Publications by authors named "Yong-Chao Xu"

The origin of genes from noncoding sequences is a long-term and fundamental biological question. However, how de novo genes originate and integrate into the existing pathways to regulate phenotypic variations is largely unknown. Here, we selected 7 genes from 782 de novo genes for functional exploration based on transcriptional and translational evidence.

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  • High mountains have a rich biodiversity, but there's limited understanding of how plants adapt to these harsh conditions.
  • Researchers completed a genome assembly for Dasiphora fruticosa, a plant found in the Qinghai-Tibetan Plateau and northern lowlands, and sequenced 592 individuals to study its adaptations.
  • Analyses revealed a genetic bottleneck after glaciation, identified 63 genes linked to adaptation between lowland and highland populations, and highlighted that reduced genetic load from inbreeding may help highland plants thrive in extreme environments, offering insights for conservation and crop breeding.
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  • Genetic load encompasses harmful mutations that can affect populations negatively, and this study focuses on how transposable element (TE) insertion contributes to this load during the range expansion of Arabidopsis thaliana.
  • The research analyzed 1,115 global natural accessions and found that TE load increases with geographic expansion, particularly in the Yangtze River basin population, with effective population size playing a significant role.
  • By mapping candidate genes and TEs, the study sheds light on the genetic factors driving TE load variation, emphasizing insights from both population genetics and quantitative genetics.
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Chloroplasts produce singlet oxygen (1O2), which causes changes in nuclear gene expression through plastid-to-nucleus retrograde signaling to increase plant fitness. However, the identity of this 1O2-triggered pathway remains unclear. Here, we identify mutations in GENOMES UNCOUPLED4 (GUN4) and GUN5 as suppressors of phytochrome-interacting factor1 (pif1) pif3 in regulating the photo-oxidative response in Arabidopsis thaliana.

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Clean and sustainable H production is crucial to a carbon-neutral world. H generation by Chlamydomonas reinhardtii is an attractive approach for solar-H from HO. However, it is currently not large-scalable because of lacking desirable strains with both optimal H productivity and sufficient knowledge of underlying molecular mechanism.

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  • Wild rice species Oryza nivara and Oryza rufipogon are important genetic resources for developing new rice cultivars, particularly in understanding their drought tolerance mechanisms.
  • While previous research has focused on phenotypic and genomic traits related to domestication, the molecular differences between wild and cultivated rice under drought stress remain underexplored, particularly regarding long noncoding NATs (lncNATs).
  • RNA sequencing revealed 1246 lncRNAs in wild and cultivated rice, with a significant number of coding-noncoding NAT pairs showing differential expression under drought, indicating the complex role of lncNATs in wild rice's response to environmental stress.
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Gene gain and loss are crucial factors that shape the evolutionary success of diverse organisms. In the past two decades, more attention has been paid to the significance of gene gain through gene duplication or genes. However, gene loss through natural loss-of-function (LoF) mutations, which is prevalent in the genomes of diverse organisms, has been largely ignored.

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Double fertilization is a key innovation for the evolutionary success of angiosperms by which the two fertilized female gametes, the egg cell and central cell, generate the embryo and endosperm, respectively. The female gametophyte (embryo sac) enclosed in the sporophyte is derived from a one-celled haploid cell lineage. It undergoes successive events of mitotic divisions, cellularization, and cell specification to give rise to the mature embryo sac, which contains the two female gametes accompanied by two types of accessory cells, namely synergids and antipodals.

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Chlorophyll biosynthesis plays essential roles in photosynthesis and plant growth in response to environmental conditions. The accumulation of excess chlorophyll biosynthesis intermediates under light results in the production of reactive oxygen species and oxidative stress. In this study, we identified a rice (Oryza sativa) mutant, oxidation under photoperiod (oxp), that displayed photobleached lesions on its leaves, reduced growth and decreased chlorophyll content during light/dark cycles or following a dark-to-light transition.

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Reproductive isolation is a prerequisite for speciation. Failure of communication between female tissues of the pistil and paternal pollen tubes imposes hybridization barriers in flowering plants. LURE1 (AtLURE1) peptides and their male receptor PRK6 aid attraction of the growing pollen tube to the ovule.

