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Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

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Science China Life Sciences 2025年第1期 232-248页

作者： Yaohan Jiang Xiao Chen Chundi Wang Liping Lyu Saleh A.Al-Farraj Naomi A.Stover Feng Gao Key Laboratory of Evolution & Marine biodiversity (Ministry of Education) and Institute of Evolution & Marine biodiversity Ocean University of China Marine College Shandong University Zoology department College of ScienceKing Saud University department of Biology Bradley University Laboratory for Marine Biology and Biotechnology Qingdao Marine Science and Technology Center

Sexual reproduction first appeared in unicellular protists and has continued to be an essential biological process in almost all *** protists, which contain both germline and somatic genomes within a single cell, have evolved a special form of sexual reproduction called conjugation that involves mitosis, meiosis, fertilization, nuclear differentiation, genome rearrangement, and the development of unique cellular structures. The molecular basis and mechanisms of conjugation vary dramatically among ciliates, and many details of the process and its regulation are still largely unknown. In order to better comprehend these processes and mechanisms from an evolutionary perspective, this study provides the first comprehensive overview of the transcriptome and proteome profiles during the entire life cycle of the newly-established marine model ciliate Euplotes vannus. Transcriptome analyses from 14 life cycle stages(three vegetative stages and 11 sexual stages) revealed over 26,000 genes that are specifically expressed at different stages, many of which are related to DNA replication,transcription, translation, mitosis, meiosis, nuclear differentiation, and/or genome rearrangement. Quantitative proteomic analyses identified 338 proteins with homologs associated with conjugation and/or somatic nuclear development in other ciliates, including dicer-like proteins, Hsp90 proteins, RNA polymerase Ⅱ and transcription elongation factors, ribosomal-associated proteins, and ubiquitin-related proteins. Four of these homologs belong to the PIWI family, each with different expression patterns identified and confirmed by RT-qPCR,which may function in small RNA-mediated genome rearrangement. Proteins involved in the nonhomologous end-joining pathway are induced early during meiosis and accumulate in the developing new somatic nucleus, where more than 80% of the germline sequences are eliminated from the somatic genome. A number of new candidate genes and proteins likely t

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Phylogenetic relationships of five genera of Xylariales and Rosasphaeria ***.(Hypocreales)

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Fungal Diversity 2012年第1期52卷 75-98页

作者： Walter M.Jaklitsch Hermann Voglmayr department of systematic and Evolutionary botany Faculty Centre of BiodiversityUniversity of ViennaRennweg 141030 WienAustria

Eight inconspicuous non-stromatic perithecial fungi immersed in plant tissue are assessed with respect to their morphology,ecology and phylogenetic *** is laid on two genera now and then placed in the family Hyponectriaceae,Xylariales:Leiosphaerella with its type species *** occurring on Vaccinium,and Pseudomassaria with its type species *** occurring on *** molecular phylogenetic analyses of LSU and ITS sequences,the generic types of these genera are closely related,but their familial affiliation within Xylariales remains *** sepincoliformis clusters with ***,whereas *** is not congeneric with Pseudomassaria and *** is combined in Leiosphaerella despite its *** species thought to belong to Leiosphaerella are re-assessed:*** that occurs on Rosa,is disposed in the new genus Rosasphaeria,which is close to Eucasphaeria in the Niessliaceae(Hypocreales),according to multi-gene phylogenetic analyses(ITS,LSU,rpb2 and tef1).For *** the genus Pseudomassariella is revived.A Leiosphaerellalike fungus on Lycopodium is described as the new species Monographella *** addition the phylogenetic relationships of two fungi forming superficial stromata are here clarified:Collodiscula japonica belongs to the Xylariaceae,while Melogramma campylosporum may currently be interpreted as representing a family of its own,the Melogrammataceae.

