Chloroplast DNA Diversity in Populations of P. sylvestris L. from Middle Siberia and the Romanian Carpathians

Characterization of the Plastid Genomes of Four Caroxylon Thunb. Species from Kazakhstan

The family Chenopodiaceae Vent. (Amaranthaceae s.l.) is known for its taxonomic complexity, comprising species of significant economic and ecological importance. Despite its significance, the availability of plastid genome data for this family remains limited. This study involved assembling and characterizing the complete plastid genomes of four Caroxylon Thunb. species within the tribe Salsoleae s.l., utilizing next-generation sequencing technology. We compared genome features, nucleotide diversity, and repeat sequences and conducted a phylogenetic analysis of ten Salsoleae s.l. species. The size of the plastid genome varied among four Caroxylon species, ranging from 150,777 bp (C. nitrarium) to 151,307 bp (C. orientale). Each studied plastid genome encoded 133 genes, including 114 unique genes. This set of genes includes 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Eight divergent regions (accD, atpF, matK, ndhF-ndhG, petB, rpl20-rpl22, rpoC2, and ycf3) were identified in ten Salsoleae s.l. plastid genomes, which could be potential DNA-barcoding markers. Additionally, 1106 repeat elements were detected, consisting of 814 simple sequence repeats, 92 tandem repeats, 88 forward repeats, 111 palindromic repeats, and one reverse repeat. The phylogenetic analysis provided robust support for the relationships within Caroxylon species. These data represent a valuable resource for future phylogenetic studies within the genus.

Molecular characterisation of Pinus sylvestris (L.) in Ireland at the western limit of the species distribution

BACKGROUND

Scots pine (Pinus sylvestris L.) underwent significant population declines across much of northwest Europe during the mid-to-late Holocene and was thought to have become extirpated in Ireland from about 400 AD. However, most extant populations are plantations reintroduced from Scotland. Others are naturalised therefrom and one in Western Ireland is a putative relict. In this paper, Scots pine in Ireland are genetically described for the first time.

RESULTS

Using two mitochondrial (mtDNA) loci, eight chloroplast (cpSSR) and 18 nuclear (nSSR) loci, the genetic composition and diversity of 19 Irish Scots pine populations is described and compared to other European populations. All trees sampled in Ireland were fixed for mitotype a, which is the most common across northwest Europe. By contrast, cpSSR (HCP = 0.967) and nSSR (He = 0.540) variation was high, and comparable with estimates for other regions across the species range. Differentiation at both sets of loci were similarly low (cpSSR FST = 0.019; nSSR FST = 0.018), but populations from continental Europe were significantly differentiated from all Irish populations based on nSSR variation.

CONCLUSIONS

All Irish Scots pine are likely part of a common Irish-Scottish gene pool which diverged from continental Scots pine following post-glacial recolonisation. A high genetic diversity and an absence of evidence of inbreeding suggests the regional decline of Scots pine did not critically reduce allelic variation. The post-glacial relationship between Irish and Scottish pine is discussed, and a suggestion from recent palaeoecological work that reintroduced Scots pine be managed as a native species is now further supported by genetic data.

New Insight into Genetic Structure and Diversity of Scots Pine (Pinus sylvestris L.) Populations in Lithuania Based on Nuclear, Chloroplast and Mitochondrial DNA Markers

We studied the genetic differentiation, structure, and diversity of Scots pine populations in Lithuania based on nuclear, chloroplast microsatellite, and mitochondrial DNA markers. We focused on revealing evolutionary history, country-wide geneflow patterns, and structuring among the Scots pine populations. We genotyped 439 Scots pine individuals of mature age from 23 natural Scots pine stands in Lithuania and used the AMOVA and a set of genetic-clustering methods. The among-population differentiation was weak for nuclear microsatellite loci (nSSRs) (FST = 0.005) but much stronger for cpSSRs (PhiST = 0.240). The populations were structured into highland and lowland populations based on cpSSRs and eastern highland versus the rest for nSSRs. We detected two mtDNA mitotypes—the universal type A and northeastern type B, and the latter occurred at a markedly higher frequency in eastern Lithuania. Within-population genetic diversity was higher in large pine-dominated forest tracts in the eastern highlands than in fragmented forests in the western highlands. We concluded that phenology-based genetic networks following the temperature climate gradients have a strong effect on shaping the genetic structure of otherwise rather homogeneous gene pools of Scots pine populations in Lithuania. The possible effects of human interference with forests on genetic diversity of Scots pine populations in Lithuania are discussed.

AutomAted RepeaT Identifier (AARTI): A tool to identify common, polymorphic, and unique microsatellites

Here we are presenting an automated computational pipeline used to mine 5976 mitochondrial genomes to identify common, polymorphic, and unique microsatellites also known as simple sequence repeats (SSRs). Microsatellites are repetitive motifs of 1-6 bases in a DNA sequence. Due to their abundance and highly polymorphic nature, microsatellites have become one of the widely used molecular/genetic markers valuable for many studies including gene tagging, genetic diversity, and species identification. Several computational tools dedicated to mine and categorize microsatellites in nucleotide sequences were developed; however, there is no tool which can identify unique, common and polymorphic microsatellites between each pair of nucleotide sequences. To explore such microsatellites, we have developed a fully automated computational pipeline named AutomAted RepeaT Identifier (AARTI). The AARTI is the only tool till date, which identifies common, polymorphic, and unique microsatellites between each pair of nucleotide sequences. The computational pipeline was constructed using the PERL programming language and the web server for the pipeline was developed with the help of PHP, HTML, CSS, and JavaScript. It was successfully tested to reproduce the results of previous study on 7 mitochondrial genomes of genus Orthotrichum. Moreover, the pipeline was also applied on 5846 (Metazoa) and 130 (Viridiplantae) mitochondrial genomes. The AARTI is freely available at https://lms.snu.edu.in/aarti/ and will certainly accelerate the studies of length variation in microsatellites between species. Additionally, it will be useful in comparative genomic studies, for the computational characterization of microsatellites, and has the potential to be a routine genome analysis pipeline for mitochondrial genomes.