High-quality reference genome decoding and population evolution analysis of prickly Sechium edule

Authors: Xiaojing Wang, Shaoqin Shen, Yanhong Fu, Rui Cao, Yunfeng Wei, Xiaoming Song

Source: Horticultural Plant Journal, Vol 11, Iss 2, Pp 827-838 (2025)

Subject Terms: Sechium edule, Whole-genome duplication, Divergence time, Genome evolution, Population structure, Cucurbitaceae, Plant culture, SB1-1110

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Relation: http://www.sciencedirect.com/science/article/pii/S2468014124000955; https://doaj.org/toc/2468-0141

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Genome assembly and population analysis of tetraploid marama bean reveal two distinct genome types

Authors: Jin Li, Christopher Cullis

Source: Scientific Reports, Vol 15, Iss 1, Pp 1-16 (2025)

Subject Terms: Marama bean, Genome assembly, Tetraploid, Plant adaptation, Phylogenetics, Whole genome duplication (WGD), Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/b0844691ceeb4a3ca387ecaf0eac2d60

Cross-species single-nucleus analysis reveals the potential role of whole-genome duplication in the evolution of maize flower development

Authors: Huawei Feng, Wenjuan Fan, Min Liu, Jiaqian Huang, Bosheng Li, Qing Sang, Baoxing Song

Source: BMC Genomics, Vol 26, Iss 1, Pp 1-12 (2025)

Subject Terms: Maize, Sorghum, Inflorescence, Evolution, Single-nucleus RNA-seq, Whole-Genome Duplication, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/72892dc828044ec38402d488426c863d

Plant AT-rich protein and zinc-binding protein (PLATZ) family in Dendrobium huoshanense: identification, evolution and expression analysis

Authors: Fangli Gu, Yanshuang Ren, Muhammad Aamir Manzoor, Tingting Wang, Renshu Huang, Naifu Chen, Cheng Song, Yingyu Zhang

Source: BMC Plant Biology, Vol 24, Iss 1, Pp 1-18 (2024)

Subject Terms: Dendrobium huoshanense, Whole genome duplication, Abiotic stress, Expression pattern, Botany, QK1-989

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2229

Access URL: https://doaj.org/article/1be01ee990944effa3ea1296b8a8d435

Differential regulation of magnesium transporters Slc41, Cnnm and Trpm6-7 in the kidney of salmonids may represent evolutionary adaptations to high salinity environments

Authors: Marius Takvam, Elsa Denker, Naouel Gharbi, Valentina Tronci, Jelena Kolarevic, Tom Ole Nilsen

Source: BMC Genomics, Vol 25, Iss 1, Pp 1-25 (2024)

Subject Terms: Whole genome duplication, Kidney function, Magnesium transporter, Euryhaline fish, Magnesium homeostasis, Nephron tubules, Biotechnology, TP248.13-248.65, Genetics, QH426-470

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Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/9e468eecb1354b389ac66dd0a04effcd

Chromosome scale genome assembly and annotation of coconut cultivar Chowghat Green Dwarf

Authors: M. K. Rajesh, Roli Budhwar, Rohit Shukla, Praveen Kumar Oraon, Shailendra Goel, Bobby Paul, Regi Jacob Thomas, Akshay Dinesh, S. Jayasekhar, K. P. Chandran, K. S. Muralikrishna, B. J. Nirmal Kumar, Alpana Das

Source: Scientific Reports, Vol 14, Iss 1, Pp 1-18 (2024)

Subject Terms: Coconut genome, Transposable elements, Whole genome duplication, Genome browser, Database, Web server, Medicine, Science

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Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/c5e8a6c197dc41618edd0ceeb3a36b68

Resolving phylogenetic conflicts in Pandanales: the dual roles of gene flow and whole-genome duplication

Authors: Tian Shi, Jian He

Source: Frontiers in Plant Science, Vol 16 (2025)

Subject Terms: Pandanales phylogeny, gene flow, whole-genome duplication, gene tree-species tree discordance, phylogenomic, Plant culture, SB1-1110

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fpls.2025.1511582/full; https://doaj.org/toc/1664-462X

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Divergent evolutionary paces among eudicot plants revealed by simultaneously duplicated genes produced billions of years ago

Authors: Yao Wang, Jiangli Wang, Yingjie Li, Yongchao Jin, Xiyin Wang

Source: Frontiers in Plant Science, Vol 16 (2025)

Subject Terms: Ks distribution, whole genome duplication, pathway enrichment analysis, Chi-square test, time correction, Plant culture, SB1-1110

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Relation: https://www.frontiersin.org/articles/10.3389/fpls.2025.1518981/full; https://doaj.org/toc/1664-462X

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Genomic, transcriptomic and metabolomic analyses of Amorphophallus albus provides insights into the evolution and resistance to southern blight pathogen

Authors: Longfei Duan, Jianfeng Qin, Gaoxin Zhou, Chuan Shen, Baofu Qin

Source: Frontiers in Plant Science, Vol 15 (2025)

