Research Articles (Microbiology and Plant Pathology)
http://hdl.handle.net/2263/1735
2024-03-29T08:32:11ZCultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe)
http://hdl.handle.net/2263/92006
Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe)
Zhang, Ticao; Qiao, Qin; Du, Xiao; Zhang, Xiao; Hou, Yali; Wei, Xin; Sun, Chao; Zhang, Rengang; Yun, Quanzheng; Crabbe, M. James C.; Van de Peer, Yves; Dong, Wenxuan
Cultivated hawthorn (Crataegus pinnatifida var.
major) is an important medicinal and edible plant
with a long history of use for health protection in
China. Herein, we provide a de novo chromosomelevel
genome sequence of the hawthorn cultivar
“Qiu Jinxing.” We assembled an 823.41Mb genome
encoding 40 571 genes and further anchored the
779.24Mb sequence into 17 pseudo‐chromosomes,
which account for 94.64% of the assembled genome.
Phylogenomic analyses revealed that cultivated
hawthorn diverged from other species within
the Maleae (apple tribe) at approximately 35.4 Mya.
Notably, genes involved in the flavonoid and
triterpenoid biosynthetic pathways have been significantly
amplified in the hawthorn genome. In addition,
our results indicated that the Maleae share a
unique ancient tetraploidization event; however, no
recent independent whole‐genome duplication
event was specifically detected in hawthorn. The
amplification of non‐specific long terminal repeat
retrotransposons contributed the most to the expansion
of the hawthorn genome. Furthermore, we
identified two paleo‐sub‐genomes in extant species
of Maleae and found that these two sub‐genomes
showed different rearrangement mechanisms. We
also reconstructed the ancestral chromosomes of
Rosaceae and discussed two possible paleopolyploid
origin patterns (autopolyploidization or allopolyploidization)
of Maleae. Overall, our study
provides an improved context for understanding the
evolution of Maleae species, and this new highquality
reference genome provides a useful resource
for the horticultural improvement of hawthorn.
SUPPLEMENTARY MATERIAL : FIGURE S1. Information of collected sample. FIGURE S2. Frequency distribution of depth of 17‐mer (upper) and K‐mer (below) in genome survey of cultivated hawthorn. FIGURE S3. The genome annotation of hawthorn. FIGURE S4. Classification statistics of cultivated hawthorn genes. FIGURE S5. The maximum likelihood phylogenetic tree of Rosaceae with bootstraps. FIGURE S6. Changes in messenger RNA (mRNA) expression in hardfleshed hawthorn “Qiujinxing”. FIGURE S7. Changes in messenger RNA (mRNA) expression in soft‐fleshed hawthorn “Ruanrou Shanlihong #3”. FIGURE S8. Triterpene biosynthesis pathway in Crataegus pinnatifida. FIGURE S9. Syntenic dot plot and Ks distribution within the apple genome. FIGURE S10. Syntenic dot plot and Ks distribution between two subgenomes of hawthorn and loquat (A), apple and loquat (B). Syntenic dot plot and Ks distribution between Gillenia trifoliata and sub‐genome A of hawthorn (C) and sub‐genome B of hawthorn (D). TABLE S1. Statistics of genome survey data. TABLE S2. Statistics of paired‐end reads based on Hi‐C technology. TABLE S3. Statistics of the lengths of 17 pseudo‐chromosomes in the cultivated hawthorn genome. TABLE S4. Predicted genes and gene features of the cultivated hawthorn. TABLE S5. Gene functional annotation of the cultivated hawthorn. TABLE S6. Predicted RNA features of the cultivated hawthorn. TABLE S7. Conserved genes using the BUSCO (Benchmarking Universal Single‐Copy Orthologs) method. TABLE S8. The enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories of species‐specific genes (P‐value <0.05) in the cultivated hawthorn. TABLE S9. The enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories of significantly (P‐value <0.05) expanded genes in the cultivated hawthorn. TABLE S10. The enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories of significantly (P‐value <0.05) differentially expressed genes between two fruit developmental stages in the hardfleshed (“Qiu Jinxing”) hawthorn cultivar. TABLE S11. The enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories of significantly (P‐value <0.05) differentially expressed genes between two fruit developmental stages in the soft‐fleshed (“Ruanrou Shanlihong #3”) hawthorn cultivar. TABLE S12. Statistics of repeat sequences, including transposable elements (TEs) in hawthorn, loquat, apple and pear genomes. TABLE S13. Statistics of orthologs between hawthorn, apple and loquat genomes. The color of the table corresponds to the squares of chromosomes in Figure 4E in the paper.
