Sub-therapeutic antibiotics are widely used as growth promoters in the poultry industry; however, the resulting antibiotic resistance threatens public health. A plant-derived growth promoter, ...Macleaya cordata extract (MCE), with effective ingredients of benzylisoquinoline alkaloids, is a potential alternative to antibiotic growth promoters. Altered intestinal microbiota play important roles in growth promotion, but the underlying mechanism remains unknown.
We generated 1.64 terabases of metagenomic data from 495 chicken intestinal digesta samples and constructed a comprehensive chicken gut microbial gene catalog (9.04 million genes), which is also the first gene catalog of an animal's gut microbiome that covers all intestinal compartments. Then, we identified the distinctive characteristics and temporal changes in the foregut and hindgut microbiota. Next, we assessed the impact of MCE on chickens and gut microbiota. Chickens fed with MCE had improved growth performance, and major microbial changes were confined to the foregut, with the predominant role of Lactobacillus being enhanced, and the amino acids, vitamins, and secondary bile acids biosynthesis pathways being upregulated, but lacked the accumulation of antibiotic-resistance genes. In comparison, treatment with chlortetracycline similarly enriched some biosynthesis pathways of nutrients in the foregut microbiota, but elicited an increase in antibiotic-producing bacteria and antibiotic-resistance genes.
The reference gene catalog of the chicken gut microbiome is an important supplement to animal gut metagenomes. Metagenomic analysis provides insights into the growth-promoting mechanism of MCE, and underscored the importance of utilizing safe and effective growth promoters.
Spinach is an important leafy vegetable enriched with multiple necessary nutrients. Here we report the draft genome sequence of spinach (Spinacia oleracea, 2n=12), which contains 25,495 ...protein-coding genes. The spinach genome is highly repetitive with 74.4% of its content in the form of transposable elements. No recent whole genome duplication events are observed in spinach. Genome syntenic analysis between spinach and sugar beet suggests substantial inter- and intra-chromosome rearrangements during the Caryophyllales genome evolution. Transcriptome sequencing of 120 cultivated and wild spinach accessions reveals more than 420 K variants. Our data suggests that S. turkestanica is likely the direct progenitor of cultivated spinach and spinach domestication has a weak bottleneck. We identify 93 domestication sweeps in the spinach genome, some of which are associated with important agronomic traits including bolting, flowering and leaf numbers. This study offers insights into spinach evolution and domestication and provides resources for spinach research and improvement.
Key message
A 7.9 kb deletion which contains a cyclin-dependent protein kinase inhibitor leads to determinate growth and dwarf phenotype in cucumber.
Plant architecture is a composite character which ...are mainly defined by shoot branching, internode elongation and shoot determinacy. Ideal architecture tends to increase the yield of plants, just like the case of “Green Revolution” increased by the application of semi-dwarf cereal crop varieties in 1960s. Cucumber (
Cucumis sativus
L.) is an important vegetable cultivated worldwide, and suitable architecture varieties were selected for different production systems. In this study, we obtained a novel dwarf mutant with strikingly shortened plant height and determinate growth habit. By bulked segregant analysis and map-based cloning, we delimited the
dw2
locus to a 56.4 kb region which contain five genes. Among all the variations between WT and
dw2
within the 56.4 kb region, a 7.9 kb deletion which resulted in complete deletion of
CsaV3_5G035790
in
dw2
was co-segregated with the dwarf phenotype. Haplotype analysis and gene expression analysis suggest that
CsaV3_5G035790
encoding a cyclin-dependent protein kinase inhibitor (
CsSMR1
) be the candidate gene responsible for the dwarf phenotype in
dw2
. RNA-seq analysis shows that several kinesin-like proteins, cyclins and reported organ size regulators are expressed differentially between WT and
dw2
, which may account for the reduced organ size in dwarf plants. Additionally, the down-regulation of
CsSTM
and
CsWOX9
in
dw2
resulted in premature termination of shoot apical meristem development, which eventually reduces the internode number and plant height. Identification and characterization of the
CsSMR1
provide a new insight into cucumber architecture modification to be applied to mechanized production system.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
The ancient gymnosperm genus Taxus is the exclusive source of the anticancer drug paclitaxel, yet no reference genome sequences are available for comprehensively elucidating the paclitaxel ...biosynthesis pathway. We have completed a chromosome-level genome of Taxus chinensis var. mairei with a total length of 10.23 gigabases. Taxus shared an ancestral whole-genome duplication with the coniferophyte lineage and underwent distinct transposon evolution. We discovered a unique physical and functional grouping of CYP725As (cytochrome P450) in the Taxus genome for paclitaxel biosynthesis. We also identified a gene cluster for taxadiene biosynthesis, which was formed mainly by gene duplications. This study will facilitate the elucidation of paclitaxel biosynthesis and unleash the biotechnological potential of Taxus.
