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Chromosomal-level genome and metabolome analyses of highly heterozygous allohexaploid Dendrocalamus brandisii elucidate shoot quality and developmental characteristics

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Journal of Integrative Plant Biology 2024年第6期66卷 1087-1105页

作者： Jutang Jiang Zeyu zhang Yucong Bai Xiaojing Wang Yuping Dou Ruiman Geng Chongyang Wu hangxiao zhang Cunfu Lu Lianfeng Gu Jian Gao Key Laboratory of National Forestry and Grassland Administration Beijing for Bamboo&Rattan Science and TechnologyInstitute of Gene Science and Industrialization for Bamboo and Rattan ResourcesInternational Center for Bamboo and RattanBeijing 100102China College of Forestry Basic Forestry and Proteomics Research CenterFujian Agriculture and Forestry UniversityFuzhou 350002China School of Life Science Peking UniversityBeijing 100871China College of Biological Sciences and Biotechnology Beijing Forestry UniversityBeijing 100083China

Dendrocalamus brandisii(Munro)Kurz is a sympodial bamboo species with inimitable taste and flavorful *** rapid growth and use as high-quality material make this bamboo species highly valued for both food processing and wood ***,genome information for *** is lacking,primarily due to its polyploidy and large genome ***,we assembled a high-quality genome for hexaploid ***,which comprises 70chromosomes with a total size of 2,756 Mb,using long-read Hi Fi ***,we accurately separated the genome into its three constituent *** used Oxford Nanopore Technologies long reads to construct a transcriptomic dataset covering 15 tissues for gene annotation to complement our genome assembly,revealing differential gene expression and post-transcriptional *** integrating metabolome analysis,we unveiled that well-balanced lignin formation,as well as abundant flavonoid and fructose contents,contribute to the superior quality of *** *** genomic,transcriptomic,and metabolomic datasets provided a solid foundation for enhancing bamboo shoot quality and developing efficient gene-editing *** study should facilitate research on *** and enhance its use as a food source and wood material by providing crucial genomic resources.

关键词： bamboo shoots Dendrocalamus brandisii(Munro)Kurz flavonoid genome lignin

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Development of an efficient expression system with large cargo capacity for interrogation of gene function in bamboo based on bamboo mosaic virus

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Journal of Integrative Plant Biology 2023年第6期65卷 1369-1382页

作者： Yandong Jin Baijie Wang Mingchuan Bao Yujie Li Shengwu Xiao Yuhua Wang Jun zhang Liangzhen Zhao hangxiao zhang Yau-Heiu Hsu Mingjie Li Lianfeng Gu College of Forestry Fujian Agriculture and Forestry UniversityFuzhou 350002China Basic Forestry and Proteomics Research Center School of Future TechnologyCollege of ForestryFujian Agriculture and Forestry UniversityFuzhou 350002China Graduate Institute of Biotechnology Chung Hsing UniversityTaichung 40227China College of crop science Fujian Agriculture and Forestry UniversityFuzhou 350002China

Bamboo is one of the fastest growing plants among monocotyledonous species and is grown extensively in subtropical *** bamboo has high economic value and produces much biomass quickly,gene functional research is hindered by the low efficiency of genetic transformation in this *** therefore explored the potential of a bamboo mosaic virus(BaMV)-mediated expression system to investigate genotype-phenotype *** determined that the sites between the triple gene block proteins(TGBps)and the coat protein(CP)of BaMV are the most efficient insertion sites for the expression of exogenous genes in both monopodial and sympodial bamboo ***,we validated this system by individually overexpressing the two endogenous genes ACE1 and DEC1,which resulted in the promotion and suppression of intemode elongation,*** particular,this system was able to drive the expression of three 2A-linked betalain biosynthesis genes(more than 4 kb in length)to produce betalain,indicating that it has high cargo capacity and may provide the prerequisite basis for the development of a DNA-free bamboo genome editing platform in the *** BaMV can infect multiple bamboo species,we anticipate that the system described in this study will greatly contribute to gene function research and further promote the molecular breeding of bamboo.

