Article
Multidisciplinary Sciences
Koji Takayama, Yoichi Tateishi, Tadashi Kajita
Summary: Through phylogeographic analyses based on nucleotide sequences of chloroplast and nuclear DNA as well as microsatellites, the historical scenario behind the pantropical distribution of Rhizophora is revealed, including the closure of the Tethys Seaway and Mid-Miocene cooling leading to lineage diversification, as well as gene exchange between the IWP and AEP lineages after 11 million years of isolation.
SCIENTIFIC REPORTS
(2021)
Article
Marine & Freshwater Biology
Gustavo Maruyama Mori, Andre Guilherme Madeira, Mariana Vargas Cruz, Yoshiaki Tsuda, Koji Takayama, Yu Matsuki, Yoshihisa Suyama, Takaya Iwasaki, Anete Pereira de Souza, Maria Imaculada Zucchi, Tadashi Kajita
Summary: The determination of species limits is crucial in biology, but can be challenging due to interspecific hybridization. In the case of mangroves, genetic data showed discrepancies with morphological traits and revealed the impact of the American continent as a barrier to gene flow. The study highlights taxonomic inconsistencies in morphology-based species designations in Rhizophora species in the Western hemisphere and South Pacific islands.
ESTUARINE COASTAL AND SHELF SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Andre Guilherme Madeira, Yoshiaki Tsuda, Yukio Nagano, Takaya Iwasaki, Maria Imaculada Zucchi, Tadashi Kajita, Gustavo Maruyama Mori
Summary: Dispersal is crucial for living beings to reach new resources and occupy new environments. However, observing the dispersal mechanisms of widespread species like mangrove trees can be costly or impractical. This study evaluates the role of ocean currents on the connectivity of Rhizophora mangle in the Southwest Atlantic. The findings suggest that isolation by distance and isolation by oceanography can explain the genetic variation of R. mangle, highlighting the importance of molecular methods and oceanographic simulations in understanding dispersal processes.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Plant Sciences
Karine E. Janner de Freitas, Railson Schreinert dos Santos, Carlos Busanello, Filipe de Carvalho Victoria, Jennifer Luz Lopes, Rod A. Wing, Antonio Costa de Oliveira
Summary: The cooking quality of Common/Asian rice varieties is highly dependent on grain starch composition, which is influenced by genetic factors. Analyzing grain quality genes in wild rice relatives can provide insights into the evolution and potential use of genetic resources. Deletion/mutation of amino acids in active sites may negatively affect specific steps of starch biosynthesis, while complete deletion of certain genes in wild species may not impact amylose content.
Article
Acoustics
Xavier Raick, Alexandre Lima Godinho, Gregorio Kurchevski, Alessia Huby, Eric Parmentier
Summary: In this study, the sounds of different species in the Pygocentrus and Serrasalmus genera were analyzed and found to exhibit distinct temporal and frequency characteristics, which can be used to differentiate taxa at both the species and genus levels.
JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA
(2023)
Article
Biotechnology & Applied Microbiology
Quanchao Wang, Tiangui Cao, Chunde Wang
Summary: In this study, bioinformatics methods were used to identify and analyze Dmrt genes in 15 bivalves, resulting in the retrieval of 55 Dmrt genes. The phylogenetic tree showed that these genes can be divided into 5 classes. The Ka/Ks ratios suggested that these genes underwent purifying selection pressure. Additionally, the spatiotemporal expression analysis indicated that different Dmrt genes may have different functions, and scallop-specific Dmrt genes may play a key role in sex determination/differentiation. Overall, this study provides a molecular basis for further investigation of the functions of Dmrt genes and phylogenomic analyses in bivalves.
Article
Agronomy
Seema Pradhan, P. Sushree Shyamli, Sandhya Suranjika, Ajay Parida
Summary: Research has shown that the R2R3-MYB transcription factor gene family plays an important role in the response of A. marina to abiotic stress, and this study is the first report of the R2R3 MYB gene family in the A. marina genome, which will aid in selecting candidates for further functional characterization.
Article
Plant Sciences
Shoukun Chen, Hongyu Ren, Yunxin Luo, Cuizhu Feng, Haifeng Li
Summary: This study identified 1858 expansin members in 40 plant species, classified into EXPA, EXPB, EXLA, and EXLB groups, with wheat containing 104 expansins. Phylogenetic analysis revealed high similarity between wheat, rice, and Arabidopsis expansins. Evolutionary analysis showed gene duplication, loss, and chromosomal rearrangement events in wheat expansins. Wheat expansin genes contain development, hormone, and abiotic stress related cis-elements, with their expression affected by environmental stresses. Overexpression of TaEXPB1A in Arabidopsis characterized its role in root and seed development, indicating the extensive functions of wheat expansins.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Evolutionary Biology
Debora Princepe, Marcus A. M. de Aguiar
Summary: This study explores how interactions between mitochondrial and nuclear DNA affect species identification accuracy and the speciation process. The findings suggest that mito-nuclear compatibility plays a crucial role in speciation and genetic data reconstruction.