2022-08-01T00:00:00ZThe neighborhood of the spike gene Is a hotspot for modular intertypic homologous and nonhomologous recombination in coronavirus genomes
http://hdl.handle.net/2263/91527
The neighborhood of the spike gene Is a hotspot for modular intertypic homologous and nonhomologous recombination in coronavirus genomes
Nikolaidis, Marios; Markoulatos, Panayotis; Van de Peer, Yves; Oliver, Stephen G.; Amoutzias, Grigorios D.
Coronaviruses (CoVs) have very large RNA viral genomes with a distinct genomic architecture of core and accessory open reading frames (ORFs). It is of utmost importance to understand their patterns and limits of homologous and nonhomologous recombination, because such events may affect the emergence of novel CoV strains, alter their host range, infection rate, tissue tropism pathogenicity, and their ability to escape vaccination programs. Intratypic recombination among closely related CoVs of the same subgenus has often been reported; however, the patterns and limits of genomic exchange between more distantly related CoV lineages (intertypic recombination) need further investigation. Here, we report computational/evolutionary analyses that clearly demonstrate a substantial ability for CoVs of different subgenera to recombine. Furthermore, we show that CoVs can obtain—through nonhomologous recombination—accessory ORFs from core ORFs, exchange accessory ORFs with different CoV genera, with other viruses (i.e., toroviruses, influenza C/D, reoviruses, rotaviruses, astroviruses) and even with hosts. Intriguingly, most of these radical events result from double crossovers surrounding the Spike ORF, thus highlighting both the instability and mobile nature of this genomic region. Although many such events have often occurred during the evolution of various CoVs, the genomic architecture of the relatively young SARS-CoV/SARS-CoV-2 lineage so far appears to be stable.
DATA AVAILABILITY : All necessary data are incorporated into the article and its
online supplementary material. Any further data are available
on request.
2022-01-01T00:00:00ZEvolution of isoform-level gene expression patterns across tissues during lotus species divergence
http://hdl.handle.net/2263/91476
Evolution of isoform-level gene expression patterns across tissues during lotus species divergence
Zhang, Yue; Yang, Xingyu; Van de Peer, Yves; Chen, Jinming; Marchal, Kathleen; Shi, Tao
Both gene duplication and alternative splicing (AS) drive the functional diversity of gene products in plants, yet the relative contributions of the two key mechanisms to the evolution of gene function are largely unclear. Here, we studied AS in two closely related lotus plants, Nelumbo lutea and Nelumbo nucifera, and the outgroup Arabidopsis thaliana, for both single-copy and duplicated genes. We show that most splicing events evolved rapidly between orthologs and that the origin of lineage-specific splice variants or isoforms contributed to gene functional changes during species divergence within Nelumbo. Single-copy genes contain more isoforms, have more AS events conserved across species, and show more complex tissue-dependent expression patterns than their duplicated counterparts. This suggests that expression divergence through isoforms is a mechanism to extend the expression breadth of genes with low copy numbers. As compared to isoforms of local, small-scale duplicates, isoforms of whole-genome duplicates are less conserved and display a less conserved tissue bias, pointing towards their contribution to subfunctionalization. Through comparative analysis of isoform expression networks, we identified orthologous genes of which the expression of at least some of their isoforms displays a conserved tissue bias across species, indicating a strong selection pressure for maintaining a stable expression pattern of these isoforms. Overall, our study shows that both AS and gene duplication contributed to the diversity of gene function during the evolution of lotus.