关键词： ACE1 bamboo BaMV-mediated overexpression DEC1 expression virus-mediated genome editing

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Profiling of circular RNA N^(6)-methyladenosine in moso bamboo(Phyllostachys edulis)using nanopore-based direct RNA sequencing

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Journal of Integrative Plant Biology 2020年第12期62卷 1823-1838页

作者： Yongsheng Wang Huihui Wang Feihu Xi Huiyuan Wang Ximei Han Wentao Wei hangxiao zhang Qianyue zhang Yushan Zheng Qiang Zhu Markus V.Kohnen Anireddy S.N.Reddy Lianfeng Gu Basic Forestry and Proteomics Research Center College of life scienceFujian Agriculture and Forestry UniversityFuzhou 350002China Basic Forestry and Proteomics Research Center College of ForestryFujian Agriculture and Forestry UniversityFuzhou 350002China College of Forestry Fujian Agriculture and Forestry UniversityFuzhou 350002China Department of Biology and Program in Cell and Molecular Biology Colorado State UniversityFort CollinsColoradoUSA

N6-methyladenosine(m^(6)A)is a prevalent modification in messenger RNAs and circular RNAs that play important roles in regulating various aspects of RNA ***,the occurrence of the m^(6)A modification in plant circular RNAs has not been reported.A widely used method to identify m^(6)A modifications relies on m^(6)A-specific antibodies followed by next-generation sequencing of precipitated RNAs(MeRIP-Seq).However,one limitation of MeRIP-Seq is that it does not provide the precise location of m^(6)A at single-nucleotide *** more recent sequencing techniques such as Nanopore-based direct RNA sequencing(DRS)can overcome such limitations,the technology does not allow sequencing of circular RNAs,as these molecules lack a poly(A)***,we developed a novel method to detect the precise location of m^(6)A modifications in circular RNAs using Nanopore *** first enriched our samples for circular RNAs,which we then fragmented and sequenced on the Nanopore platform with a customized *** this method,we identified 470 unique circular RNAs from DRS reads based on the back-spliced junction *** exonic circular RNAs,about 10%contained m^(6)A sites,which mainly occurred around acceptor and donor splice *** study demonstrates the utility of our antibody-independent method in identifying total and methylated circular RNAs using Nanopore *** method has the additional advantage of providing the exact location of m^(6)A sites at single-base resolution in circular RNAs or linear transcripts from non-coding RNA without poly(A)tails.

关键词： circular precise overcome

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Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma bamboo(Dendrocalamus latiflorus Munro)

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Journal of Integrative Plant Biology 2022年第3期64卷 649-670页

作者： Yushan Zheng Deming Yang Jundong Rong Liguang Chen Qiang Zhu Tianyou He Lingyan Chen Jing Ye Lili Fan Yubang Gao hangxiao zhang Lianfeng Gu College of Forestry Fujian Agriculture and Forestry UniversityFuzhou 350002China College of Landscape Architecture Fujian Agriculture and Forestry UniversityFuzhou 350002China Basic Forestry and Proteomics Research Center College of ForestryFujian Provincial Key Laboratory of Haixia Applied PlantSystems BiologyFujian Agriculture and Forestry UniversityFuzhou 350002China

Dendrocalamus latiflorus Munro is a woody clumping bamboo with rapid shoot *** genetic transformation and clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)gene editing techniques are available for ***,enabling reverse genetic ***,*** has the potential to be a model bamboo ***,the genome sequence of *** has remained unreported due to its polyploidy and large genome ***,we sequenced the *** genome and assembled it into three allele-aware subgenomes(AABBCC),representingthe largest genome of a major bamboo *** assembled 70 allelic chromosomes(2,737 Mb)for hexaploid *** using both singlemolecule sequencing from the Pacific Biosciences(Pac Bio)Sequel platform and chromosome conformation capture sequencing(Hi-C).Repetitive sequences comprised 52.65%of the *** *** annotated 135231 protein-coding genes in the genome based on transcriptomes from eight different *** sequencing using RNA-Seq and Pac Bio singlemolecule real-time long-read isoform sequencing revealed highly differential alternative splicing(AS)between non-abortive and abortive shoots,suggesting that AS regulates the abortion rate of bamboo *** high-quality hexaploid genome and comprehensive strand-specific transcriptome datasets for this Poaceae family member will pave the way for bamboo research using *** as a model species.

