Article
Plant Sciences
Dhafer A. Alzahrani
Summary: Abutilon fruticosum, an endemic plant in Saudi Arabia, has a complete chloroplast genome with 114 unique genes. Comparative analyses show similarities with other Malvaceae species in gene content and structure, and variability in gene position. Phylogenetic analysis suggests a close relationship with Althaea officinalis, contradicting previous systematic positions. This study provides valuable insights for further phylogenetic and evolutionary studies within the Malvaceae family.
Article
Multidisciplinary Sciences
Xinyu Sun, Ying Zhan, Songlin Li, Yu Liu, Qiang Fu, Xin Quan, Jinyu Xiong, Huixin Gang, Lijun Zhang, Huijuan Qi, Aoxue Wang, Junwei Huo, Dong Qin, Chenqiao Zhu
Summary: This study assembled the complete chloroplast genomes of blackcurrant, red currant, white currant, and gooseberry for the first time, providing valuable genomic data for their systematic classification and molecular breeding. The phylogenetic analysis revealed the relationships within Grossulariaceae and the Ribes genus, challenging the current classification based on morphology.
Article
Forestry
Jingyao Ping, Xiaona Zhong, Ting Wang, Yingjuan Su
Summary: Plant chloroplast (cp) gene clusters are genes arranged closely together on the cp genome. Broken gene clusters have been observed in gymnosperms. The study found that disruption of gene clusters leads to increased evolutionary rates and selection pressure in associated genes.
Article
Plant Sciences
Salvador Guzman-Diaz, Fabian Augusto Aldaba Nunez, Emily Veltjen, Pieter Asselman, Isabel Larridon, Marie-Stephanie Samain
Summary: Chloroplast genomes in Magnoliaceae are considered highly conserved but intergenic regions show significant nucleotide diversity, contributing to phylogenetically informative data. The gene content is consistent across species, with a length of about 160kb, and differences between genera are greater than within genera. Phylogenetic analyses confirm that the current infrageneric classification in Magnolia does not reflect natural relationships.
Article
Plant Sciences
Yun Song, Fan Jiang, Junxia Shi, Chaonan Wang, Ning Xiang, Shuifang Zhu
Summary: This study examined the classification and phylogenetic relationships of Phytolacca using the whole chloroplast genome and three markers. The results showed that Phytolacca is monophyletic and that Central America is the center of species diversity. Birds may play a key role in the dispersal of Phytolacca due to the fleshy fruiting of the genus.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Joonhyung Jung, Changkyun Kim, Joo-Hwan Kim
Summary: This study provides detailed information on 15 complete plastid genomes of Commelinoideae taxa, revealing structural variations and resolving problematic positions among genera in the family.
Article
Biotechnology & Applied Microbiology
Nan Lin, Rui Liu, Yakun Wang, Peng Guo, Yihan Wang, Yanpei Liu, Fude Shang
Summary: The complete chloroplast genome of Ulmus mianzhuensis was sequenced and compared with other Ulmus species, revealing a highly conserved gene structure. It was also found that U. mianzhuensis should be considered as a subspecies of U. parvifolia. This study highlights the valuable information provided by the chloroplast genome in genetic variation and phylogenetic analysis of Ulmus species.
Article
Biotechnology & Applied Microbiology
Kewang Xu, Chenxue Lin, Shiou Yih Lee, Lingfeng Mao, Kaikai Meng
Summary: This study compared the chloroplast genomes of Ilex species and estimated their phylogenetic relationships. The results showed shared genomic structures and gene rearrangements among Ilex species. Hypervariable and repetitive regions were also identified, which could be useful for future phylogenetic and population genetic studies.
Article
Plant Sciences
Bartosz Ulaszewski, Sandra Jankowska-Wroblewska, Katarzyna Swilo, Jaroslaw Burczyk
Summary: The study found that Aria edulis, Chamaemespilus alpina, and Torminalis glaberrima were more closely related to each other rather than to Sorbus s.s., providing additional support for considering them as separate genera.
