Browsing by Author "Liu, Jianquan"
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Item Evidences for a role of two Y-specific genes in sex determination in Populus deltoides(2020) Xue, Liangjiao; Wu, Huaitong; Chen, Yingnan; Li, Xiaoping; Hou, Jing; Lu, Jing; Wei, Suyun; Dai, Xiaogang; Olson, Matthew S.; Liu, Jianquan; Wang, Mingxiu; Charlesworth, Deborah; Tongming, YinAlmost all plants in the genus Populus are dioecious (i.e. trees are either male or female), but it is unknown whether dioecy evolved in a common ancestor or independently in different subgenera. Here, we sequence the small peritelomeric X- and Y-linked regions of P. deltoides chromosome XIX. Two genes are present only in the Y-linked region. One is a duplication of a non-Y-linked, female-specifically expressed response regulator, which produces siRNAs that block this gene’s expression, repressing femaleness. The other is an LTR/Gypsy transposable element family member, which generates long non-coding RNAs. Overexpression of this gene in A. thaliana promotes androecium development. We also find both genes in the sex-determining region of P. simonii, a different poplar subgenus, which suggests that they are both stable components of poplar sex-determining systems. By contrast, only the duplicated response regulator gene is present in the sex-linked regions of P. davidiana and P. tremula. Therefore, findings in our study suggest dioecy may have evolved independently in different poplar subgenera.Item Evolution of a ZW sex chromosome system in willows(2023) Hu, Nan (TTU); Sanderson, Brian J.; Guo, Minghao (TTU); Feng, Guanqiao (TTU); Gambhir, Diksha (TTU); Hale, Haley; Wang, Deyan; Hyden, Brennan; Liu, Jianquan; Smart, Lawrence B.; DiFazio, Stephen P.; Ma, Tao; Olson, Matthew S. (TTU)Transitions in the heterogamety of sex chromosomes (e.g., XY to ZW or vice versa) fundamentally alter the genetic basis of sex determination, however the details of these changes have been studied in only a few cases. In an XY to ZW transition, the X is likely to give rise to the W because they both carry feminizing genes and the X is expected to harbour less genetic load than the Y. Here, using a new reference genome for Salix exigua, we trace the X, Y, Z, and W sex determination regions during the homologous transition from an XY system to a ZW system in willow (Salix). We show that both the W and the Z arose from the Y chromosome. We find that the new Z chromosome shares multiple homologous putative masculinizing factors with the ancestral Y, whereas the new W lost these masculinizing factors and gained feminizing factors. The origination of both the W and Z from the Y was permitted by an unexpectedly low genetic load on the Y and this indicates that the origins of sex chromosomes during homologous transitions may be more flexible than previously considered.Item A General Model to Explain Repeated Turnovers of Sex Determination in the Salicaceae(2021) Yang, Wenlu; Wang, Deyan; Li, Yiling; Zhang, Zhiyang; Tong, Shaofei; Li, Mengmeng; Zhang, Xu; Zhang, Lei; Ren, Liwen; Ma, Xinzhi; Zhou, Ran; Sanderson, Brian J.; Keefover-Ring, Ken; Yin, Tongming; Smart, Lawrence B.; Liu, Jianquan; DiFazio, Stephen P.; Olson, Matthew; Ma, TaoDioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly in multiple plant lineages. However, the specific mechanisms by which sex systems evolve and their commonalities among plant species remain poorly understood. With both XY and ZW sex systems, the family Salicaceae provides a system to uncover the evolutionary forces driving sex chromosome turnovers. In this study, we performed a genome-wide association study to characterize sex determination in two Populus species, P. euphratica and P. alba. Our results reveal an XY system of sex determination on chromosome 14 of P. euphratica, and a ZW system on chromosome 19 of P. alba. We further assembled the corresponding sex-determination regions, and found that their sex chromosome turnovers may be driven by the repeated translocations of a Helitron-like transposon. During the translocation, this factor may have captured partial or intact sequences that are orthologous to a type-A cytokinin response regulator gene. Based on results from this and other recently published studies, we hypothesize that this gene may act as a master regulator of sex determination