Subject Terms: Amorphophallus albus, genome evolution, transcriptomic and metabolomic, whole genome duplication, Sclerotium rolfsii (SR), Plant culture, SB1-1110

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Relation: https://www.frontiersin.org/articles/10.3389/fpls.2024.1518058/full; https://doaj.org/toc/1664-462X

Access URL: https://doaj.org/article/120278c9fe4547dd834fb03f49fb0977

Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis

Authors: Federico A Vignale, Andrea Hernandez Garcia, Carlos P Modenutti, Ezequiel J Sosa, Lucas A Defelipe, Renato Oliveira, Gisele L Nunes, Raúl M Acevedo, German F Burguener, Sebastian M Rossi, Pedro D Zapata, Dardo A Marti, Pedro Sansberro, Guilherme Oliveira, Emily M Catania, Madeline N Smith, Nicole M Dubs, Satish Nair, Todd J Barkman, Adrian G Turjanski

Source: eLife, Vol 14 (2025)

Subject Terms: Ilex paraguariensis, yerba mate, genome, caffeine, convergent evolution, whole-genome duplication, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/104759; https://doaj.org/toc/2050-084X

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An ancient whole-genome duplication in barnacles contributes to their diversification and intertidal sessile life adaptation

Authors: Jianbo Yuan, Xiaojun Zhang, Xiaoxi Zhang, Yamin Sun, Chengzhang Liu, Shihao Li, Yang Yu, Chengsong Zhang, Songjun Jin, Min Wang, Jianhai Xiang, Fuhua Li

Source: Journal of Advanced Research, Vol 62, Iss , Pp 91-103 (2024)

Subject Terms: Barnacle genome, Whole-genome duplication, Comparative genomics, Intertidal adaptation, Transcriptome analysis, Medicine (General), R5-920, Science (General), Q1-390

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Relation: http://www.sciencedirect.com/science/article/pii/S2090123223002643; https://doaj.org/toc/2090-1232

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Ecology, Evolution and Diversity of Plants

Contributors: Meng, Hong-Hu, Song, Yi-Gang

Subject Terms: Ficus, Indo-Burma, genetic structure, human cultivation, nSSRs, species abundance distribution (SAD), neutral process, Tiankeng forests, negative terrain, plant refuge, chloroplast DNA, ITS, Stilpnolepis, allopatric divergence, genetic diversity, spatial genetic structure, mating system, Rhizophora apiculata, Avicennia marina, habitat destruction, conservation, restoration, phylogeny, biogeography, divergence, critically endangered, rare species, genetic divergence, isolation by distance, biodiversity conservation, xerophytic relict plant, source-sink metapopulations, ddRAD-seq, Asia, Biogeography, Bauhinia, Fabaceae, late Eocene, vegetation restoration, phytoplankton, Shengjin Lake, environmental factors, flower-visitor, insect pollination, plant species, urbanization, diversity, functional group, pollination network, green space, Polygonum criopolitanum, distyly, style-morph ratios, seed sets, strict self-incompatibility, weed seeds, seed identification, target detection, convolutional neural network, YOLOv5, early seedling growth, Eremurus anisopterus, hermaphrodite–gynomonoecious sexual system, inbreeding depression, offspring fitness, seed germination, seed mass, Xizang, Rhodiola namlingensis, Rhodiola wangii, new species, taxonomy, radiation, Salvia miltiorrhiza, subg. Glutinaria, plastid genome, phylogenomics, latitudinal diversity gradient, species richness, biodiversity pattern, climate change, diversification, speciation, extinction, flora, vegetation, origin, evolution, Yunnan, SW China, character evolution, bulbil, inflorescence architecture, floral color, perianth opening degree, Bletilla striata, compound system of bamboo and orchid, endophytic fungi, fungal diversity, symbiotic relationship, Gastrochilus, niche, Asian Monsoon, endangered species, integrative evidence, Pyrus hopeiensis, Pyrus ussuriensis, taxonomic uncertainty, aril, conservation genetics, Eleutharrhena macrocarpa, evolutionary distinctiveness, Himalayan uplift, Menispermaceae, southern Yunnan rainforests, Tiliacoreae, Elaeagnus moorcroftii Wall., PacBio’s high-fidelity sequencing, Hi-C-assisted assembly, whole genome duplication, xerophyte, drylands, Paris polyphylla, transcriptome, polyphyllin, EST-SSR markers, biodiversity, T. doichangensis, gene flow, conservation priority, endemic taxa, Viburnum, geographical pattern, abiotic stress, genotyping, okra, phenotyping, molecular markers, SSR, land plants, molecular systematics, morphology, tree of life, distribution, habitat suitability, Nymphaea, land use, Orchidaceae, investigation, mountains, Poyang Lake basin, germplasm resource, database, numerical taxonomy, random forest, bipartite networks, modularity analysis, apparent competition, minimum spanning tree, Renyi diversity, new syntaxa, CART, MCSN, taxonomy modeling, classifier modeling, biodiversity loss, conservation genomics, Fengshui/shrine/temple forests, human impact, hemiparasite–host species, phylogenetic, Cassytha, Lauraceae, woody plants, Taraxacum kok-saghyz, Hevea brasiliensis, Eucommia ulmoides, genome-wide, SPLs, expression pattern, Technology: general issues

