Article
Forestry
Huijuan Zhou, Xiaoxiao Gao, Keith Woeste, Peng Zhao, Shuoxin Zhang
Summary: Chloroplast (cp) DNA genomes of Castanea species show similar genomic structures with differences in gene loss and pseudogenization in certain genes. These findings contribute to a better understanding of the evolutionary history and phylogenetic relationships of chestnut species.
Article
Multidisciplinary Sciences
Eckart Stolle, Rodrigo Pracana, Federico Lopez-Osorio, Marian K. Priebe, Gabriel Luis Hernandez, Claudia Castillo-Carrillo, Maria Cristina Arias, Carolina Ivon Paris, Martin Bollazzi, Anurag Priyam, Yannick Wurm
Summary: The study investigates the role of supergene regions in Solenopsis fire ants, which determine whether colonies have multiple queens or not. By analyzing genomes, the researchers find that the supergene variant responsible for multiple-queen colonies evolved in one species and spread to other species through introgressive hybridization.
NATURE COMMUNICATIONS
(2022)
Article
Plant Sciences
Darren C. J. Wong, Rod Peakall
Summary: In this study, transcriptome data were used for phylogenetic analysis of orchid plants, revealing important results and suggesting potential applications of transcriptome data in other studies.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Marine & Freshwater Biology
Kathryn L. Dawkins, James M. Furse, Jane M. Hughes
Summary: Research on the biogeographic history of mesic Australian fauna with Gondwanan origins is limited. This study focused on the burrowing clade of Australian freshwater crayfish to analyze their origin, distribution, and diversification patterns. The results suggest that the clade originated during the early fragmentation of Gondwana in southern Australia, with divergence between extant taxa likely a result of both short- and long-distance dispersal events, influenced by fluctuating sea levels and changing climate into the Eocene.
Article
Plant Sciences
Xia Liu, Zhaoshan Wang, Wei Wang, Qinqin Huang, Yanfei Zeng, Yu Jin, Honglei Li, Shuhui Du, Jianguo Zhang
Summary: This study examines the origin and biogeography of the Populus genus using phylogenetic analysis of chloroplast fragments. The results suggest that the early divergences of the Salicaceae family occurred in Eurasia after the Cretaceous-Paleogene mass extinction, with subsequent spread to other regions. Modern Populus species began to diversify during the early Oligocene, potentially facilitated by climate changes. Populus species from Eurasia colonized North America via the Bering Land Bridges. The present-day distribution of Populus can be explained by differences in extinction rates in different regions. Further research is needed to test these hypotheses. This study highlights the importance of combining phylogenetic analysis and biogeographic interpretations to understand the origin and distribution of biodiversity in temperate plant floras.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Physiology
Sergio Diez-Hermano, Maria D. Ganfornina, Arne Skerra, Gabriel Gutierrez, Diego Sanchez
Summary: This study proposed a novel phylogenetic tree topology for chordate Lipocalins, revealing the evolutionary history of Lipocalins in fish and mammals, and discussing the functional impact of early diverging Lipocalins.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Plant Sciences
Chenqian Tang, Xin Chen, Yunfei Deng, Liyang Geng, Jianhui Ma, Xueyan Wei
Summary: This study analyzed the chloroplast genomes of Sorbus s.s. plants to investigate their phylogenetic relationships. The results showed that Sorbus s.s. is monophyletic, while Sorbus s.l. is polyphyletic. The current subgenus and section classifications were found to be problematic. The conserved genome structure of Sorbus s.s. can be used for population genetics, species delimitation, and phylogenetic studies, while hypervariable regions and repeat sequences are promising molecular markers.
Article
Biodiversity Conservation
Jiahui Tian, Yongjia Zhan, Chengmin Shi, Hirotsugu Ono, Lihong Tu
Summary: This study reconstructed the phylogeny of Solenysa and other linyphiids based on molecular data, revealing that Solenysa diverged from other linyphiids in the early Cretaceous and diversified further in the middle Oligocene. The results suggest that Solenysa is a relict group from the Cretaceous period with low species diversity due to a long-time lag in its early evolutionary history.