关键词： Collodiscula Eucasphaeria.Leiosphaerella Massarina Melogramma Metasphaeria New genus Phylogenetic reconstruction Pseudomassaria Pseudomassariella systematics

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Evolution of the platycodonoid group with particular references to biogeography and character evolution

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Journal of Integrative Plant Biology 2014年第10期56卷 995-1008页

作者： Qiang Wang Xiao-Quan Wang Hang Sun Yan Yu Xing-Jin He De-Yuan Hong State Key Laboratory of systematic and Evolutionary botany Institute of Botany the Chinese Academy of Sciences Key Laboratory of biodiversity and Biogeography Kunming Institute of Botany the Chinese Academy of Sciences College of Life Sciences Sichuan University

The Qinghai‐Tibet Plateau（QTP）is an important center of origin and diversification for many northern temperate *** hypothesis＂out‐of‐QTP＂suggests that the majority of northern temperate plants have originated and dispersed from the QTP and adjacent *** interesting question is whether the biogeographic history of the platycodonoids（Campanulaceae）,a group mainly distributed in the QTP and adjacent regions,coincides with the hypothesis＂out‐of‐QTP＂？Furthermore,how have the diagnostic characters of the platycodonoids evolved？In the present study,all 10genera of the platycodonoids were sampled for molecular phylogeny and dating analyses,and ancestral states of distribution and characters were *** results do not support the platycodonoids as an＂out‐of‐QTP＂group,but instead they might have descended from Tethyan *** dispersal and diversification of the platycodonoids in Asia might have been driven by the uplift of the *** present study highlights the importance of the Tethyan Tertiary flora for the origin of the Sino‐Himalayan flora and the influence of the uplift of QTP on diversification of northern temperate *** addition,character state reconstruction reveals that the inferior ovary,capsule,long‐colpate pollen,and chromosome number 2n=14 are probably ancestral states.

关键词： Biogeography Campanulaceae character evolution platycodonoids Qinghai‐Tibet Plateau

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Spatio-temporal evolution of Allium L. in the Qinghaie-Tibet-Plateau region: Immigration and in situ radiation

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Plant Diversity 2017年第4期39卷 167-179页

作者： Frank Hauenschild Adrien Favre Jan Schnitzler Ingo Michalak Martin Freiberg Alexandra N. Muellner-Riehl Leipzig University Department of Molecular Evolution and Plant Systematics & Herbarium (LZ) Johannisallee 21-23 04103 Leipzig Germany Leipzig University Department of Systematic Botany and Functional Biodiversity Research Johannisallee 21-23 04103 Leipzig Germany German Centre for Integrative biodiversity Research (iDly) Halle-lena-Leipzig Deutscher Platz 5e 04103 Leipzig Germany

A plethora of studies investigating the origin and evolution of diverse mountain taxa has assumed a causal link between geological processes （orogenesis） and a biological response （diversification）. Yet, a substantial delay （up to 30 Myr） between the start of orogenesis and diversification is often observed. Evolutionary biologists should therefore identify alternative drivers of diversification and maintenance of biodiversity in mountain systems. Using phylogenetic, biogeographic, and diversification rate analyses, we could identify two independent processes that most likely explain the diversity of the widespread genus Allium in the Qinghai-Tibet Plateau （QTP） region：（1） While the QTP-related taxa of the subgenus Melanocrommyum diversified in situ, （2） QTP-related taxa of other subgenera migrated into the QTP from multiple source areas. Furthermore, shifts in diversification rates within Allium could not be attributed spatially and temporally to the uplift history of the QTP region. Instead, global cooling and climate oscillations in the Quaternary were major contributors to increased speciation rates in three clades of AUium. Our study therefore adds to the growing evidence supporting the ＂mountain-geo-biodiversity hypothesis＂, which highlights the role of climate oscillations for the diversification of mountain organisms.