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Access URL: https://directory.doabooks.org/handle/20.500.12854/137712
https://mdpi.com/books/pdfview/book/8941

Ongoing chromothripsis underpins osteosarcoma genome complexity and clonal evolution

Authors: Espejo Valle-Inclan, Jose ^{1, 6, 8}, De Noon, Solange ^{2, 3, 6}, Trevers, Katherine ^{2, 3}, Elrick, Hillary ¹, van Belzen, Ianthe A.E.M. ¹, Zumalave, Sonia ¹, Sauer, Carolin M. ¹, Tanguy, Mélanie ⁴, Butters, Thomas ^{2, 3}, Muyas, Francesc ¹, Rust, Alistair G. ¹, Amary, Fernanda ^{2, 3}, Tirabosco, Roberto ^{2, 3}, Giess, Adam ⁴, Sosinsky, Alona ⁵, Elgar, Greg ⁴, Flanagan, Adrienne M. ^{2, 3, 7, ∗}, Cortés-Ciriano, Isidro ^{1, 7, 9, ∗∗}

Source: In Cell 23 January 2025 188(2):352-370

Evolution and function of galectins in Xenopus laevis: Comparison with mammals and new perspectives

Authors: Ogawa, Takashi ^{a, b, ⁎}, Nonaka, Yasuhiro ^a, Shoji, Hiroki ^c, Nakamura, Takanori ^a

Source: In BBA Advances 2025 7

The Monochoria genome provides insights into the molecular mechanisms underlying floral heteranthery

Authors: Yang, Jingshan ^{a, b}, Chen, Jinming ^a, He, Xiangyan ^{a, b}, Wang, Guangxi ^c, Barrett, Spencer C.H. ^{d, ⁎}, Li, Zhizhong ^{a, ⁎}

Source: In Journal of Genetics and Genomics February 2025

Unveiling kiwifruit TCP genes: evolution, functions, and expression insights

Authors: Donglin Li, Haibo Li, Huimin Feng, Ping Qi, Zhicheng Wu

Source: Plant Signaling & Behavior, Vol 19, Iss 1 (2024)

Subject Terms: kiwifruit, tcp gene family, actinidia chinensis, actinidia eriantha, whole-genome duplication, expression profiles, conserved motif, Plant ecology, QK900-989, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1559-2316; https://doaj.org/toc/1559-2324

Access URL: https://doaj.org/article/cb63b7a72b93447095ca5c48e0727e6e

The Carthamus tinctorius L. genome sequence provides insights into synthesis of unsaturated fatty acids

Authors: Yuanyuan Dong, Xiaojie Wang, Naveed Ahmad, Yepeng Sun, Yuanxin Wang, Xiuming Liu, Na Yao, Yang Jing, Linna Du, Xiaowei Li, Nan Wang, Weican Liu, Fawei Wang, Xiaokun Li, Haiyan Li

Source: BMC Genomics, Vol 25, Iss 1, Pp 1-13 (2024)

Subject Terms: Safflower, Whole genome duplication, Evolutionary history, Fatty acid biosynthesis, Biotechnology, TP248.13-248.65, Genetics, QH426-470

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Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/4e9743ee17864a21bb0a126d91c29874

Karyotype and LTR-RTs analysis provide insights into oak genomic evolution

Authors: Rui-Bin Cao, Ran Chen, Ke-Xin Liao, He Li, Gang-Biao Xu, Xiao-Long Jiang

Source: BMC Genomics, Vol 25, Iss 1, Pp 1-13 (2024)

Subject Terms: Whole-genome duplication, Long terminal repeat retrotransposons, Karyotype, Oak, Chromosomal structure, Genomic evolution, Biotechnology, TP248.13-248.65, Genetics, QH426-470

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Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/6ceee0ac2902437993f7406c85eb6480

A chromosome-level genome reveals genome evolution and molecular basis of anthraquinone biosynthesis in Rheum palmatum

Authors: Tianyi Zhang, Lipan Zhou, Yang Pu, Yadi Tang, Jie Liu, Li Yang, Tao Zhou, Li Feng, Xumei Wang

Source: BMC Plant Biology, Vol 24, Iss 1, Pp 1-20 (2024)

Subject Terms: Rheum palmatum, Genome, Transposable element, Anthraquinone, Whole genome duplication, Botany, QK1-989

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Relation: https://doaj.org/toc/1471-2229

Access URL: https://doaj.org/article/8e1505f5528e44fc9d00f7243554d0d5

Branching Out to Speciation in a Model of Fractionation: The Malvaceae

Authors: Zhang, Y., Zheng, C., Islam, S., Kim, Y., Sankoff, D.

Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics IEEE/ACM Trans. Comput. Biol. and Bioinf. Computational Biology and Bioinformatics, IEEE/ACM Transactions on. 18(5):1875-1884 Jan, 2021