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Summary: With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many polyploid species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly.We developed a novel subgenome‐phasing algorithm, SubPhaser, specifically designed for a neoallopolyploid or a homoploid hybrid. SubPhaser first searches for the subgenome‐specific sequence (k‐mer), then assigns homoeologous chromosomes into subgenomes, and further provides tools to annotate and investigate specific sequences.SubPhaser works well on neoallopolyploids and homoploid hybrids containing subgenome‐specific sequences like wheat, but fails on autopolyploids lacking subgenome‐specific sequences like alfalfa, indicating that SubPhaser can phase neoallopolyploid/homoploid hybrids with high accuracy, sensitivity and performance.This highly accurate, highly sensitive, ancestral data free chromosome phasing algorithm, SubPhaser, offers significant application value for subgenome phasing in neoallopolyploids and homoploid hybrids, and for the subsequent exploration of genome evolution and related genetic/epigenetic mechanisms. [ABSTRACT FROM AUTHOR]

In the soil, plant roots associated with fungi often encounter uneven distribution of nitrate (NO3−)/ammonium (NH4+) patches, but the mechanism underlying N form‐influenced plant–fungal interactions remains limited. We inoculated Arabidopsis with a root endophyte Phomopsis liquidambaris, and evaluated the effects of P. liquidambaris on plant performance under NO3− or NH4+ nutrition. Under NO3− nutrition, P. liquidambaris inoculation promoted seedling growth, whereas under NH4+ nutrition, P. liquidambaris suppressed seedling growth. Under high NH4+ conditions, fungus‐colonized roots displayed increased NH4+ accumulation and NH4+ efflux, similar to the effect of ammonium stress caused by elevated NH4+ levels. Notably, this fungus excluded NH4+ during interactions with host roots, thereby leading to increased NH4+ levels at the plant–fungal interface under high NH4+ conditions. A nitrite reductase‐deficient strain that excludes NO3− but absorbs NH4+, decreased NH4+ levels in Arabidopsis shoots and rescued plant growth and nitrogen metabolism under high NH4+ levels. Transcriptomic analysis highlighted that P. liquidambaris had altered transcriptional responses associated with plant response to inorganic N forms. Our results demonstrate that fungus‐regulated NO3−/NH4+ dynamics at the plant–fungal interface alters plant response to NO3−/NH4+ nutrition. This study highlights the essential functions of root endophytes in plant adaptation to soil nitrogen nutrients. Brief Summary: We determined how to root endophyte affects plant response to different forms of N. Our results suggest that root endophyte differentially regulates plant response to NO3− and NH4+ nutrition through modulating N fluxes at the plant–fungal interface rather than through regulating defense responses. [ABSTRACT FROM AUTHOR]

Previously, the application of the fungal endophyte Phomopsis liquidambari B3 exhibited notable effect in alleviating soil obstacles caused by continuous cropping of peanut. It was supposed that P. liquidambari B3 could enhance the efficiency of nodulation and nitrogen fixation by enriching the diversity of nodular endophytic bacteria under continous monocropping system. To verify this hypothesis, a pot experiment was conducted under natural conditions. Four treatments were set as follow: discontinuous cropping soil (NS), continuous cropping soil (CK), continuous cropping soil inoculate with actived P. liquidambari B3 (CSB3), and continuous cropping soil inoculate with sterilized P. liquidambari B3 (CSIB3). As a result, a total of 120 isolates were obtained. Our study clearly declared that the addition of fungal endophyte effectively enriched the genetic diversity and the community composition in CSB3. In contrast, a low genetic diversity level and simplex community structure were exhibited in CK and CSIB3. Meanwhile, the positive percentage rate and corresponding community composition of the plant growth-promoting isolates in NS and CSB3 were larger and more abundant than the other. This is the first time to describe the effects of fungal endophytes on the diversity of the nodular culturable endophytic bacteria associated with continuous cropping of peanut. [ABSTRACT FROM AUTHOR]

Huge numbers of bacteria reside in the digestive tract of host and these microorganisms play a vital role in the host health, especially in the digestion of food and the development of immune system. Host phylogeny and diet, especially long-term diet, both have great influence on the gut bacterial community. Other aspects of host, such as gender, age, and the geography and weather they lived, are also correlated to their gut bacterial community. Feces are usually used for gut bacteria study and fecal bacteria can represent the distal gut bacteria. In order to determine the influence of the host phylogeny and diet on the composition of distal gut bacterial community and to interpret bacterial population and diversity in the intestinal of animals, the distal gut bacterial community of four kinds of primates and five kinds of carnivora (including herbivorous, omnivorous, and carnivorous) were investigated using high-throughput sequencing and the isolation of the Actinobacteria from fresh feces of several primates was processed. The results showed the host phylogeny had a greater influence on the distal gut bacterial community of the primates and carnivora than the host diet. A total of 44 bacteria phyla and two archaea phyla were detected, which indicated that the distal gut bacteria of these animals were abundant. The distal gut bacteria were relatively stable and wildly shared in primates and carnivora. The difference in distal gut bacteria of the two animal orders is mainly determined by relative abundance of most distal gut bacteria rather than by the taxa of these bacteria. [ABSTRACT FROM AUTHOR]

In the soil, plant roots associated with fungi often encounter uneven distribution of nitrate (NO 3 - )/ammonium (NH 4 + ) patches, but the mechanism underlying N form-influenced plant-fungal interactions remains limited. We inoculated Arabidopsis with a root endophyte Phomopsis liquidambaris, and evaluated the effects of P. liquidambaris on plant performance under NO 3 - or NH 4 + nutrition. Under NO 3 - nutrition, P. liquidambaris inoculation promoted seedling growth, whereas under NH 4 + nutrition, P. liquidambaris suppressed seedling growth. Under high NH 4 + conditions, fungus-colonized roots displayed increased NH 4 + accumulation and NH 4 + efflux, similar to the effect of ammonium stress caused by elevated NH 4 + levels. Notably, this fungus excluded NH 4 + during interactions with host roots, thereby leading to increased NH 4 + levels at the plant-fungal interface under high NH 4 + conditions. A nitrite reductase-deficient strain that excludes NO 3 - but absorbs NH 4 + , decreased NH 4 + levels in Arabidopsis shoots and rescued plant growth and nitrogen metabolism under high NH 4 + levels. Transcriptomic analysis highlighted that P. liquidambaris had altered transcriptional responses associated with plant response to inorganic N forms. Our results demonstrate that fungus-regulated NO 3 - /NH 4 + dynamics at the plant-fungal interface alters plant response to NO 3 - /NH 4 + nutrition. This study highlights the essential functions of root endophytes in plant adaptation to soil nitrogen nutrients., (© 2022 John Wiley & Sons Ltd.)