glucosidase gene in Solanum tuberosum cultivar DM 1-3 516 R44.

Results

The current analysis revealed that single transcription start sites (TSSs) were present in 12/19 (63.2%) of promoter regions analyzed. The predictive score at a cutoff value of 0.8 for the majority (84.2%) of the promoter regions ranged from 0.90 to 1.00. The locations for 42% of the TSSs were below −500 bp relative to the start codon (ATG). MβGII was identified as the common promoter motif for 94.4% of the genes with an E value of 3.5e−001. The CpG analysis showed low CpG density in the promoter regions of most of the genes except for gene ID102593331 and ID: 102595860. The number of SSRs per gene ranged from 2 to 9 with repeat lengths of 2 to 6 bp. Evolutionary distances ranged from 0.685 to 0.770 (mean = 0.73), demonstrating narrower genetic diversity range. Phylogeny was inferred using the UPGMA method, and gene sequences from different species were found to be clustered together.

Conclusion

In silico identified regulatory elements in promoter regions will contribute to our understanding of the regulatory mechanism of glucan endo-1,3-beta-glucosidase genes and provide a promising target for genetic engineering to improve disease resistance in potatoes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-021-00240-0.

Gene duplication and transposition of mobile elements drive evolution of the Rpv3 resistance locus in grapevine

A wild grape haplotype (Rpv3-1) confers resistance to Plasmopara viticola. We mapped the causal factor for resistance to an interval containing a TIR-NB-LRR (TNL) gene pair that originated 1.6-2.6 million years ago by a tandem segmental duplication. Transient coexpression of the TNL pair in Vitis vinifera leaves activated pathogen-induced necrosis and reduced sporulation compared with control leaves. Even though transcripts of the TNL pair from the wild haplotype appear to be partially subject to nonsense-mediated mRNA decay, mature mRNA levels in a homozygous resistant genotype were individually higher than the mRNA trace levels observed for the orthologous single-copy TNL in sensitive genotypes. Allelic expression imbalance in a resistant heterozygote confirmed that cis-acting regulatory variation promotes expression in the wild haplotype. The movement of transposable elements had a major impact on the generation of haplotype diversity, altering the DNA context around similar TNL coding sequences and the GC-content in their proximal 5'-intergenic regions. The wild and domesticated haplotypes also diverged in conserved single-copy intergenic DNA, but the highest divergence was observed in intraspecific and not in interspecific comparisons. In this case, introgression breeding did not transgress the genetic boundaries of the domesticated species, because haplotypes present in modern varieties sometimes predate speciation events between wild and cultivated species.

Nucleotide composition of transposable elements likely contributes to AT/GC compositional homogeneity of teleost fish genomes

BACKGROUND

Teleost fish genome size has been repeatedly demonstrated to positively correlate with the proportion of transposable elements (TEs). This finding might have far-reaching implications for our understanding of the evolution of nucleotide composition across vertebrates. Genomes of fish and amphibians are GC homogenous, with non-teleost gars being the single exception identified to date, whereas birds and mammals are AT/GC heterogeneous. The exact reason for this phenomenon remains controversial. Since TEs make up significant proportions of genomes and can quickly accumulate across genomes, they can potentially influence the host genome with their own GC content (GC%). However, the GC% of fish TEs has so far been neglected.

RESULTS

The genomic proportion of TEs indeed correlates with genome size, although not as linearly as previously shown with fewer genomes, and GC% negatively correlates with genome size in the 33 fish genome assemblies analysed here (excluding salmonids). GC% of fish TE consensus sequences positively correlates with the corresponding genomic GC% in 29 species tested. Likewise, the GC contents of the entire repetitive vs. non-repetitive genomic fractions correlate positively in 54 fish species in Ensembl. However, among these fish species, there is also a wide variation in GC% between the main groups of TEs. Class II DNA transposons, predominant TEs in fish genomes, are significantly GC-poorer than Class I retrotransposons. The AT/GC heterogeneous gar genome contains fewer Class II TEs, a situation similar to fugu with its extremely compact and also GC-enriched but AT/GC homogenous genome.

