Plant Molecular Phylogenetics and Evolutionary Genomics II

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (20 December 2021) | Viewed by 14727

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Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Moscow 119991, Russia
Interests: plant molecular phylogeny and systematics; genome evolution; biodiversity; phytoplanktonic metagenome
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Dear Colleagues,

"Nothing in biology makes sense except in the light of evolution", as Theodosius Dobzhansky stated. The primary aim of molecular phylogenetics is to infer the evolutionary relationships of living organisms by comparing the structures of their information macromolecules (semantids). However, this does not limit its role in biological research studies.

The molecular phylogenetic approach is applied in a wide range of studies on taxonomy, biodiversity and its conservation, biogeography, population genetics, molecular ecology, and agrobiology. Now, the phylogenetic approach serves as a blueprint for investigations in almost all biological disciplines. In the Genomic era, the evolutionary paradigm is a framework for studying the structural and functional basis of living beings.

This Special Issue of Plants is open to research articles on all aspects of plant molecular evolution, including molecular phylogenetics and systematics, phylogenomics, comparative genomics, barcoding and biogeography, molecular ecology, and evo-devo, as well as the bioinformatic and laboratory methods of the aforementioned studies.

Prof. Dr. Alex Troitsky
Guest Editor

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Keywords

  • evolutionary genomics
  • molecular phylogeny
  • phylogenomics
  • genomic biodiversity
  • taxonomy

Published Papers (5 papers)