关键词： alternative splicing bamboo shoots chromosome conformation capture sequencing D.latiflorus genome assembly single-molecular sequencing

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Mitochondrial genome sequences of Artemia tibetiana and Artemia urmiana:assessing molecular changes for high plateau adaptation

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Science China Life Sciences 2013年第4期56卷 440-452页

作者： zhang hangxiao LUO QiBin SUN Jing LIU Fei WU Gang YU Jun WANG WeiWei CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences University of Chinese Academy of Sciences Department of Genome Oriented Bioinformatics Technische Universit t MünchenWissenschaftszentrum WeihenstephanFreising 85350Germany Division of Gastroenterology Department of MedicineUniversity of AlbertaEdmonton T6G 2V2AlbertaCanada

Brine shrimps,Artemia(Crustacea,Anostraca),inhabit hypersaline environments and have a broad geographical distribution from sea level to high *** therefore possess significant genetic diversity,which gives them their outstanding *** understand this remarkable plasticity,we sequenced the mitochondrial genomes of two Artemia tibetiana isolates from the Tibetan Plateau in China and one Artemia urmiana isolate from Lake Urmia in Iran and compared them with the genome of a low-altitude Artemia,*** compared the ratio of the rate of nonsynonymous(Ka) and synonymous(Ks) substitutions(Ka/Ks ratio) in the mitochondrial protein-coding gene sequences and found that atp8 had the highest Ka/Ks ratios in comparisons of *** with either *** or *** and that atp6 had the highest Ka/Ks ratio between *** and ***6 may have experienced strong selective pressure for high-altitude adaptation because although *** and *** are closely related they live at different *** identified two extended termination-associated sequences and three conserved sequence blocks in the D-loop region of the mitochondrial *** propose that sequence variations in the D-loop region and in the subunits of the respiratory chain complexes independently or collectively contribute to the adaptation of Artemia to different altitudes.

关键词： mitochondrial genome Artemia tibetiana sequence variation high plateau species

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Multi-omics of Circular RNAs and Their Responses to Hormones in Moso Bamboo(Phyllostachys edulis)

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Genomics, Proteomics & Bioinformatics 2023年第4期21卷 866-885页

作者： Yongsheng Wang Huihui Wang Huiyuan Wang Ruifan Zhou Ji Wu Zekun zhang Yandong Jin Tao Li Markus V.Kohnen Xuqing Liu Wentao Wei Kai Chen Yubang Gao Jiazhi Ding hangxiao zhang Bo Liu Chentao Lin Lianfeng Gu Basic Forestry and Proteomics Research Center College of ForestryFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhou 350002China College of Forestry Fujian Agriculture and Forestry UniversityFuzhou 350002China Department of Molecular Cell and Developmental BiologyUniversity of California at Los AngelesLos AngelesCA 90095USA

Circular RNAs(circRNAs)are endogenous non-coding RNAs with covalently closed structures,which have important functions in ***,their biogenesis,degradation,and function upon treatment with gibberellins(GAs)and auxins(1-naphthaleneacetic acid,NAA)remain ***,we systematically identified and characterized the expression patterns,evolutionary conservation,genomic features,and internal structures of circRNAs using RNase R-treated libraries from moso bamboo(Phyllostachys edulis)***,we investigated the biogenesis of circRNAs dependent on both cis-and *** explored the function of circRNAs,including their roles in regulating microRNA(miRNA)-related genes and modulating the alternative splicing of their linear ***,we developed a customized degradome sequencing approach to detect miRNA-mediated cleavage of ***,we presented a comprehensive view of the participation of circRNAs in the regulation of hormone metabolism upon treatment of bamboo seedlings with GA and ***,our study provides insights into the biogenesis,function,and miRNA-mediated degradation of circRNAs in moso bamboo.

关键词： Alternative splicing Circular RNA Degradome Phyllostachys edulis Phytohormone

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Transcriptomic Profile Reveals Blastocyst-derived Signalling Molecules Involved in the Embryo-uterine Crosstalk during Implantation in Mice

Transcriptomic Profile Reveals Blastocyst-derived Signalling...

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中国生理学会生殖科学专业委员会—中国动物学会生殖生物学分会第二次联合学术年会暨“生殖科学专业委员会第二次学术交流会”和“生殖生物学分会第十六次学术年会”

作者： hangxiao zhang Bo He Shuangbo Kong Jinhua Lu Haibin Wang State key laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of Sciences Reproductive Medical Center The First Affiliated Hospital of Xiamen University Fujian Provincial Key Laboratory of Reproductive Health Research Medical College of Xiamen University

The implantation is the first embryo-uterus dialog during pregnancy,which needs a competent blastocyst and a receptive *** researches suggest that the blastocysts need to be activated to initiate the crosstalk with the endometrium and whether this process happens normally can determine the pregnancy ***,the molecular signals from blastocysts

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林木原生质体细胞壁再生研究进展

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分子植物育种 2023年第11期21卷 3719-3732页

作者：张千悦魏文桃张航晓顾连峰福建农林大学林学院基础林学与蛋白质组学中心福州350002 福建农林大学林学院福建省海峡植物应用系统生物学重点实验室福州350002