Article
Genetics & Heredity
Yongjuan Jiao, Guangyan Feng, Linkai Huang, Gang Nie, Zhou Li, Yan Peng, Dandan Li, Yanli Xiong, Zhangyi Hu, Xinquan Zhang
Summary: In this study, comparative genomic analyses and phylogenetic inferences were conducted on 14 cp genomes of Dactylis glomerata from the Mediterranean and Eurasia. The results revealed that the main divergence time of D. glomerata dates back to the Miocene era, and nine highly variable regions were identified among the subspecies based on cp sequence divergence.
Article
Genetics & Heredity
Yin Sun, Peishan Zou, Nannan Jiang, Yifu Fang, Guofeng Liu
Summary: This study sequenced the complete chloroplast genomes of six Paphiopedilum species and identified ten highly variable regions that could serve as potential DNA barcodes or phylogenetic markers. The results also demonstrated that chloroplast genome sequencing is an effective means in resolving the complex relationship in Paphiopedilum.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Marco F. Cerna, Mariela M. Moreno, Byron G. Fuertes, Mario L. Iza, Gerardo E. Medina, Celso G. Recalde
Summary: The tropical Andes serve as a natural barrier between the Pacific Ocean and the Atlantic, with a variety of ecosystems and biodiversity, including the unique Dracula orchids. Geographical patterns and geophysical conditions in the Andes play a crucial role in shaping the biodiversity of the Dracula genus.
ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS
(2021)
Article
Evolutionary Biology
Naoko Takezaki
Summary: This study found that Elopomorpha may be the first basal group of teleost fish to have diverged, supporting the recent prevailing view of morphological studies. Using species and genes with low sequence divergence can increase the accuracy of phylogenetic construction.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Hany K. M. Dweck, Gaelle J. S. Talross, Yichen Luo, Shimaa A. M. Ebrahim, John R. Carlson
Summary: Salt taste perception in invertebrates, specifically in Drosophila, is dependent on Ir56b, an atypical member of the ionotropic receptor family. Ir56b acts in conjunction with two coreceptors, Ir25a and Ir76b. It is expressed in neurons that also sense sugars and can induce salt taste responses when expressed in bitter-sensing neurons. Ir56b is unique in that it lacks an N-terminal region, a feature that is evolutionarily conserved. This study sheds light on the molecular basis of salt taste perception.
Article
Ecology
Xue Li Zhu, Jiao Jiao Yuan, Li Yang Zhou, Luca Bartolozzi, Xia Wan
Summary: This study constructed the first phylogenetic relationship for Cyclommatus stag beetles, identifying two well-supported clades that are divided based on geographical distribution. The results also indicate the divergence time and further diversification of these beetles. Additionally, the study suggests that the two clades should be classified into separate genera based on their genetic and morphological differences. Overall, this research provides important insights into the classification, genetics, and evolution of stag beetles in the Oriental region.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Fredy Archila L. Morales, Monika M. Lipinska, Magdalena Dudek, Dariusz L. Szlachetko
Summary: Guatemala is known for its diverse flora and fauna, with over 1200 orchid species. In the Baja Verapaz department, a new orchid species, Schiedeella bajaverapacensis, was discovered. The discovery was based on morphological evidence and confirmed through phylogenetic analyses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Veterinary Sciences
Kornsorn Srikulnath, Syed Farhan Ahmad, Thitipong Panthum, Suchinda Malaivijitnond
Summary: Research has shown that macaque bioresources play an indispensable role in advancing scientific discoveries in human physiology, pathology, and other fields, advocating for the establishment of a macaque research center to integrate relevant resources. In addition, detailed genetic studies on macaque bioresources of Thai origin are expected to accelerate the development of vaccines.
JOURNAL OF MEDICAL PRIMATOLOGY
(2022)
Review
Fisheries
Syed Farhan Ahmad, Maryam Jehangir, Kornsorn Srikulnath, Cesar Martins
Summary: The rapid transformation of fish genomics and the availability of high-quality datasets provide important roadmaps for research, highlighting fish genomes as vital resources for genomic studies.
REVIEWS IN FISH BIOLOGY AND FISHERIES
(2022)
Article
Agriculture, Dairy & Animal Science
Watcharaporn Thapana, Nattakan Ariyaraphong, Parinya Wongtienchai, Nararat Laopichienpong, Worapong Singchat, Thitipong Panthum, Syed Farhan Ahmad, Ekaphan Kraichak, Narongrit Muangmai, Prateep Duengkae, Kornsorn Srikulnath
Summary: The evolutionary patterns and phylogenetic utility of duplicate control regions (CRs) in Varanus salvator macromaculatus and other varanids were observed in this study. The results showed an independent evolution of CRs in varanids, with lower divergence between orthologous copies compared to paralogous copies. Recombination events were also found between CRs, and CR2 was identified as a potential phylogenetic marker. These findings contribute to a better understanding of the molecular evolutionary processes in varanid genomes.