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Research

14 pages, 3420 KiB  
Article
Genome-Wide Identification, Characterization and Expression Analysis of Lipoxygenase Gene Family in Artemisia annua L.
by Ying Meng, Yu Liang, Baosheng Liao, Wenrui He, Qianwen Liu, Xiaofeng Shen, Jiang Xu and Shilin Chen
Plants 2022, 11(5), 655; https://doi.org/10.3390/plants11050655 - 28 Feb 2022
Cited by 6 | Viewed by 2491
Abstract
Lipoxygenase (LOX) is a ubiquitous oxygenase found in animals and plants and plays a pivotal role in diverse biological processes, including defense and development. Artemisinin, which can only be obtained from Artemisia annua L., is the most effective therapeutic drug for malaria without [...] Read more.
Lipoxygenase (LOX) is a ubiquitous oxygenase found in animals and plants and plays a pivotal role in diverse biological processes, including defense and development. Artemisinin, which can only be obtained from Artemisia annua L., is the most effective therapeutic drug for malaria without serious side effects. This study identified and analyzed LOX gene family members in the A. annua genome at the chromosomal level. Twenty LOX genes with various molecular weights, isoelectric points, and amino acid numbers were identified and named AaLOX, which were located in the cytoplasm or chloroplast. The average protein length of all AaLOX was 850 aa. Phylogenetic tree analysis revealed that the AaLOX was divided into two major groups, 9-LOX and 13-LOX. The exon numbers ranged from 1 to 12, indicating that different AaLOX genes have different functions. The secondary structure was mainly composed of alpha helix and random coil, and the tertiary structure was similar for most AaLOX. Upstream promoter region analysis revealed that a large number of cis-acting elements were closely related to plant growth and development, light response, hormone, and other stress responses. Transcriptome data analysis of different tissues suggested that the gene family was differently expressed in the roots, stems, leaves, and flowers of two A. annua strains HAN1 and LQ9. qRT-PCR confirmed that AaLOX5 and AaLOX17 had the highest expression in flowers and leaves. This study provides a theoretical basis for the further functional analysis of the AaLOX gene family. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics II)
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29 pages, 20262 KiB  
Article
Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion
by Salvador Guzmán-Díaz, Fabián Augusto Aldaba Núñez, Emily Veltjen, Pieter Asselman, Isabel Larridon and Marie-Stéphanie Samain
Plants 2022, 11(3), 448; https://doi.org/10.3390/plants11030448 - 6 Feb 2022
Cited by 9 | Viewed by 2874
Abstract
Chloroplast genomes are considered to be highly conserved. Nevertheless, differences in their sequences are an important source of phylogenetically informative data. Chloroplast genomes are increasingly applied in evolutionary studies of angiosperms, including Magnoliaceae. Recent studies have focused on resolving the previously debated classification [...] Read more.
Chloroplast genomes are considered to be highly conserved. Nevertheless, differences in their sequences are an important source of phylogenetically informative data. Chloroplast genomes are increasingly applied in evolutionary studies of angiosperms, including Magnoliaceae. Recent studies have focused on resolving the previously debated classification of the family using a phylogenomic approach and chloroplast genome data. However, most Neotropical clades and recently described species have not yet been included in molecular studies. We performed sequencing, assembly, and annotation of 15 chloroplast genomes from Neotropical Magnoliaceae species. We compared the newly assembled chloroplast genomes with 22 chloroplast genomes from across the family, including representatives from each genus and section. Family-wide, the chloroplast genomes presented a length of about 160 kb. The gene content in all species was constant, with 145 genes. The intergenic regions showed a higher level of nucleotide diversity than the coding regions. Differences were higher among genera than within genera. The phylogenetic analysis in Magnolia showed two main clades and corroborated that the current infrageneric classification does not represent natural groups. Although chloroplast genomes are highly conserved in Magnoliaceae, the high level of diversity of the intergenic regions still resulted in an important source of phylogenetically informative data, even for closely related taxa. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics II)
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26 pages, 10624 KiB  
Article
When Morphology and Biogeography Approximate Nuclear ITS but Conflict with Plastid Phylogeny: Phylogeography of the Lotus dorycnium Species Complex (Leguminosae)
by Tatiana E. Kramina, Maya V. Lysova, Tahir H. Samigullin, Mehmet U. Özbek and Dmitry D. Sokoloff
Plants 2022, 11(3), 410; https://doi.org/10.3390/plants11030410 - 2 Feb 2022
Cited by 5 | Viewed by 2247
Abstract
Lotus dorycnium s.l. is a complex of taxa traditionally regarded as members of Dorycnium. It has a wide Mediterranean range, extending in the north to Central and Eastern Europe, and in the east to the Crimea, the Caucasus, and the Western Caspian [...] Read more.