for the entire family. We propose a general model to explain how the XY and ZW sex systems in this family can be determined by the same RR gene. Our study provides new insights into the diversification of incipient sex chromosomes in flowering plants by showing how transposition and rearrangement of a single gene can control sex in both XY and ZW systems.Item Genomic effects of population collapse in a critically endangered ironwood tree Ostrya rehderiana(2018) Yang, Yongzhi; Ma, Tao; Wang, Zefu; Lu, Zhiqiang; Li, Ying; Fu, Chengxin; Chen, Xiaoyong; Zhao, Mingshui; Olson, Matthew S.; Liu, JianquanIncreased human activity and climate change are driving numerous tree species to endangered status, and in the worst cases extinction. Here we examine the genomic signatures of the critically endangered ironwood tree Ostrya rehderiana and its widespread congener O. chinensis. Both species have similar demographic histories prior to the Last Glacial Maximum (LGM); however, the effective population size of O. rehderiana continued to decrease through the last 10,000 years, whereas O. chinensis recovered to Pre-LGM numbers. O. rehderiana accumulated more deleterious mutations, but purged more severely deleterious recessive variations than in O. chinensis. This purging and the gradually reduced inbreeding depression together may have mitigated extinction and contributed to the possible future survival of the outcrossing O. rehderiana. Our findings provide critical insights into the evolutionary history of population collapse and the potential for future recovery of the endangered trees.Item Global divergent responses of primary productivity to water, energy, and CO2(2019) Liu, Zhiyong; Chen, Lei; Smith, Nicholas G.; Yuan, Wenping; Chen, Xiaohong; Zhou, Guoyi; Alam, Syed Ashraful; Lin, Kairong; Zhao, Tongtiegang; Zhou, Ping; Chu, Chengjin; Ma, Hanqing; Liu, JianquanThe directionality of the response of gross primary productivity (GPP) to climate has been shown to vary across the globe. This effect has been hypothesized to be the result of the interaction between multiple bioclimatic factors, including environmental energy (i.e. temperature and radiation) and water availability. This is due to the tight coupling between water and carbon cycling in plants and the fact that temperature often drives plant water demand. Using GPP data extracted from 188 sites of FLUXNET2015 and observation-driven terrestrial biosphere models (TBMs), we disentangled the confounding effects of temperature, precipitation and carbon dioxide on GPP, and examined their long-term effects on productivity across the globe. Based on the FLUXNET2015 data, we observed a decline in the positive effect of temperature on GPP, while the positive effects of precipitation and CO2 were becoming stronger during 2000–2014. Using data derived from TBMs between 1980 and 2010 we found similar effects globally. The modeled data allowed us to investigate these effects more thoroughly over space and time. In arid regions, the modeled response to precipitation increased since 1950, approximately 30 years earlier than in humid regions. We further observed the negative effects of summer temperature on GPP in arid regions, suggesting greater aridity stress on productivity under global warming. Our results imply that aridity stress, triggered by rising temperatures, has reduced the positive influence of temperature on GPP, while increased precipitation and elevated CO2 may alleviate negative aridity impacts.Item Repeated turnovers keep sex chromosomes young in willows(2022) Wang, Deyan; Li, Yiling; Li, Mengmeng; Yang, Wenlu; Ma, Xinzhi; Zhang, Lei; Wang, Yubo; Feng, Yanlin; Zhang, Yuanyuan; Zhou, Ran; Sanderson, Brian J (TTU); Keefover‑Ring, Ken; Yin, Tongming; Smart, Lawrence B; DiFazio, Stephen P; Liu, Jianquan; Olson, Matthew (TTU); Ma, TaoBackground Salicaceae species have diverse sex determination systems and frequent sex chromosome turnovers. However, compared with poplars, the diversity of sex determination in willows is poorly understood, and little is known about the evolutionary forces driving their turnover. Here, we characterized the sex determination in two Salix species, S. chaenomeloides and S. arbutifolia, which have an XY system on chromosome 7 and 15, respectively. Results Based on the assemblies of their sex determination