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GEOZS, IJS, IMTLJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK, ZAGLJ
The circadian clock is a critical regulator of plant physiology and development, controlling key agricultural traits in crop plants. In addition, natural variation in circadian rhythms is important ...for local adaptation. However, quantitative modulation of circadian rhythms due to artificial selection has not yet been reported. Here we show that the circadian clock of cultivated tomato (Solanum lycopersicum) has slowed during domestication. Allelic variation of the tomato homolog of the Arabidopsis gene EID1 is responsible for a phase delay. Notably, the genomic region harboring EID1 shows signatures of a selective sweep. We find that the EID1 allele in cultivated tomatoes enhances plant performance specifically under long day photoperiods, suggesting that humans selected slower circadian rhythms to adapt the cultivated species to the long summer days it encountered as it was moved away from the equator.
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IJS, NUK, SBMB, UL, UM, UPUK
27.
The multi‐omics basis of potato heterosis Li, Dawei; Lu, Xiaoyue; Zhu, Yanhui ...
Journal of integrative plant biology,
March 2022, Volume:
64, Issue:
3
Journal Article
Peer reviewed
Open access
ABSTRACT
Heterosis is a fundamental biological phenomenon characterized by the superior performance of hybrids over their parents. Although tremendous progress has been reported in seed crops, the ...molecular mechanisms underlying heterosis in clonally propagated crops are largely unknown. Potato (Solanum tuberosum L.) is the most important tuber crop and an ongoing revolution is transforming potato from a clonally propagated tetraploid crop into a seed‐propagated diploid hybrid potato. In our previous study, we developed the first generation of highly homozygous inbred lines of potato and hybrids with strong heterosis. Here, we integrated transcriptome, metabolome, and DNA methylation data to explore the genetic and molecular basis of potato heterosis at three developmental stages. We found that the initial establishment of heterosis in diploid potato was mainly due to dominant complementation. Flower color, male fertility, and starch and sucrose metabolism showed obvious gene dominant complementation in hybrids, and hybrids devoted more energy to primary metabolism for rapid growth. In addition, we identified ~2 700 allele‐specific expression genes at each stage, which likely function in potato heterosis and might be regulated by CHH allele‐specific methylation level. Our multi‐omics analysis provides insight into heterosis in potato and facilitates the exploitation of heterosis in potato breeding.
An integrated examination of transcriptome, metabolome and DNA methylation data to explore the genetic and molecular basis of potato heterosis at three developmental stages showed that the initial establishment of heterosis in diploid potato was mainly due to dominant complementation.
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FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
The oomycete Phytophthora infestans was the causal agent of the Irish Great Famine and is a recurring threat to global food security. The pathogen can reproduce both sexually and asexually, with high ...potential to adapt to various environments and great risk to break disease resistance genes in potato. As are other oomycetes, P. infestans is regarded to be diploid during the vegetative phase of its life cycle, although some studies reported trisomy and polyploidy. Using microsatellite fingerprinting, genome-wide assessment of single nucleotide polymorphisms, nuclear DNA quantification, and microscopic counting of chromosome numbers, we assessed the ploidy level of a comprehensive selection of isolates. All progenies from sexual populations of P. infestans in nature were found to be diploid, in contrast nearly all dominant asexual lineages, including the most important pandemic clonal lineages US-1 and 13_A2 were triploid. Such triploids possess significantly more allelic variation than diploids. We observed that triploid genotype can change to a diploid genome constitution when exposed to artificial stress conditions. This study reveals that fluctuations in the ploidy level may be a key factor in the adaptation process of this notorious plant destroyer and imposes an extra challenge to control this disease.
Statistically, the accessions in Hap 1 showed significantly lower root Na+/K+ ratios than those in the larger group Hap2 (P = 1.78 × 10−10). Since root Na+/K+ ratio is negatively correlated with salt ...resistance in tomato, Hap1 and Hap2 were defined as the tolerant and sensitive alleles of SlSOS1, respectively (Figure 1b). To assess whether the variations in this cis‐element contribute to SlSOS1 expression, we analysed the binding capacity of the CRT/DRE variants with SlDREB2, a known salt‐inducible DREB transcription factor in tomato recognizing CRT/DRE motif and inducing the expression of target genes (Hichri et al., 2016). Furthermore, phenotype analysis showed that slsos1‐1 and slsos1‐2 mutants were clearly more sensitive to salt stress than wild type plants (Figure 1n and o), which indicates that, like the Arabidopsis SOS1 (Shi et al., 2003), SlSOS1 also plays a crucial role in salt tolerance in tomato. Overall, our findings indicate that natural variations in the promoter of SlSOS1 disrupting the SlDREB2‐binding cis‐element result in reduced expression of SlSOS1 and increased salt sensitivity in the cultivated tomato due to selection during domestication.
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BFBNIB, DOBA, FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UILJ, UKNU, UL, UM, UPUK
Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental ...questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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