原生质体细胞壁再生不仅在细胞全能性的研究中具有重要作用,同时在研究核质基因重组和体细胞胚胎发生等方面具有重要的应用。因此本研究从植物原生质体的分离、纯化入手对原生质体细胞壁再生研究进展进行了综述,详细阐述了制备、培养及... 详细信息

原生质体细胞壁再生不仅在细胞全能性的研究中具有重要作用,同时在研究核质基因重组和体细胞胚胎发生等方面具有重要的应用。因此本研究从植物原生质体的分离、纯化入手对原生质体细胞壁再生研究进展进行了综述,详细阐述了制备、培养及植株再生过程的研究进展,分析了影响原生质体培养再生植株的相关因素,此外,还对原生质体培养的方法、方式以及原生质体再生细胞壁过程中细胞的生理生化变化进行了概述,总结了原生质体再生细胞壁得到再生植株的应用。最后对今后的应用前景进行展望,为植物原生质体细胞壁再生得到再生植株技术的发展提供参考。

关键词：植物原生质体原生质体培养细胞壁再生遗传改良

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环状RNA的产生、研究方法及功能

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遗传 2019年第6期41卷 469-485页

作者：刘旭庆高宇帮赵良真蔡宇晨王汇源苗苗顾连峰张航晓福建农林大学林学院基础林学与蛋白质组学中心福州350002 福建农林大学生命科学学院福州350002

随着高通量测序技术的发展,环状RNA(circular RNAs,circRNAs)逐渐成为非编码RNA研究领域的热点。本文系统综述了环状RNA侧翼内含子自身互补配对驱动、RNA结合蛋白驱动以及套索驱动这3种环状RNA形成模型,并从高通量文库构建、生物信息学... 详细信息

随着高通量测序技术的发展,环状RNA(circular RNAs,circRNAs)逐渐成为非编码RNA研究领域的热点。本文系统综述了环状RNA侧翼内含子自身互补配对驱动、RNA结合蛋白驱动以及套索驱动这3种环状RNA形成模型,并从高通量文库构建、生物信息学鉴别和常用的实验验证等3个方面对环状RNA的研究方法进行了介绍。同时,本文详细归纳了环状RNA作为microRNA(miRNA)或蛋白的海绵体、调控宿主基因的选择性剪接和表达、翻译成多肽等多种功能。最后通过系统综述植物环状RNA的特征及最新研究进展,为环状RNA在植物学中的进一步研究提供了新的视野。

关键词：环状RNA 反向剪接选择性剪接海绵体

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短枝木麻黄半同胞家系苗期遗传变异及选择

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热带作物学报 2023年第8期44卷 1596-1604页

作者：徐惠昌聂森余锦林尤龙辉叶功富张航晓程分生苏亲桂福建省林业科学研究院福建福州350012 福建农林大学林学院福建福州350002 福州市林业局福建福州350007 福建省惠安赤湖国有防护林场福建泉州362131

为探究短枝木麻黄半同胞家系苗期生长与分枝性状遗传变异规律,初步筛选优良种质,以40个短枝木麻黄半同胞家系1年生幼苗为材料,对其苗高、地径、干重、根冠比、侧枝数、侧枝角和侧枝长等7个性状进行遗传分析;通过聚类分析和布雷金多性状... 详细信息

为探究短枝木麻黄半同胞家系苗期生长与分枝性状遗传变异规律,初步筛选优良种质,以40个短枝木麻黄半同胞家系1年生幼苗为材料,对其苗高、地径、干重、根冠比、侧枝数、侧枝角和侧枝长等7个性状进行遗传分析;通过聚类分析和布雷金多性状综合评价法,进行优良家系选择。结果表明,短枝木麻黄半同胞家系苗期生长与分枝性状变异丰富,7个性状在家系间差异均达到极显著水平;各性状家系遗传力变化范围为0.36~0.83,受中度或强度遗传控制。以10%入选率,选出4个优良家系,分别为3-265、5-373、1-266和2-343家系,入选家系苗高、地径、干重、侧枝数和侧枝长的现实增益分别为21.14%、19.10%、41.83%、19.97%和18.88%,遗传增益分别是17.55%、15.66%、29.70%、15.57%和15.10%,选择效果较为显著。短枝木麻黄幼苗在家系间具有很大的选育潜能,本研究选择出的优良家系既丰富了短枝木麻黄优良种质资源,也为后续短枝木麻黄遗传改良和林分营建提供了较好的种质材料。

关键词：短枝木麻黄半同胞家系遗传变异苗期选择

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