regions, we found that the sex determination mechanism of willows may have underlying similarities with poplars, both involving intact and/or partial homologs of a type A cytokinin response regulator (RR) gene. Comparative analyses suggested that at least two sex turnover events have occurred in Salix, one preserving the ancestral pattern of male heterogamety, and the other changing heterogametic sex from XY to ZW, which could be partly explained by the “deleterious mutation load” and “sexually antagonistic selection” theoretical models. We hypothesize that these repeated turnovers keep sex chromosomes of willow species in a perpetually young state, leading to limited degeneration. Conclusions Our findings further improve the evolutionary trajectory of sex chromosomes in Salicaceae species, explore the evolutionary forces driving the repeated turnovers of their sex chromosomes, and provide a valuable reference for the study of sex chromosomes in other species.Item Warming-induced increase in carbon uptake is linked to earlier spring phenology in temperate and boreal forests(2022) Gu, Hongshuang; Qiao, Yuxin; Xi, Zhenxiang; Rossi, Sergio; Smith, Nicholas G (TTU); Liu, Jianquan; Chen, Lei (TTU)Under global warming, advances in spring phenology due to rising temperatures have been widely reported. However, the physiological mechanisms underlying the advancement in spring phenology still remain poorly understood. Here, we investigated the effect of temperature during the previous growing season on spring phenology of current year based on the start of season extracted from multiple long-term and large-scale phenological datasets between 1951 and 2018. Our findings indicate that warmer temperatures during previous growing season are linked to earlier spring phenology of current year in temperate and boreal forests. Correspondingly, we observed an earlier spring phenology with the increase in photosynthesis of the previous growing season. These findings suggest that the observed warming-induced earlier spring phenology is driven by increased photosynthetic carbon assimilation in the previous growing season. Therefore, the vital role of warming-induced changes in carbon assimilation should be considered to accurately project spring phenology and carbon cycling in forest ecosystems under future climate warming.Item A willow sex chromosome reveals convergent evolution of complex palindromic repeats(2020) Zhou, Ran; Macaya-Sanz, David; Carlson, Craig H.; Schmutz, Jeremy; Jenkins, Jerry W.; Kudrna, David; Sharma, Aditi; Sandor, Laura; Shu, Shengqiang; Barry, Kerrie; Tuskan, Gerald A.; Ma, Tao; Liu, Jianquan; Olson, Matthew S.; Smart, Lawrence B.; DiFazio, Stephen P.Background: Sex chromosomes have arisen independently in a wide variety of species, yet they share common characteristics, including the presence of suppressed recombination surrounding sex determination loci. Mammalian sex chromosomes contain multiple palindromic repeats across the non-recombining region that show sequence conservation through gene conversion and contain genes that are crucial for sexual reproduction. In plants, it is not clear if palindromic repeats play a role in maintaining sequence conservation in the absence of homologous recombination. Results: Here we present the first evidence of large palindromic structures in a plant sex chromosome, based on a highly contiguous assembly of the W chromosome of the dioecious shrub Salix purpurea. The W chromosome has an expanded number of genes due to transpositions from autosomes. It also contains two consecutive palindromes that span a region of 200 kb, with conspicuous 20-kb stretches of highly conserved sequences among the four arms that show evidence of gene conversion. Four genes in the palindrome are homologous to genes in the sex determination regions of the closely related genus Populus, which is located on a different chromosome. These genes show distinct, floral-biased expression patterns compared to paralogous copies on autosomes. Conclusion: The presence of palindromes in sex chromosomes of mammals and plants highlights the intrinsic importance of these features in adaptive evolution in the absence of recombination. Convergent evolution is driving both the independent establishment of sex chromosomes as well as their fine-scale sequence structure.