Review
Biology
Kornsorn Srikulnath, Syed Farhan Ahmad, Worapong Singchat, Thitipong Panthum
Summary: Transposable elements (TEs) play critical roles in eukaryotic genomes, particularly in sex chromosomes, by mediating genomic novelties and contributing to sex chromosome differentiation. The abundance of TEs in sex-determining regions is linked to the emergence of these regions and is considered a hallmark of chromosome degeneration. Recent approaches have been developed to study the roles and effects of TEs in sex chromosome differentiation and evolution.
Article
Green & Sustainable Science & Technology
Worapong Singchat, Aingorn Chaiyes, Wongsathit Wongloet, Nattakan Ariyaraphong, Kitipong Jaisamut, Thitipong Panthum, Syed Farhan Ahmad, Warut Chaleekarn, Warong Suksavate, Mitree Inpota, Chavin Chaisongkram, Naris Kaewsalubnil, Narongrit Muangmai, Wiyada Chamchumroon, Yoichi Matsuda, Prateep Duengkae, Kornsorn Srikulnath
Summary: This study investigates the genetic diversity and potential distribution areas of red junglefowl in Thailand. It reveals that protected areas are suitable habitats for red junglefowl with high genetic diversity. Understanding red junglefowl can contribute to improved resource management, species reintroduction, and sustainable development, supporting local food security objectives.
Review
Green & Sustainable Science & Technology
Kornsorn Srikulnath, Nattakan Ariyaraphong, Worapong Singchat, Thitipong Panthum, Artem Lisachov, Syed Farhan Ahmad, Kyudong Han, Narongrit Muangmai, Prateep Duengkae
Summary: Mitochondrial displacement loop (mt D-loop) sequence analyses have improved assessments of genetic diversity and population dynamics of endangered species facing climate change and habitat loss. Tracking population haplotypes of these species using mitochondrial-based markers has advanced conservation genomics and biodiversity research. Studies on Asian elephants have used mt D-loop sequences to assess genetic diversity and population-scale hypotheses, shedding light on evolutionary processes and facilitating conservation efforts.
Article
Green & Sustainable Science & Technology
Wongsathit Wongloet, Prach Kongthong, Aingorn Chaiyes, Worapong Singchat, Warong Suksavate, Nattakan Ariyaraphong, Thitipong Panthum, Artem Lisachov, Kitipong Jaisamut, Jumaporn Sonongbua, Trifan Budi, Wannapa Wannakan, Worawit Thienpreecha, Paanwaris Paansri, Syed Farhan Ahmad, Kriangsak Sribuarod, Umphornpimon Prayoon, Pakpoom Aramsirirujiwet, Wiyada Chamchumroon, Narongrit Muangmai, Prateep Duengkae, Kornsorn Srikulnath
Summary: Developing successful conservation programs for genetically depleted species is challenging, as survival and adaptive potential are related to genetic and habitat factors. The greater mouse-deer, a true forest species, has experienced a significant decline in the wild and currently only exists in captive populations. A restoration program has been successful in increasing their population, but maintaining genetic diversity in small captive populations is crucial for long-term recovery.
Article
Agriculture, Dairy & Animal Science
Wongsathit Wongloet, Worapong Singchat, Aingorn Chaiyes, Hina Ali, Surachai Piangporntip, Nattakan Ariyaraphong, Trifan Budi, Worawit Thienpreecha, Wannapa Wannakan, Autchariyapron Mungmee, Kittipong Jaisamut, Thanyapat Thong, Thitipong Panthum, Syed Farhan Ahmad, Artem Lisachov, Warong Suksavate, Narongrit Muangmai, Rattanaphon Chuenka, Mitsuo Nunome, Wiyada Chamchumroon, Kyudong Han, Aniroot Nuangmek, Yoichi Matsuda, Prateep Duengkae, Kornsorn Srikulnath
Summary: This study investigated the socio-cultural, environmental, and genetic aspects of the Mae Hong Son chicken breed in North Thailand. The breed was found to have high levels of genetic diversity and a unique DNA fingerprint. Genetic introgression from red junglefowl and indigenous breeds was identified, supporting the hypothesis of its crossbreeding origin. These findings contribute to our understanding of the genetic blueprint and potential for improving domestic chickens using this breed.