SYSTEMATIC BIOLOGY
(2021)
Article
Plant Sciences
Mariana Y. Lopez-Chavez, Dulce Infante-Mata, T. Alvarez-Legorreta, Michael F. Dunn, Ricardo A. Castro-Chan, Karina Guillen-Navarro
Summary: This study aimed to evaluate the impact of a common glyphosate-based herbicide on mangrove and water chestnut trees. The results showed that different concentrations of glyphosate had different effects on plant growth, with continuous application leading to reduced growth. Additionally, glyphosate also decreased the release of carbon dioxide from the soil. These findings contribute to the understanding of the adverse effects of glyphosate on ecologically important trees and their ecosystem services in coastal areas.
Article
Genetics & Heredity
M. Shijili, Ravisankar Valsalan, Deepu Mathew
Summary: In this study, MATE proteins, which are crucial for the survival of mangrove plants under challenging environments, were identified in the genomes of various mangrove species. The proteins were classified into different clusters based on their phylogenetic analysis and their predicted functions were determined. The study also provided detailed information on the amino acid sequences, exon-intron structure, motif details, and subcellular localization pattern of all the identified MATE proteins. Additionally, custom designed repeat masking libraries for each genome were provided, which will be useful for researchers worldwide. This study provides comprehensive insights into the molecular mechanisms enabling the survival of mangroves under hostile conditions.
Article
Biochemistry & Molecular Biology
Mingxing Cheng, Huanran Yuan, Ruihua Wang, Jianing Zou, Ting Liang, Fang Yang, Shaoqing Li
Summary: In this study, 53 MT genes were identified from six Oryza species and clustered into four groups based on phylogenetic analysis. The uneven distribution of MT genes on chromosomes, with almost half clustered on chromosome 12, suggests a fragment duplication event. The duplicated MT genes were under strong negative selection, as indicated by Ka/Ks values. OsMT genes were found to be induced under different stress conditions and mainly located in chloroplasts. These results provide valuable insights into the evolution and function of the MT gene family in the Oryza genus.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Fisheries
Chona Camille VinceCruz-Abeledo, Kenneth Jay Solis, Anthony D. Angeles, Joseph Emmanuel C. Valdez, Courtney Anne Ngo, Ma Carmen Ablan-Lagman
Summary: Morphological species identification in juvenile Scylla is possible through image analysis of frontal lobe spines, with distinct features still needed for easy differentiation. This study identified the most distinguishable ratio for S. olivacea and highlighted its emerging market potential in the soft-shell crab industry. Ongoing tests are exploring visual detectability of the ratio and alternative features based on local practices.
Article
Ecology
Ronghui Fan, Keyi Tang, Liang Dou, Changkun Fu, Abu ul Hassan Faiz, Xuming Wang, Yufan Wang, Shunde Chen, Shaoying Liu
Summary: In this study, the phylogenetic relationship of the elegant water shrew, Nectogale elegans, was inferred using sequencing of mitochondrial and nuclear genes. The results revealed two species within the genus Nectogale: N. elegans and N. sikhimensis. The split between these two species may be related to the uplift of the Qinghai-Tibet Plateau, which is supported by both molecular and morphological evidence.
ECOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Jinxin Liu, Mengmeng Shi, Zhaolei Zhang, Hongbo Xie, Weijun Kong, Qiuling Wang, Xinlei Zhao, Chunying Zhao, Yulin Lin, Xiaoxia Zhang, Linchun Shi
Summary: This study reveals the extensive discordance and complexity of the relationships across the members of the Atractylodes lancea complex according to cytonuclear genomic data, which may be caused by interspecific hybridization or gene introgression.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biodiversity Conservation
Zixiao Guo, Xinnian Li, Ziwen He, Yuchen Yang, Wenqing Wang, Cairong Zhong, Anthony J. Greenberg, Chung-I Wu, Norman C. Duke, Suhua Shi
GLOBAL CHANGE BIOLOGY
(2018)
Article
Ecology
Zixiao Guo, Wuxia Guo, Haidan Wu, Xiaoting Fang, Wei Lun Ng, Xianggang Shi, Ying Liu, Zhicheng Huang, Weixi Li, Lu Gan, Sining He, Cairong Zhong, Shuguang Jian, Xun Gong, Suhua Shi, Yelin Huang
JOURNAL OF BIOGEOGRAPHY
(2018)
Article
Biochemistry & Molecular Biology
Shaohua Xu, Ziwen He, Zixiao Guo, Zhang Zhang, Gerald J. Wyckoff, Anthony Greenberg, Chung-I. Wu, Suhua Shi
MOLECULAR BIOLOGY AND EVOLUTION
(2017)
Article
Multidisciplinary Sciences
Shaohua Xu, Ziwen He, Zhang Zhang, Zixiao Guo, Wuxia Guo, Haomin Lyu, Jianfang Li, Ming Yang, Zhenglin Du, Yelin Huang, Renchao Zhou, Cairong Zhong, David E. Boufford, Manuel Lerdau, Chung-I Wu, Norman C. Duke, Suhua Shi
NATIONAL SCIENCE REVIEW
(2017)
Article
Genetics & Heredity
Haomin Lyu, Xinnian Li, Zixiao Guo, Ziwen He, Suhua Shi
Article
Biochemistry & Molecular Biology
Zuyao Liu, Guoling Chen, Tianqi Zhu, Zhaochi Zeng, Zhitong Lyu, Jian Wang, Kevin Messenger, Anthony Greenberg, Zixiao Guo, Ziheng Yang, Suhua Shi, Yingyong Wang
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2018)
Article
Biotechnology & Applied Microbiology
Lu Liu, Zixiao Guo, Cairong Zhong, Suhua Shi
Article
Plant Sciences
Wei Xie, Cairong Zhong, Xinnian Li, Zixiao Guo, Suhua Shi
Article
Plant Sciences
Zheng-Zhen Wang, Zi-Xiao Guo, Cai-Rong Zhong, Hao-Min Lyu, Xin-Nian Li, Norman C. Duke, Su-Hua Shi
Summary: Through a study on the mangrove tree, Avicennia marina, we found comprehensive genetic divergence among subspecies, higher than among geographical populations within subspecies. The level of genetic diversity differs significantly among the three subspecies, hinting at a degree of separation among their gene pools.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2022)
Article
Plant Sciences
Xiaomeng Mao, Wei Xie, Xinnian Li, Suhua Shi, Zixiao Guo
Summary: Mangrove ecosystems in China are under threat, and DNA barcoding technology can help in rapid species identification to enhance conservation efforts.
Article
Biochemistry & Molecular Biology
Rufan Zhang, Zixiao Guo, Lu Fang, Cairong Zhong, Norman C. Duke, Suhua Shi
Summary: The study found that the populations of Aegiceras corniculatum are shaped by historical climate changes and sea-level fluctuations, with two main groups identified: Indo-Malayan and Pan-Australasia. Genetic drift in a bottleneck event likely led to the genetic break between the southern and northern South China Sea subgroups of the coastal plant. This case highlights how bottleneck events can promote population subdivision and has implications for other taxa beyond coastal plants.
Article
Biochemistry & Molecular Biology
Wei Xie, Zixiao Guo, Jiayan Wang, Ziwen He, Yulong Li, Xiao Feng, Cairong Zhong, Suhua Shi
Summary: Understanding how plants adapt and diverge in extreme environments is important for plant evolution and ecology. This study explores the genomic and phenotypic characteristics of mangroves, finding that mangroves with atypical phenotypes also have distinctive genomic features.
Article
Plant Sciences
Zixiao Guo, Shaohua Xu, Wei Xie, Shao Shao, Xiao Feng, Ziwen He, Cairong Zhong, Kaichi Huang, Chung- Wu, Suhua Shi
Summary: This study analyzed the genomes of Xylocarpus species using single-molecule real-time sequencing and identified genomic features associated with mangroves. These features include positive selection in genes related to salt tolerance and root development, higher non-synonymous to synonymous substitution ratios, and active elimination of long terminal repeats. The study also found that some of these features are present in a terrestrial relative of mangroves, suggesting pre-adaptive traits. The study establishes a framework to study genomic features acquired during adaptation to new environments.
Article
Biochemistry & Molecular Biology
Sen Li, Xiaomeng Mao, Ziwen He, Shaohua Xu, Zixiao Guo, Suhua Shi
Summary: While most species in the Goodeniaceae family are native to Australasia, S. taccada and S. hainanensis have spread to tropical coastlines in the Atlantic and Indian Oceans. S. taccada is well adapted to sandy coastal areas and has become invasive. S. hainanensis is mainly found in salt marshes near mangrove forests and is in danger of extinction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Jiayan Wang, Wei Xie, Fa Si, Ziwen He, Xinfeng Wang, Shao Shao, Suhua Shi, Zixiao Guo
Summary: This study sequenced and analyzed the genomes of Heritiera fomes and Heritiera littoralis, two coastal plants with buoyant fruits, to uncover the genomic evolution and temporal transcriptional regulation of sea-surfing plant propagules.