Lotus dorycnium s.l. is a complex of taxa traditionally regarded as members of Dorycnium. It has a wide Mediterranean range, extending in the north to Central and Eastern Europe, and in the east to the Crimea, the Caucasus, and the Western Caspian region. Molecular phylogenetic data support placement of the L. dorycnium complex in the genus Lotus. The present study investigated the phylogeny, phylogeography and morphological variability of the L. dorycnium complex across its distribution range to reveal the main trends in genetic and morphological differentiation in this group. The results of the morphological analyses demonstrated some degree of differentiation, with L. d. ssp. herbaceus, ssp. gracilis, and ssp. anatolicus more or less well defined, whereas ssp. dorycnium, ssp. germanicus, and ssp. haussknechtii can be hardly distinguished from each other using morphology. Analyses of the L. dorycnium complex based on nrITS revealed a tendency towards a geographic differentiation into Western, Eastern, and Turkish groups. Phylogenetic and phylogeographic analyses of the same set of specimens using concatenated plastid markers trnL-F, rps16, and psbA-trnH demonstrated a low resolution between the L. dorycnium complex and L. hirsutus, as well as among the taxa within the L. dorycnium complex, which can be interpreted as evidence of an incomplete lineage sorting or hybridization. The evolutionary processes responsible for incongruence in phylogenetic signals between plastid and nuclear sequences of the morphologically well-defined species L. dorycnium and L. hirsutus were most likely localized in the Eastern Mediterranean. A possibility of rare gene exchange between the L. dorycnium complex and the group of L. graecus is revealed for the first time. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics II)
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17 pages, 3401 KiB  
Article
Plastome Characterization and Phylogenomic Analysis Yield New Insights into the Evolutionary Relationships among the Species of the Subgenus Bryocles (Hosta; Asparagaceae) in East Asia
by JiYoung Yang, Mi-Jung Choi, Seon-Hee Kim, Hyeok-Jae Choi and Seung-Chul Kim
Plants 2021, 10(10), 1980; https://doi.org/10.3390/plants10101980 - 22 Sep 2021
Cited by 5 | Viewed by 2327
Abstract
The genus Hosta, which has a native distribution in temperate East Asia and a number of species ranging from 23 to 40, represents a taxonomically important and ornamentally popular plant. Despite its taxonomic and horticultural importance, the genus Hosta has remained taxonomically [...] Read more.
The genus Hosta, which has a native distribution in temperate East Asia and a number of species ranging from 23 to 40, represents a taxonomically important and ornamentally popular plant. Despite its taxonomic and horticultural importance, the genus Hosta has remained taxonomically challenging owing to insufficient diagnostic features, continuous morphological variation, and the process of hybridization and introgression, making species circumscription and phylogenetic inference difficult. In this study, we sequenced 11 accessions of Hosta plastomes, including members of three geographically defined subgenera, Hosta, Bryocles, and Giboshi, determined the characteristics of plastomes, and inferred their phylogenetic relationships. We found highly conserved plastomes among the three subgenera, identified several mutation hotspots that can be used as barcodes, and revealed the patterns of codon usage bias and RNA editing sites. Five positively selected plastome genes (rbcL, rpoB, rpoC2, rpl16, and rpl20) were identified. Phylogenetic analysis suggested (1) the earliest divergence of subg. Hosta, (2) non-monophyly of subg. Bryocles and its two sections (Lamellatae and Stoloniferae), (3) a sister relationship between H. sieboldiana (subg. Giboshi) and H. ventricosa (subg. Bryocles), and (4) reciprocally monophyletic and divergent lineages of H. capitata in Korea and Japan, requiring further studies of their taxonomic distinction. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics II)
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18 pages, 3068 KiB  
Article
Genome-Wide Identification and Characterization of the Abiotic-Stress-Responsive GRF Gene Family in Diploid Woodland Strawberry (Fragaria vesca)
by Zhiqi Li, Qian Xie, Jiahui Yan, Jianqing Chen and Qingxi Chen
Plants 2021, 10(9), 1916; https://doi.org/10.3390/plants10091916 - 15 Sep 2021
Cited by 16 | Viewed by 3515
Abstract
Growth regulatory factors (GRF) are plant-specific transcription factors that play an important role in plant resistance to stress. This gene family in strawberry has not been investigated previously. In this study, 10 GRF genes were identified in the genome of the diploid woodland [...] Read more.
Growth regulatory factors (GRF) are plant-specific transcription factors that play an important role in plant resistance to stress. This gene family in strawberry has not been investigated previously. In this study, 10 GRF genes were identified in the genome of the diploid woodland strawberry (Fragaria vesca). Chromosome analysis showed that the 10 FvGRF genes were unevenly distributed on five chromosomes. Phylogenetic analysis resolved the FvGRF proteins into five groups. Genes of similar structure were placed in the same group, which was indicative of functional redundance. Whole-genome duplication/segmental duplication and dispersed duplication events effectively promoted expansion of the strawberry GRF gene family. Quantitative reverse transcription-PCR analysis suggested that FvGRF genes played potential roles in the growth and development of vegetative organs. Expression profile analysis revealed that FvGRF3, FvGRF5, and FvGRF7 were up-regulated under low-temperature stress, FvGRF4 and FvGRF9 were up-regulated under high-temperature stress, FvGRF6 and FvGRF8 were up-regulated under drought stress, FvGRF3, FvGRF6, and FvGRF8 were up-regulated under salt stress, FvGRF2, FvGRF7, and FvGRF9 were up-regulated under salicylic acid treatment, and FvGRF3, FvGRF7, FvGRF9, and FvGRF10 were up-regulated under abscisic acid treatment. Promoter analysis indicated that FvGRF genes were involved in plant growth and development and stress response. These results provide a theoretical and empirical foundation for the elucidation of the mechanisms of abiotic stress responses in strawberry. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics II)
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