OPEN RESEARCH BADGES : This article has earned an Open Data badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at The transcriptome dataset of Nelumbo lutea generated for this work is accessible through NCBI Sequence Read Archive (SRA) under accession number PRJNA777451 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA777451) and PRJNA705058 (URL: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA705058). The assembled genomes of Nelumbo nucifera and Nelumbo lutea are downloaded from the Nelumbo Genome Database (URL: http://nelumbo.biocloud.net). The transcriptome dataset of Nelumbo nucifera is downloaded from the published paper (doi: http://10.1093/dnares/dsz010), and the transcriptome dataset of Arabidopsis is downloaded from the published paper (doi: http://10.1111/tpj.13312).; DATA AVAILABILITY STATEMENT : The Oxford Nanopore full-length sequencing dataset generated for this work is accessible through the NCBI Sequence Read Archive (SRA) under accession number PRJNA777451. The Illumina RNA-seq dataset is accessible through the NCBI SRA under accession number PRJNA705058.; SUPPLEMENTARY FIGURES : FIGURE S1 Density distribution of consensus full-length transcripts obtained by Nanopore sequencing.
FIGURE S2. Distribution of the number of isoforms per gene in N. lutea, N. nucifera, and Arabidopsis.
FIGURE S3. Pipeline to identify conserved AS events in the same ortholog group.
FIGURE S4. RT-PCR validation of interspecies conserved AS events.
FIGURE S5. Box plots showing the distribution of the number of AS events per gene in genes with different copies in N. lutea, N. nucifera, and Arabidopsis.
FIGURE S6. Percentages of single-copy and duplicated genes that undergo AS events.
FIGURE S7. Bar graph showing the percentages of single-copy and duplicated genes with at least one interspecies conserved AS event in N. lutea and N. nucifera.
FIGURE S8. Bar chart showing the average number of AS events per gene.
FIGURE S9. Intraspecies conserved AS events in paralogous gene pairs.
FIGURE S10. Heatmap showing the presence/absence of the N. nucifera lineage-specific isoforms in other N. nucifera cultivars as obtained from transcriptome analysis.
FIGURE S11. Heatmap of WGCNA module–tissue association in N. lutea, N. nucifera, and Arabidopsis.
FIGURE S12. Distribution of the polymorphism value (PV) for the genes in N. lutea, N. nucifera, and Arabidopsis.
FIGURE S13. Distribution of the number of isoforms of duplicated genes displaying single- or multiple-tissue biased expression patterns.
FIGURE S14. Verification of matching tissues between N. lutea, N. nucifera, and Arabidopsis.
FIGURE S15. Schematic of genes with single- and multiple-tissue bias and the conserved tissue bias between orthologous genes.
FIGURE S16. Examples of the conservation of tissue-specific expression for orthologous gene pairs that either show single-tissue or multiple-tissue biased expression.
FIGURE S17. Phylogenetic analysis of MADS-box genes from the two Nelumbo species and Arabidopsis.
FIGURE S18. Tissue-specific module networks of isoforms for the ‘ABCE’ module in Arabidopsis thaliana.; SUPPLEMENTARY TABLES : TABLE S1. Summary of the RNA-seq samples in this study.
TABLE S2. Summary of the genes, isoforms, and AS events in N. lutea, N. nucifera, and Arabidopsis.
TABLE S3. Summary of the interspecies conserved AS events.
TABLE S4. RT-PCR primers for validating the interspecies conserved AS events.
TABLE S5. Intraspecies conserved AS events in N. lutea, N. nucifera, and Arabidopsis.
TABLE S6. The nodes of the isoform coexpression networks for N. lutea, N. nucifera, and Arabidopsis.
TABLE S7. Summary of the conserved tissue bias patterns in different comparisons between N. lutea, N. nucifera, and Arabidopsis.
2022-11-01T00:00:00ZIn vitro dual activity of Aloe marlothii roots and its chemical constituents against Plasmodium falciparum asexual and sexual stage parasites
http://hdl.handle.net/2263/90762
In vitro dual activity of Aloe marlothii roots and its chemical constituents against Plasmodium falciparum asexual and sexual stage parasites
Mianda, S.M.; Invernizzi, Luke; Van der Watt, Mariette Elizabeth; Reader, Janette; Moyo, Phanankosi; Birkholtz, Lyn-Marie; Maharaj, Vinesh J.
Please abstract in the article.
2022-10-01T00:00:00Z