Biology subjects

Xun, H.

Publications and source records attributed to Xun, H..

3 recordsLinked to original sources

bioRxiv2025

T2T Gap-free Genome Assembly of Gp03, a Soybean Cultivar with High Genetic Transformation Efficiency

Soybean is a major cultivated crop worldwide, serving as a crucial source of edible oil, plant protein, and animal feed. The continuous growth of the global population necessitates accelerated soybean breeding. High-quality reference genomes are foundational for soybean functional genomics and breeding research. Several telomere-to-telomere (T2T) reference genomes have been released, facilitating subsequent functional studies. However, soybean varieties show varying efficiencies in genetic transformation, with currently available reference genomes having low transformation efficiencies. Here, we report the complete T2T genome assembly of Gp03, a soybean cultivar with high genetic transformation efficiency, developed in Northeast China. Gp03 exhibited high transformation efficiency in comparative studies and favorable agronomic traits for dense planting. The assembly comprises 20 chromosomes with a total size of 1.01 GB, an N50 length of 51.5 Mb, and includes 40 telomeres and 20 putative centromere regions. Genome annotation identified 61,832 genes and 545.8 Mb of repetitive sequences, accounting for 53.8% of the genome. This work provides a valuable genetic resource for soybean breeding and is expected to accelerate molecular breeding efforts.

plant biology↗

bioRxiv2021

Effects of homoeologous exchange on gene expression and alternative splicing in a newly formed allotetraploid wheat

Homoeologous exchange (HE) is a major mechanism generating post-polyploidization genetic variation with important evolutionary consequences. However, the direct impacts of HE without entangling with additional evolutionary forces on gene expression remains to be fully understood. Here, we analyzed high-throughput RNA-seq data of young leaves from individuals of a synthetic allotetraploid wheat (AADD), which contain variable numbers of HEs. We aimed to investigate if and to which extent HE directly impacts gene expression and alternative splicing (AS). We found that HE impacts expression of genes located within HE regions primarily via cis-acting dosage effect, which led to significant changes in the total expression of homoeolog pairs, especially for homoeologs whose original expression was biased. In parallel, HE influences expression of a large amount of genes residing in non-HE regions by trans-regulation leading to convergent expression of homoeolog pairs. Intriguingly, when taking into account of the original relative homoeolog expression states, homoeolog pairs under trans-effect are more prone to showing convergent response to HE whereas those under cis-effect trended to show subgenome-specific expression. Moreover, HE induced quantitative, largely individual-specific, changes of alternative splicing (AS) events. Like homoeologs expression, homoeo-AS events which related to trans effect were more responsive to HE. HE therefore exerts multifaceted immediate effects on gene expression and, to a less extent, also transcript diversity in nascent allopolyploidy.

plant biology↗

bioRxiv2019

The kynurenine pathway is essential for rhodoquinone biosynthesis in Caenorhabditis elegans

A key metabolic adaptation for some species that face hypoxia as part of their life-cycle involves an alternative electron transport chain in which rhodoquinone (RQ) is required for fumarate reduction and ATP production. RQ biosynthesis in bacteria and protists requires ubiquinone (Q) as a precursor. In contrast, Q is not a precursor for RQ biosynthesis in animals such as parasitic helminths, and this pathway has remained elusive. We used Caenorhabditis elegans as a model animal to elucidate several key steps in RQ biosynthesis. Through RNA interference and a series of mutants, we found that arylamine metabolites from the kynurenine pathway are essential precursors for RQ biosynthesis de novo. Deletion of kynu-1, which encodes a kynureninase that converts L-kynurenine (KYN) into anthranilic acid (AA), and 3-hydroxykynurenine (HKYN) into 3-hydroxyanthranilic acid (3HAA), completely abolishes RQ biosynthesis, but does not affect Q levels. Deletion of kmo-1, which encodes a kynurenine 3-monooxygenase that converts KYN to HKYN, drastically reduces RQ, but not Q levels. Knockdown of the Q biosynthetic genes, coq-5 and coq-6, affects both Q and RQ levels demonstrating that common enzymes are used in both biosynthetic pathways. Our study reveals that two pathways for RQ biosynthesis have independently evolved. In contrast to bacteria, where amination is the last step in RQ biosynthesis, worms begin with the arylamine precursor, AA or 3HAA. Since RQ is absent in mammalian hosts of helminths, inhibition of RQ biosynthesis may have broad implications for targeting parasitic infections which cause important neglected tropical diseases.

biochemistry↗