Haoyang Xin's research while affiliated with Michigan State University and other places

... With increasing chromatin accessibility and dynamic histone modifications, enhancers can be activated and brought into the proximity of their target gene promoters to form enhancer-promoter chromatin loops 12,17,18 . Through recruiting TFs and co-factors, they can physically interact with target gene promoters and then trigger their expression [18][19][20][21][22] . Although GAME genes represent a well-known metabolic gene cluster, so far, any putative involvement of enhancers in controlling their expression remained unexplored. ...

... J. effusus (soft rush; 2n = 42) is a species with an almost cosmopolitan distribution, having biotechnological importance for phytoremediation of contaminated water and medicinal properties (Liao et al., 2011;Vymazal, 2014). Two recently performed genome assemblies of J. effusus and J. inflexus confirmed their monocentricity (Hofstatter et al., 2022;Planta et al., 2022). However, the repeat composition and centromeric organization were not investigated in detail. ...

... In recent years, the significant increase in research focused on plant rDNA (Hemleben et al., 2021) has led to the discovery of many unexpected features of the evolutionary dynamics of 5S rDNA. These include the insertion of 5S rDNA CDS into the spacer regions of 35S rDNA in liverworts, gymnosperms, and asterids (Garcia et al., 2010;Garcia and Kovařík, 2013;Sousa et al., 2020), as well as 5S rDNA-related pseudogene expansion in the genomes of some species of Tulipa (Liu et al., 2022) and horizontal transfer of IGS fragments between phylogenetically distant angiosperm taxa (Tynkevich et al., 2022a). However, studies on 5S rDNA have not yet been carried out for the majority of higher plant families. ...

... After comparing the 5S rDNA obtained in previous studies with ours, both perfectly reflect the extensive diversity in P. nepalensis, in which all 18 chromosomes can be distinguished according to the signal position, signal intensity, and signal number. Nevertheless, 5S rDNA was quite conserved and dormant in numerous species, such as C. campanulatus, C. sativa, H. rhamnoides, J. regia, M. atropurpureum, P. stratiotes, P. trichocarpa, and Sanguisorba L. [9,16,22,33,36,71,72]; leaving a question about the big difference in 5S rDNA among the above species. There are several plausible hypotheses under investigation, such as (i) chromosome rearrangement (e.g., deletion, duplication, inversion, translocation), (ii) polyploidization, (iii) self-incompatibility, and (iv) chromosome satellites. ...

... Besides, it is known that GISH hardly discriminate the parental genomes of the hybrids which are from two close species or two species with weak reproductive isolation (Zhu et al. 2023). The drawback of GISH may be partly overcome by FISH, because FISH could discriminate variable karyotypes of close species or within species, such as in Alstroemeria (Kamstra et al. 1997;Zhou et al. 2003), Lilium (Lim et al. 2001;Sultana et al. 2010), Tulip (Marasek and Okazaki 2008;Lan et al. 2018), Chrysanthemum (Dai et al. 2005Qi et al. 2015). FISH analysis of 15 Narcissus cultivars shows that 13 of them are autotetraploid (EEEE: 2n = 4x = 28 E ), 'Jinzhanyintai' is an autotriploid (AAA: 2n = 3x = 30 A ), 'Bride Crown' is a F 1 hybrid (AB: 2n = 2x = 10 A + 7 B ), and 'Pink Parasol' is identified as an allotetraploid (CCDD: 2n = 4x = 20 C + 10 D ) (Zeng et al. 2020). ...

... Because these oligos can be artificially designed from single-copy sequences, oligo probes are repeat-free and can be developed for any plant species with a sequenced genome (Han et al. 2015;Jiang 2019). Thus, oligo-FISH has been successfully applied to the cytogenetics of several plants, such as maize, rice, potatoes, cucumbers and poplars (Albert et al. 2019;Braz et al. 2018;Han et al. 2015;Hou et al. 2018;Xin et al. 2018). Moreover, because the single-copy sequences used for oligo design are mainly from conserved genic regions, oligo probes designed for one species are likely useful in other related species. ...

... This application detects the location, distribution and mapping of particular genes in several genomes. 45S and 5S ribosomal DNA (rDNA) segments termed as chromosomal markers are utilized as FISH probes to identify differences in chromosomal structure because they are localized in many tandem repeats (Ramzan et al., 2018;Khan 2009;Xin et al., 2017). ...

... China is considered as a center of origin for Lilium, yet a small number of studies have been carried out on the researches of wild Lilium' evaluation and utilization, especially abiotic tolerances. Previous studies about Chinese Lilium have focused on morphological characterization Xiang et al., 2005), taxonomic (Liu et al., 2017), phylogenetic (Kim et al., 2019;Zhou et al., 2020), genetic variability, and diversity (Wang et al., 2016). Thus, we want to develop a comprehensive understanding of the realized niche of Lilium in this study, which can provide a new insight into the tolerance evaluation of Lilium. ...

... However, pachytene chromosomes are not fully compressed and always intertwine with each other during chromosome preparation. In order to obtain a more dispersed pachytene chromosome, profile a squashing method is usually used [18]. However, slight slithering of the coverslip during squashing will result in mechanical stretching of the chromosome local region [19]. ...

... foliar epidermal anatomy, leaf structure, Lilium rosthornii, morphological adaptations, stomatal size 1 | INTRODUCTION Lilium rosthornii, also referred to as Rosthorn's Lily, is a lily species that is only found in certain areas of China (Liu et al., 2016). The observed species have distinctive morphological characteristics, such as the presence of three to five golden-orange blooms positioned at the tips of each of the shorter 3 00 long stalks (Wang et al., 2021). ...