CONCLUSION

Our results reveal a previously overlooked correlation between GC% of fish genomes and their TEs. This applies to both TE consensus sequences as well as the entire repetitive genomic fraction. On the other hand, there is a wide variation in GC% across fish TE groups. These results raise the question whether GC% of TEs evolves independently of GC% of the host genome or whether it is driven by TE localization in the host genome. Answering these questions will help to understand how genomic GC% is shaped over time. Long-term accumulation of GC-poor(er) Class II DNA transposons might indeed have influenced AT/GC homogenization of fish genomes and requires further investigation.

In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa

Pathogenesis related (PR) proteins are low molecular weight family of proteins induced in plants under various biotic and abiotic stresses. They play an important role in plant-defense mechanism. PRs have wide range of functions, acting as hydrolases, peroxidases, chitinases, anti-fungal, protease inhibitors etc. In the present study, an attempt has been made to analyze promoter regions of PR1, PR2, PR5, PR9, PR10 and PR12 of Arabidopsis thaliana and Oryza sativa. Analysis of cis-element distribution revealed the functional multiplicity of PRs and provides insight into the gene regulation. CpG islands are observed only in rice PRs, which indicates that monocot genome contains more GC rich motifs than dicots. Tandem repeats were also observed in 5' UTR of PR genes. Thus, the present study provides an understanding of regulation of PR genes and their versatile roles in plants.

Evidence-based gene models for structural and functional annotations of the oil palm genome

Background

Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes. Classification and characterization of genes associated with traits of interest, such as those for fatty acid biosynthesis and disease resistance, were also limited. Lipid-, especially fatty acid (FA)-related genes are of particular interest for the oil palm as they specify oil yields and quality. This paper presents the characterization of the oil palm genome using different gene prediction methods and comparative genomics analysis, identification of FA biosynthesis and disease resistance genes, and the development of an annotation database and bioinformatics tools.

Results

Using two independent gene-prediction pipelines, Fgenesh++ and Seqping, 26,059 oil palm genes with transcriptome and RefSeq support were identified from the oil palm genome. These coding regions of the genome have a characteristic broad distribution of GC₃ (fraction of cytosine and guanine in the third position of a codon) with over half the GC₃-rich genes (GC₃ ≥ 0.75286) being intronless. In comparison, only one-seventh of the oil palm genes identified are intronless. Using comparative genomics analysis, characterization of conserved domains and active sites, and expression analysis, 42 key genes involved in FA biosynthesis in oil palm were identified. For three of them, namely EgFABF, EgFABH and EgFAD3, segmental duplication events were detected. Our analysis also identified 210 candidate resistance genes in six classes, grouped by their protein domain structures.

Conclusions

We present an accurate and comprehensive annotation of the oil palm genome, focusing on analysis of important categories of genes (GC₃-rich and intronless), as well as those associated with important functions, such as FA biosynthesis and disease resistance. The study demonstrated the advantages of having an integrated approach to gene prediction and developed a computational framework for combining multiple genome annotations. These results, available in the oil palm annotation database (http://palmxplore.mpob.gov.my), will provide important resources for studies on the genomes of oil palm and related crops.

Reviewers

This article was reviewed by Alexander Kel, Igor Rogozin, and Vladimir A. Kuznetsov.

Electronic supplementary material

The online version of this article (doi:10.1186/s13062-017-0191-4) contains supplementary material, which is available to authorized users.

Efficient transposition of the youngest miniature inverted repeat transposable element family of yellow fever mosquito in yeast

Miniature inverted repeat transposable elements (MITEs) are often the most numerous DNA transposons in plant and animal genomes. The dramatic amplification of MITE families during evolution is puzzling, because the transposase sources for the vast majority of MITE families are unknown. The yellow fever mosquito genome contains > 220-Mb MITE sequences; however, transposition activity has not been demonstrated for any of the MITE families. The Gnome elements are the youngest MITE family in this genome, with at least 116 identical copies. To test whether the putative autonomous element Ozma is capable of mobilizing Gnome and its two sibling MITEs, analyses were performed in a yeast transposition assay system. Whereas the wild-type transposase resulted in very low transposition activity, mutations in the region containing a putative nuclear export signal motif resulted in a dramatic (at least 4160-fold) increase in transposition frequency. We have also demonstrated that each residue of the novel DD37E motif is required for the activity of the Ozma transposase. Footprint sequences left at the donor sites suggest that the transposase may cleave between the second and the third nucleotides from the 5' ends of the elements. The excised elements reinsert specifically at dinucleotide 'TA', ~ 55% of them in yeast genes. The elements described in this article could potentially be useful as genetic tools for genetic manipulation of mosquitoes.