关键词： Allium Evolution Hengduan mountains Historical biogeography Molecular dating Qinghai-Tibet plateau

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Effects of patch size, disturbances on diversity and structural traits of tropical semi-evergreen forest in the lowland Indo Burma hotspot: implication on conservation of the threatened tree species

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Journal of Mountain Science 2016年第8期13卷 1397-1410页

作者： Koushik MAJUMDAR Badal Kumar DATTA Plant Taxonomy and biodiversity Laboratory Department of Botany Tripura University

Information on geographic distribution, population and threat status of most globally red listed species in the Indo Burma zone are inadequate. Given the increase in the prevalence of isolated forest patches in the part of this hotspot, evaluation is necessary on how size of the remnant forest patches and on-going disturbances affects structure and diversity of remaining habitats including the population of some globally threatened tree species. Quantitative vegetation inventory by 500 m long and lO m wide （0.5 ha） line transects were randomly set in nine fragmented tropical semi-evergreen forest patches in Tripura, Northeast India. The studied forests patches grouped into small, medium and large based on their respected sizes. Spatial variability was analysed in woody species diversity and structure along the patch size gradients and their response to both patch size and anthropogenic disturbances. Out of 167 species, 13 identified as red-listed species by IUCN under the present inventory. Most of the diversity and structural parameters showed statistically significant positive response with the forest patch size, except for stand dominance, disturbance, sapling density and number of aggregated distribution pattern decreased when patch size increased. In addition, most of the diversity and structural attributes showed negative response with disturbances. Present baseline data would serve as an effective tool for management and protection of this important forest type. Future habitat restoration programme and strategies for relocation of additional population and re-introduction of those globally threatened trees are recommended.

关键词： Forest diversity Semi-evergreen forest Threatened species Population composition IndoBurma zone

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Glacial Refugia of Ginkgo biloba and Human Impact on Its Genetic Diversity:Evidence from Chloroplast DNA

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Journal of Integrative Plant Biology 2008年第3期50卷 368-374页

作者： Wei Gong Zhen Zeng Ye-Ye Chen Chuan Chen Ying-Xiong Qiu Cheng-Xin Fu Laboratory of systematic Evolutionary botany and biodiversity and State Conservation Center for Gene Resources of Endangered Wildlife College of Life Sciences Zhejiang University Hangzhou 310058 China

Variations in the trnK region of chloroplast DNA were investigated in the present study using polymerase chain reactionrestriction fragment length polymorphism to detect the genetic structure and to infer the possible glacial refugia of Ginkgo biloba L. in China. In total, 220 individuals from 12 populations in China and three populations outside China were analyzed, representing the largest number of populations studied by molecular markers to date. Nineteen haplotypes were produced and haplotype A was found in all populations. Populations in south-western China, including WC, JF, PX, and SP, contained 14 of the 19 haplotypes and their genetic diversity ranged from 0.771 4 to 0.867 6. The TM population from China also showed a high genetic diversity （H = 0.848 5）. Most of the genetic variation existed within populations and the differentiation among populations was low （GsT = 0.2）. According to haplotype distribution and the historical record, we suggest that populations of G. biloba have been subjected to extensive human impact, which has compounded our attempt to infer glacial refugia for Ginkgo. Nevertheless, the present results suggest that the center of genetic diversity of Ginkgo is mainly in south-western China and in situ conservation is needed to protect and preserve the genetic resources.

关键词： chloroplast DNA Ginkgo biloba glacial refugia human activities polymerase chain reaction-restriction fragment length polymorphism

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Changes of woody species diversity, horizontal and vertical distribution of stems across interior to outside within a primate rich habitat of Northeast India

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Journal of Forestry Research 2016年第4期27卷 787-798页

作者： Koushik Majumdar Bal Krishan Choudhary Badal Kumar Datta Plant Taxonomy and biodiversity Lab. Department of Botany Tripura University

