Zhang et al. show that #plastome and nrDNA are effective super-#barcodes for spp. discrimination in Chimonocalamus and, with Skmer analysis for molecular identification, help ID cryptic new #species.
https://doi.org/10.1111/jse.70027
@WileyEcolEvol
@WileyEcology
#systematics #DataScience #botany
Genetic Polymorphism of Invasive Species of Knotweed (Reynoutria) Assessed by the matK and rpl32-trnL (UAG) Regions of Chloroplast DNA
Genetic Polymorphism of Invasive Species of Knotweed... ##bioinformaticanalysis ##chloroplastdna ##geneticpolymorphism ##molecularevolution ##moleculargenomics ##bioinformatics ##chloroplasts ##plastome ##molecularphylogeny ##genomics ##knotweed ##reynoutria ##matk ##rpl32trnl
Abstract An important model system for studying the role of genetic diversity and hybridization in plant invasions is the species complex of the genus Reynoutria Houtt. Within the secondary distribution range, two species of this genus are widespread, R. japonica Houtt. and R. sachalinensis (F. Schmidt) Nakai, as well as their derivatives, the hexaploid R. × bohemica Chrtek & Chrtková and the tetraploid R. × moravica (Hodálová and Mereďa) Olshanskyi and Antonenko, which are recognized as separate species. The genetic diversity of the species of the genus Reynoutria in Ukraine is still almost unexplored by molecular methods. In this work, we determined chloroplast haplotypes for samples of R. japonica, R. sachalinensis and R. × bohemica from Ukraine and other European countries and compared them with haplotypes of Reynoutria from the primary distribution range in China and Korea. The genetic diversity of R. japonica from the primary distribution range was significantly higher compared to European samples, which are mainly represented by the haplotype J1.1. At the same time, we identified haplotypes J1.2 and J1.3 specific to the Eastern European area, which probably arose as a consequence of the divergence of the chloroplast genome within the secondary distribution range. Of the five samples morphologically identified as R. × bohemica, three carry the haplotype J1.1, which is consistent with the idea that R. japonica var. japonica was involved as a maternal form in the formation of R. × bohemica. However, a chloroplast haplotype identical to R. sachalinensis was detected in two samples from the Alpine region of Europe. These samples likely represent another hybrid species of R. × moravica. Therefore, the use of chloroplast DNA markers is crucial for identifying the donor of maternal subgenomes in hybrid forms of the genus Reynoutria.
New cover, who dis?🤳...
Calling all #bryophyte lovers! Li et al. have reconstructed the ordinal and familial #phylogeny of bryophytes using the largest #plastome data set to date! https://doi.org/10.1111/jse.13063
@WileyEcolEvol
#PlantSci #JSE #taxonomy #evolution #mosses #botany
Pulsatilla patens is a rare and endangered species in Europe and its population resources have significantly decreased over the past decades. Previous genetic studies of this species made it possible to estimate the genetic diversity of the European population and to describe the structure of chloroplast and mitochondrial genomes. The main aim of these studies was to characterize the variability of chloroplast and mitochondrial genomes in more detail at the intra-population and inter-population levels. Our study presents new organelle genome reference sequences that allow the design of novel markers that can be the starting point for testing hypotheses, past and modern biogeography of rare and endangered species P. patens, and adaptive responses of this species to changing environments. The study included sixteen individuals from five populations located in Northeastern Poland. Comparative analysis of 16 P. patens plastomes from 5 populations enabled us to identify 160 point mutations, including 64 substitutions and 96 InDels. The most numerous detected SNPs and Indels (75%) were accumulated in three intergenic spacers: ndhD—ccsA, rps4—rps16, and trnL(UAG)—ndhF. The mitogenome dataset, which was more than twice as large as the plastome (331 kbp vs. 151 kbp), revealed eight times fewer SNPs (8 vs. 64) and six times fewer InDels (16 vs. 96). Both chloroplast and mitochondrial genome identified the same number of haplotypes—11 out of 16 individuals, but both organellar genomes slightly differ in haplotype clustering. Despite the much lower variation, mitogenomic data provide additional resolution in the haplotype detection of P. patens, enabling molecular identification of individuals, which were unrecognizable based on the plastome dataset.
J of Systematics and Evolution
cytgen
Cytology and Genetics
JIPB
Kuba.Sawicki