Article
Plant Sciences
Kuan Liu, Rong Wang, Xiu-Xiu Guo, Xue-Jie Zhang, Xiao-Jian Qu, Shou-Jin Fan
Summary: This study sequenced and analyzed the chloroplast genomes of 13 Eragrostideae species, identifying useful molecular markers for phylogenetic analysis. The study revealed Enneapogon as the earliest diverging lineage, Eragrostis as the sister to Uniola including Harpachne, and discussed the classification of Harpachne harpachnoides based on morphological and molecular evidence.
Article
Horticulture
Anna Pikunova, Svetlana Goryunova, Olga Golyaeva, Maria Dolzhikova, Anna Pavlenko, Oleg Kurashev, Evgeniia Sotnikova, Oksana Polivanova, Anastasia Sivolapova, Oleg Kazakov, Denis Goryunov
Summary: The complete chloroplast genomes of red currant and gooseberry cultivars were sequenced and assembled, revealing differences in genome length and protein-coding genes. Phylogenetic analysis showed that Ribes species clustered together, with Ribes fasciculatum being the most distant. All Ribes species share a similar set of protein-coding genes in their plastome sequences. Negative selection was observed for most genes in both the Ribes group and Saxifragales, while positive selection was observed for ycf4 and clpP genes in the Ribes group. Pseudogenization events of ycf genes may reflect their importance in Ribes' adaptation. The study provides valuable genomic resources and clarifications for marker development and phylogenomics of the Ribes genus.
Article
Genetics & Heredity
Samaila Samaila Yaradua, Kowiyou Yessoufou
Summary: This study sequenced the complete chloroplast genome of Hypoestes forskaolii and explored its evolutionary patterns and phylogenetic relationships within Justiceae. The results showed highly conserved genomic structure and gene contents within Justiceae, with slight differences in gene locations. Variable hotspots in the cp genome were identified as potential DNA barcodes for evolutionary analysis.
Article
Genetics & Heredity
Jialong Pei, Yong Wang, Juan Zhuo, Huibin Gao, Naresh Vasupalli, Dan Hou, Xinchun Lin
Summary: This study sequenced and analyzed the complete chloroplast genome of Dendrocalamus farinosus, a bamboo species used for food and timber in southwestern China. The genome structure, gene content, repeat sequences, and phylogenetic relationship with other Dendrocalamus species were investigated. Comparative analysis showed differences between the genomes, with higher divergence in non-coding regions and greater conservation in inverted repeat regions. The study also identified a potential gene marker for distinguishing bamboo species and provided insights into the evolutionary pathways of bamboo species based on their geographic distribution and rhizome types.
Article
Biology
Lin Yang, Jinhong Tian, Liu Xu, Xueli Zhao, Yuyang Song, Dawei Wang
Summary: This study sequenced six new chloroplast genomes of the endangered Magnoliaceae family and analyzed the phylogenetic relationships of 37 published chloroplast genomes in the family. The findings showed the typical quadripartite structure of chloroplast genomes in Magnoliaceae and provided insights into the intergeneric relationships of the family. These findings will contribute to adjusting the phylogenetic position of Magnoliaceae at the molecular level.
Article
Plant Sciences
Alexa S. Tyszka, Eric C. Bretz, Holly M. Robertson, Miles D. Woodcock-Girard, Karolis Ramanauskas, Drew A. Larson, Gregory W. Stull, Joseph F. Walker
Summary: Chloroplasts and mitochondria have their own genomes and have been important for inferring land plant phylogeny. This study examined the genomes of 226 land plants to investigate the similarity between the evolutionary histories of these organelles. The results showed mostly concordant topologies, except for a few conflicting relationships that need further investigation. The findings suggest significant differences in molecular evolution between the chloroplast and mitochondrial genomes, indicating the need for separate evolutionary models.
FRONTIERS IN PLANT SCIENCE
(2023)