Article
Biology
Nattakan Ariyaraphong, Wongsathit Wongloet, Pish Wattanadilokchatkun, Thitipong Panthum, Worapong Singchat, Thanyapat Thong, Artem Lisachov, Syed Farhan Ahmad, Narongrit Muangmai, Kyudong Han, Prateep Duengkae, Yosapong Temsiripong, Kornsorn Srikulnath
Summary: Morphological divergence between Siamese and other crocodiles has been observed, leading to questions about potential crocodile hybrids. Genetic analysis revealed evidence of introgression between Siamese and saltwater crocodiles, highlighting the importance of identifying hybrids for conservation efforts.
Article
Virology
Akihiko Koga, Syed Farhan Ahmad, Thitipong Panthum, Worapong Singchat, Kornsorn Srikulnath
Summary: Through analyzing the genome of the tammar wallaby, we conclude that walbRep was formed in the red-necked wallaby lineage after its divergence from the tammar wallaby.
Article
Biology
Ryan Rasoarahona, Pish Wattanadilokchatkun, Thitipong Panthum, Thanyapat Thong, Worapong Singchat, Syed Farhan Ahmad, Aingorn Chaiyes, Kyudong Han, Ekaphan Kraichak, Narongrit Muangmai, Akihiko Koga, Prateep Duengkae, Agostinho Antunes, Kornsorn Srikulnath
Summary: The research aims to enhance the ant colony optimization algorithm by integrating marker effectiveness indicators, providing cost-effective solutions for genetic assessments, breeding, and conservation efforts. The study addresses the trade-off between accuracy and cost, and provides valuable insights into real-world genetic studies.
Article
Fisheries
Thitipong Panthum, Pish Wattanadilokchatkun, Kitipong Jaisamut, Worapong Singchat, Syed Farhan Ahmad, Narongrit Muangmai, Prateep Duengkae, Agostinho Antunes, Kornsorn Srikulnath
Summary: In this study, the male-linked region of the jade perch was identified on chromosome 19, and a remnant of the amh gene was found in this region, which is considered a candidate gene for sex determination in teleosts.
Article
Biochemistry & Molecular Biology
Wattanawan Jaito, Thitipong Panthum, Syed Farhan Ahmad, Worapong Singchat, Narongrit Muangmai, Kyudong Han, Akihiko Koga, Prateep Duengkae, Kornsorn Srikulnath
Summary: In this study, sex-specific and linked loci were identified in the Siamese cobra through in silico chromosome mapping. These loci were mainly mapped on the Z sex chromosome, and a putative sex-determining region was found, with one specific locus homologous to the TOPBP1 gene. The findings contribute to our understanding of the genetic basis and sex-specific traits in the Siamese cobra.
Article
Biology
Thitipong Panthum, Nattakan Ariyaraphong, Wongsathit Wongloet, Pish Wattanadilokchatkun, Nararat Laopichienpong, Ryan Rasoarahona, Worapong Singchat, Syed Farhan Ahmad, Ekaphan Kraichak, Narongrit Muangmai, Prateep Duengkae, Yusuke Fukuda, Sam Banks, Yosapong Temsiripong, Tariq Ezaz, Kornsorn Srikulnath
Summary: Hybrids between the Siamese crocodile and saltwater crocodile pose a challenge for conservation efforts. This study used DArT sequencing to identify genome-wide SNPs in both species and confirm hybrid scenarios. PCR-based detection of SNP loci successfully distinguished species and hybridization levels.
Article
Fisheries
Pish Wattanadilokchatkun, Thitipong Panthum, Kitipong Jaisamut, Syed Farhan Ahmad, Sahabhop Dokkaew, Narongrit Muangmai, Prateep Duengkae, Worapong Singchat, Kornsorn Srikulnath
Summary: The study identified and characterized microsatellites in the Siamese fighting fish genome and compared their organization across different species. The identified microsatellites can be used for cross-species amplification, and two microsatellites were successfully validated in different species. The polymorphic markers identified in this study have potential applications in assessing genetic diversity, population structure, and marker-assisted selection.