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Genome-Wide Identification and Functional analysis of Genes Expressed Ubiquitously in Rice

Molecular Plant 2015年第2期8卷 276-289页

作者： Ki-Hong Jung Sung-Ruyl Kim Hoi-Khoanh Giong Minh Xuan Nguyen Hyun-Jung Koh Gynheung An Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute Kyung Hee University Yongin 446-701 Korea Graduate School of Biotechnology Kyung Hee University Yongin 446-701 Korea These authors contributed equally to the article.

Genes that are expressed ubiquitously throughout all developmental stages are thought to be necessary for basic biological or cellular functions. Therefore, determining their biological roles is a great challenge. We identified 4034 of these genes in rice after studying the results of Agilent 44K and Affymetrix meta- anatomical expression profiles. Among 105 genes that were characterized by loss-of-function analysis, 79 were classified as members of gene families, the majority of which were predominantly expressed. Using T-DNA insertional mutants, we examined 43 genes and found that loss of expression of six genes caused developing seedor seedling-defective phenotypes. Of these, three are singletons without similar family members and defective phenotypes are expected from mutations. phylogenomic analyses integrating genome-wide transcriptome data revealed the functional dominance of three ubiquitously expressed fam- ily genes. Among them, we investigated the function of OsO3g19890, which is involved in ATP generation within the mitochondria during endosperm development. We also created and evaluated functional net- works associated with this gene to understand the molecular mechanism. Our study provides a useful strategy for pheonome analysis of ubiquitously expressed genes in rice.

关键词： functional redundancy phylogenomic analysis rice systematic phenotype screening ubiquitouslyexpressed genes

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phylogenomics of non-model ciliates based on transcriptomic analyses

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Protein & Cell 2015年第5期6卷 373-385页

作者： Xiao Chen Xiaolu Zhao Xiaohui Liu Alan Warren Fangqing Zhao Miao Miao College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao 266003 China Department of Life Sciences Natural History Museum Cromwell Road London SW7 5BD UK Beijing Institutes of Life Science Chinese Academy of Sciences Beijing 100101 China

Ciliates are one of the oldest living eukaryotic unicellular organisms, widely distributed in the waters around the world. As a typical marine oligotrich ciliate, Strombidium sulcatum plays an important role in marine food webs and energy flow. Here we report the first deep se- quencing and analyses of RNA-Seq data from Strombidium sulcatum. We generated 42,640 unigenes with an N50 of 1,451 bp after de novo assembly and removing rRNA, mitochondrial and bacteria contaminants. We employed SPOCS to detect orthologs from S. sulcatum and 17 other ciliates, and then carried out the phyloge- nomic reconstruction using 127 single copy orthologs. In phylogenomic analyses, concatenated trees have similar topological structures with concordance tree on the class level. Together with phylogenetic networks analysis, it aroused more doubts about the placement of Protocruzia, Mesodinium and Myrionecta. While epi- plasmic proteins are known to be related to morphological characteristics, we found the potential relationship between gene expression of epiplasmic proteins and morphological characteristics. This work supports the use of high throughput approaches for phylogenomic analysis as well as correlation analysis between expression level of target genes and morphological characteristics.

关键词： Strombidium protozoa transcriptome,non-model ciliate phylogenomic analysis

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Systematic arrangement within the family Clitocybaceae (Tricholomatineae, Agaricales): phylogenetic and phylogenomic evidence, morphological data and muscarine-producing innovation

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Fungal Diversity 2023年第6期123卷 1-47页

作者： Zheng-Mi He Zuo-Hong Chen Tolgor Bau Geng-Shen Wang Zhu L.Yang CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China Yunnan Key Laboratory for Fungal Diversity and Green Development Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China College of Life Sciences Hunan Normal UniversityChangsha 410081China Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi Jilin Agricultural UniversityChangchun 130118China

The Clitocybaceae is a recently established ***,the infrafamilial divisions and relationships within the family are vague due to limited sampling and genes employed for phylogenetic *** mushrooms of the family contain the neurotoxic muscarine,which has caused many severe and even deadly poisonings ***,the taxonomic distribution and evolution of the toxin within the family is largely *** this study,phylogenetic analyses based on nucleotide sequences of ITS and of six molecular loci(ITS,LSU,TEF1,RPB1,RPB2 and ATP6),plus a phylogenomic analysis based on 485 single-copy orthologous genes,were performed to reconstruct the framework of *** analysis was used to estimate the divergence times within the ***,biochemical analysis for muscarine was conducted of 32 representative *** on these analyses,an updated classification of Clitocybaceae into six genera(Clitocybe,Collybia,Dendrocollybia,Lepista,Pseudolyophyllum,and Singerocybe)is *** genus Collybia is emended to accommodate four subgenera(Collybia,Crassicybe,Leucocalocybe,and Macrosporocybe).Seventeen new Chinese species and 15 new combinations are *** to the genera of Clitocybaceae and the subgenera of Collybia,as well as to the known species of Clitocybe and Collybia *** in China,are *** addition,muscarine was detected in 18 species,and these muscarine-containing species formed a major monophyletic clade within Collybia ***,our phylogenetic,phylogenomic,chemotaxonomic and molecular dating results indicate that the Clitocybaceae is a natural group estimated to have arisen some 60 million years ago,and in this family,muscarine has evolved only once circa 20 million years ago without later losses.

关键词： Clitocybe Clitocyboid Collybia Muscarine phylogenomic analysis Single-copy gene

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The first complete mitogenome of Cyclommatus stag beetles(Coleoptera: Lucanidae) with the phylogenetic implications

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Entomotaxonomia 2017年第4期39卷 294-299页

作者：刘静李成功游硕万霞安徽大学资源与环境工程学院生态系安徽合肥230000 大理大学云南省生物医药研发重点实验室云南大理671000

The first complete mitogenome of Cyclommatus stag beetles, Cyclommatus vitalisi（Coleoptera： Lucanidae） is sequenced using the next generation sequening. The genomic structure is a closed circular molecule with 17,853 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes（t RNAs）, 2 ribosomal RNAs（r RNAs） and a control region. The sequence has neither a gene rearrangement nor a non-coding region. The nucleotide composition is A（36. 31%）, C（21. 48%）, T（31. 20%） and G（11. 01%）, with overall AT content of 73. 61%. The phylogenetic analysis of 13 stag beetles and another three scarab beetles show that Cyclommatus vitalisi shares a close ancestry with Lucanus mazama and Lucanus fortunei.

关键词： Cyclommatus vitalisi mitogenome phylogenomic analysis

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