The interior forest of protected area（PA）recover quickly in terms of greater diversity and structural complexity than peripheral and outsides, which may be due to high plant-frugivore interactions in the interior forest than the disturbed outsides. To describe the structural and functional differences in tree communities from interior to outside forests with in small PA, we quantitatively analyzed the vegetation of Trishna Wildlife Sanctuary, a rich primate habitat of Northeast India. Vegetation was sampled at C10 cm girth at breast height by 10 m 9 500 m sized20 line transects（10 ha） laid in the interior（N = 7）,peripheral（N = 7） and outside（N = 6） zones of this sanctuary. All transects were ordinated by Principal Component Analysis based on correlation between diversity and existing disturbance indices. We found significant differences（P ／ 0.05） in taxonomic richness and diversity indices between the habitat. Van diagram confirmed greater unique species richness in the interior zone（64） than peripheral（28） and outside（6） zones. Overall density（ha-1） did not differed across the zones, but basal area（m2ha-1） was significantly（P ／ 0.01） high in peripheral zone. Vertical distribution of stem density was linearly declined across zones（r2adj[ 0.70; P ／ 0.01） with increase in the canopy height. Horizontal distribution of adult stems showed significant inverse quadratic relationship（r2adj[ 0.80; P ／ 0.001）, which suggests very low density of canopy forming voluminous trees in the interior *** protection, restoration and management of interior regions are required to preserve local plant genetic diversity and also to maintain suitable habitat for threatened wildlife.

关键词： interior outside habitat restoration Northeast disturbance quickly inverse preserve quadratic

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Ethno-medicinal plants used by Bengali communities in Tripura, northeast India

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Journal of Forestry Research 2014年第3期25卷 713-716页

作者： Joydeb Majumder Partha P. Bhattacharjee Badal K. Datta Basant K. Agarwala Ecology & biodiversity Laboratories Department of Zoology Tripura University Plant Taxonomy & biodiversity Laboratory Department of Botany Tripura University

Northeastern India has high medicinal plant diversity due to variance in topography and physiognomy. We documented the uses of various medicinal plants by the Bengali people of West district and South district of Tripura state for their own health care as well as for domesti-cated animals. Based on semi structured interviews, group discussions and information from local informants, a total of 93 species of medicinal plants of 52 families and 83 genera were documented. These plants were used to treat more than 55 different human diseases and 6 diseases of livestock. Sixty-eight plant species were used singly and the rest were used in combination with other species for therapeutic formulations of various diseases. Leaves of plants were most often used for most of the ethnobotanical preparations. Maximum consensus value of 96% was recorded for Chromolaena odorata （L.） King ＆amp;H. Rob., and the mini-mum was 15%for Bambusa balcooa Robx. Of the 93 plant species, 75 species showed pharmacological properties. Prospects for augmenting existing knowledge and enhancing the use of traditional medicinal plants are discussed.

关键词： ethnobotanical survey Bengali community traditionalknowledge Tripura state Northeast India

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Effect of shifting cultivation and fallow on soil quality index in Mokokchung district,Nagaland,India

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Ecological Processes 2022年第1期11卷 561-576页

作者： Wati Temjen Maibam Romeo Singh Tali Ajungla department of botany Nagaland University798627 LumamiIndia Centre for biodiversity Department of BotanyNagaland University798627 LumamiIndia

Background:Shifting cultivation is a major agriculture practice in the Nagaland state of *** study examines the effect of shifting cultivation and the length of the fallow period on soil quality index(SQI).Four sites were selected for the study,viz.,a shifting cultivation site(SCS),a 3-year-old fallow land(FL-3),a 7-year-old fallow land(FL-7),and a 12-year-old fallow land(FL-12).Soil parameters were recorded seasonally and SQI was calculated from the minimum data ***:With the increase in the fallow period,the values of conductivity,soil organic carbon,available nitrogen,available phosphorus,exchangeable potassium,moisture,clay,and cation exchange capacity of soil ***,soil pH and bulk density decreased with fallow *** additive SQI_(a)values were in the order SCS

关键词： Shifting cultivation Jhum Soil quality index Soil health Seasonal variation Nagaland India

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A new model of speciation

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National Science Review 2019年第2期6卷 289-290页

作者： Loren H.Rieseberg department of botany and biodiversity Research Centre University of British Columbia NSR

In the first paragraph of ‘On the origin of species’, Darwin [1]refers to speciation as that ‘mystery of mysteries’. Although the means by which new species arise is no longer mysterious, some puzzles remain. One such puzzle, which is addressed in a recent paper from Chung-I Wu’s group on mangrove speciation [2],concerns the popular allopatric speciation model. In this model,

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