TamiR1123 originated from a family of miniature inverted-repeat transposable elements (MITE) including one inserted in the Vrn-A1a promoter in wheat

More than half of spring wheat cultivars have a dominant Vrn-A1a allele that has an insertion of a miniature inverted-repeat transposable element (MITE) in its promoter. In this study, we found that the MITE present in the Vrn-A1a gene (MITE_VRN) is a nearly perfect palindrome and it can form highly stable hairpin loops when expressed as RNA. MITE_VRN also possessed sequences of a microRNA in Triticum aestivum (TamiR1123). The P(32) labeled TamiR1123 probe detected two RNA molecules on a small RNA gel blot, one expected for MITE_VRN, and the other expected for TamiR1123. These results demonstrated that MITE_VRN was expressed as RNAs and TamiR1123 was originated from the MITE_VRN family. The isogenic line TDD carrying the dominant Vrn-A1a allele with MITE_VRN showed higher TamiR1123 and Vrn-A1a transcript levels than the isogenic line TDE carrying the recessive vrn-A1a allele without MITE_VRN. TamiR1123 were greatly up-regulated by plant age but slightly down-regulated by low temperature and short days. These findings have pointed to alternative regulatory mechanisms for plant development governed by Vrn-A1a in spring wheat.

Phylogenomic study of lipid genes involved in microalgal biofuel production-candidate gene mining and metabolic pathway analyses

Optimizing microalgal biofuel production using metabolic engineering tools requires an in-depth understanding of the structure-function relationship of genes involved in lipid biosynthetic pathway. In the present study, genome-wide identification and characterization of 398 putative genes involved in lipid biosynthesis in Arabidopsis thaliana Chlamydomonas reinhardtii, Volvox carteri, Ostreococcus lucimarinus, Ostreococcus tauri and Cyanidioschyzon merolae was undertaken on the basis of their conserved motif/domain organization and phylogenetic profile. The results indicated that the core lipid metabolic pathways in all the species are carried out by a comparable number of orthologous proteins. Although the fundamental gene organizations were observed to be invariantly conserved between microalgae and Arabidopsis genome, with increased order of genome complexity there seems to be an association with more number of genes involved in triacylglycerol (TAG) biosynthesis and catabolism. Further, phylogenomic analysis of the genes provided insights into the molecular evolution of lipid biosynthetic pathway in microalgae and confirm the close evolutionary proximity between the Streptophyte and Chlorophyte lineages. Together, these studies will improve our understanding of the global lipid metabolic pathway and contribute to the engineering of regulatory networks of algal strains for higher accumulation of oil.

Mutator-like elements with multiple long terminal inverted repeats in plants

Mutator-like transposable elements (MULEs) are widespread in plants and the majority have long terminal inverted repeats (TIRs), which distinguish them from other DNA transposons. It is known that the long TIRs of Mutator elements harbor transposase binding sites and promoters for transcription, indicating that the TIR sequence is critical for transposition and for expression of sequences between the TIRs. Here, we report the presence of MULEs with multiple TIRs mostly located in tandem. These elements are detected in the genomes of maize, tomato, rice, and Arabidopsis. Some of these elements are present in multiple copies, suggesting their mobility. For those elements that have amplified, sequence conservation was observed for both of the tandem TIRs. For one MULE family carrying a gene fragment, the elements with tandem TIRs are more prevalent than their counterparts with a single TIR. The successful amplification of this particular MULE demonstrates that MULEs with tandem TIRs are functional in both transposition and duplication of gene sequences.