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  • The less-is-more hypothesis suggests that gene loss can drive evolutionary change, with loss-of-function (LoF) mutations helping in adaptation and diversification.
  • Researchers identified over 60,000 LoF variants in Arabidopsis genomes, revealing that 34% of protein-coding genes lack these mutations.
  • Findings show correlations between LoF variants and genetic diversity, and some variants are linked to climate change, indicating their significant role in plant adaptation and trait diversity.
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Rapid phenotypic changes in traits of adaptive significance are crucial for organisms to thrive in changing environments. How such phenotypic variation is achieved rapidly, despite limited genetic variation in species that experience a genetic bottleneck is unknown. , an annual and inbreeding forb (Brassicaceae), is a great system for studying this basic question.

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Transposable elements (TEs) are mobile genetic elements with very high mutation rates that play important roles in shaping genome architecture and regulating phenotypic variation. However, the extent to which TEs influence the adaptation of organisms in their natural habitats is largely unknown. Here, we scanned 201 representative resequenced genomes from the model plant Arabidopsis thaliana and identified 2,311 polymorphic TEs from noncentromeric regions.

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  • Organisms must adapt to their changing environments, and studying their range expansions helps us understand these adaptations, particularly regarding climate change.
  • The plant Arabidopsis thaliana, originally from the Iberian Peninsula and North Africa, has spread to regions like the Yangtze River basin, which has a contrasting climate.
  • Research revealed the Yangtze population of A. thaliana is unique, having diverged over 61,000 years ago, and adaptations, especially in flowering time genes, are key to their survival in this new habitat.
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  • Balancing selection helps maintain genetic variation in populations, contrasting with positive selection which fixes beneficial traits; however, its broad impacts on gene adaptation remain underexplored.
  • A study examined genes under balancing selection in two plant species, uncovering five specific genes associated with stress response and adaptation, showing significant ecological differences between haplotype groups.
  • Findings suggest that many more genes than just the well-known ones are under balancing selection, highlighting their crucial role in adapting to different environments, particularly regarding resistance to stress.
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  • Researchers studied a type of RNA called lncRNA HOTTIP to see how it affects colorectal cancer (CRC) patients.
  • They found that lncRNA HOTTIP is more active in cancer tissues than in healthy tissues and is linked to more severe cancer stages.
  • Higher levels of lncRNA HOTTIP could mean patients have a worse prognosis, suggesting it might help doctors understand how serious the cancer is for future patients.
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Leaf senescence is an important biological process that contributes to grain yield in crops. To study the molecular mechanisms underlying natural leaf senescence, we harvested three different developmental ear leaves of maize, mature leaves (ML), early senescent leaves (ESL), and later senescent leaves (LSL), and analyzed transcriptional changes using RNA-sequencing. Three sets of data, ESL vs.

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Objective: To explore the common types of massive intraoperative bleeding, clinical characteristics, treatment philosophy and operating skills in pelvic cancer surgery.

Methods: We treated massive intraoperative bleeding in 19 patients with pelvic cancer in our department from January 2003 to March 2012. Their clinical data were retrospectively analyzed.

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Objective: To investigate the approach and efficacy of dealing the rectal ligament in resection of rectal cancer in obese male patients.

Methods: A total of 92 patients (BMI>25 kg/m(2)) undergoing resection of rectal cancer from December 2008 to December 2010 in Henan Tumor hospital were assigned into 2 groups according to the surgical technique, the modified group (paralleled clipping of rectal ligament, 48 patients) and traditional group (44 patients). Operative time, intra-operational bleeding, rectal ulceration, ureteral injury, mesorectal integrity, and positive rate of lateral margin of pelvic wall were compared between two groups.

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Objective: To evaluate the association of early diarrhea(postoperative day 1 to 7) and anastomotic leakage after low anterior resection for rectal cancer.

Methods: Clinical data of 192 cases (group A, tumor from the anal verge 4-7 cm) from May 2004 to May 2007 and 236 cases(group B) from July 2007 to May 2010 in our hospital who received low anterior resection of rectal cancer were analyzed retrospectively.

Results: In group A, the incidence of early postoperative diarrhea was 19.

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