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| 1 | Organellar genome assembly methods and comparative analysis of horticultural plants显示文摘Although organellar genomes(including chloroplast and mitochondrial genomes)are smaller than nuclear genomes in size and gene number,organellar genomes are very important for the investigation of plant evolution and molecular ecology mechanisms.Few studies have focused on the organellar genomes of horticultural plants.Approximately 1193 chloroplast genomes and 199 mitochondrial genomes of land plants are available in the National Center for Biotechnology Information(NCBI),of which only 39 are from horticultural plants.In this paper,we report an innovative and efficient method for high-quality horticultural organellar genome assembly from next-generation sequencing(NGS)data.Sequencing reads were first assembled by Newbler,Amos,and Minimus software with default parameters.The remaining gaps were then filled through BLASTN search and PCR.The complete DNA sequence was corrected based on Illumina sequencing data using BWA(Burrows–Wheeler Alignment tool)software.The advantage of this approach is that there is no need to isolate organellar DNA from total DNA during sample preparation.Using this procedure,the complete mitochondrial and chloroplast genomes of an ornamental plant,Salix suchowensis,and a fruit tree,Ziziphus jujuba,were identified.This study shows that horticultural plants have similar mitochondrial and chloroplast sequence organization to other seed plants.Most horticultural plants demonstrate a slight bias toward A+T rich features in the mitochondrial genome.In addition,a phylogenetic analysis of 39 horticultural plants based on 15 protein-coding genes showed that some mitochondrial genes are horizontally transferred from chloroplast DNA.Our study will provide an important reference for organellar genome assembly in other horticultural plants.Furthermore,phylogenetic analysis of the organellar genomes of horticultural plants could accurately clarify the unanticipated relationships among these plants. | Xuelin Wang Feng Cheng Dekai Rohlsen Changwei Bi Chunyan Wang Yiqing Xu Suyun Wei Qiaolin Ye Tongming Yin Ning Ye | 2018 | Horticulture Research2018，5，1： | 4 |
| 2 | Genome-wide identification and characterization of WUSCHEL-related homeobox(WOX) genes in Salix suchowensis显示文摘Members of the WUSCHEL-related homeobox(WOX)transcription factor family are essential for determining cell fate and regulating diverse developmental processes in plants.Many WOX genes have been systematically investigated in woody plants such as Populus trichocarpa,but not in Salix suchowensis.Whole-genome sequence data for S.suchowensis is now available for comprehensive study of WOX genes in S.suchowensis.We thus surveyed the genome of S.suchowensis and demonstrated active expression of 15 WOX genes.In a phylogenetic analysis of WOX genes,the 15 SsWOX genes clustered among the modern/WUS,intermediate and ancient clades similar to the WOX genes of Arabidopsis thaliana.Based on the conserved intron/exon structure,SsWOX genes in the same subgroup had similar conserved exon–intron structures and motif domains.Furthermore,among several SsWOX subgroups,WUS(Wuschel)-box and EAR(the ERF-associated amphiphilic repression)-like motifs were conserved.Expression profiles of WOX genes in roots,stems and leaves indicate that SsWOX genes have various conserved roles in the tissues.Comparative analysis of the expression patterns in Salix suchowensis with that of Arabidopsis suggests that different shoot regeneration abilities are controlled by different WOX genes in plants.The analysis provide an overview of differentially expressed SsWOX genes during shoot regeneration,but also contribute to understanding the evolution of WOX genes in Salicaceae and the interrelations of WOX genes and other transcription factors,providing targets for further study. | Xuelin Wang Changwei Bi Chunyan Wang Qiaolin Ye Tongming Yin Ning Ye | 2019 | Journal of Forestry Research2019，30，5： | 3 |
| 3 | Particle Size Distributions and Organic-Inorganic Compositions of Suspended Particulate Matters Around the Bohai Strait显示文摘Laser in situ scattering and transmissometry(LISST) significantly improves our ability to assess particle size distribu-tion(PSD) in seawater, while wide-ranging measurements of the organic-inorganic compositions of suspended particulate matters(SPM) are still difficult by using traditional methods such as microscopy. In this study, PSD properties and SPM compositions around the Bohai Strait(China) were investigated based on the measurements by LISST in combination with hydro-biological parameters collected from a field survey in summer 2014. Four typical PSD shapes were found in the region, namely right-peak, left-peak, dou-ble-peak and negative-skew shapes. The double-peak and negative-skew shapes may interconvert into each other along with strong hydrodynamic variation. In the upper layer of the Bohai Sea, organic particles were in the majority, with inorganic particles rarely observed. In the bottom layer, SPM were the mixture of organic and inorganic matters. LISST provided valuable baseline information on size-resolved organic-inorganic compositions of SPM: the size of organic particles mainly ranged from 4 to 20 μm and 40 to 100 μm, while most SPM ranging from 20 to 40 μm were composed of inorganic sediment. | WANG Xiao BIAN Changwei BI Rong JIANG Wensheng ZHANG Hua ZHANG Xueqing | 2017 | Journal of Ocean University of China2017，16，1： | 0 |
| 4 | Assembly and analysis of the Populus deltoides mitochondrial genome:the first report of a multicircular mitochondrial conformation for the genus Populus显示文摘Genomics research of Populus deltoides,an important timber species that is widely planted worldwide,is an important part of poplar breeding.Currently,the nuclear and chloroplast genome of P.deltoides have been sequenced,but its mitochondrial genome(mitogenome)has not been reported.To further explore the evolution and phylogeny of P.deltoides,the mitogenome of P.deltoides I-69 was assembled using reads from Nanopore and Illumina sequencing platforms and found to consist of 802,637 bp and three circular chromosomes(336,205,280,841,and 185,591 bp)containing 58 genes(34 protein-coding genes,21 tRNA genes,and 3 rRNA genes).RNA analysis in combination with several species showed signifi cantly fewer RNA editingsites in the mitogenomes of poplar and other angiosperms than in gymnosperms.Sequence transfer analysis showed extensive mitogenome rearrangements in Populus species,and with evolution from lower to higher plants,tRNA transfer from chloroplasts to mitochondria became increasingly frequent.In a phylogenetic analysis,the evolutionary status of P.deltoides was determined,and the section Populus was supported.Our results based on the fi rst report of a multicircular conformation of the Populus mitogenome provide a basis for further study of the evolution and genetics of P.deltoides and other Populus species and for breeding programs. | Yanshu Qu Pengyan Zhou Chunfa Tong Changwei Bi Li’an Xu | 2023 | Journal of Forestry Research2023，34，3： | 0 |
| 5 | The first mitogenome of Lauraceae(Cinnamomum chekiangense)显示文摘There are three distinct genetic systems in higher plants,the dominant nuclear genome and the semi-autonomous organelle genomes(plastids and mitochondria).In contrast to the conserved plastid genome(plastome),the plant mitochondrial genome(mitogenome)is characterized by an intriguing“evolutionary paradox”distinguished by a remarkably low mutation rate but with a significantly high rearrangement rate(Palmer and Herbon,1988;Lai et al.,2022). | Changwei Bi Ning Sun Fuchuan Han Kewang Xu Yong Yang David K.Ferguson | 2024 | Plant Diversity2024，46，1： | 0 |
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