Genetic and demographic signatures accompanying the evolution of the selfing syndrome in Daphne kiusiana, an evergreen shrub

BACKGROUND AND AIMS

The evolution of mating systems from outcrossing to self-fertilization is a common transition in flowering plants. This shift is often associated with the 'selfing syndrome', which is characterized by less visible flowers with functional changes to control outcrossing. In most cases, the evolutionary history and demographic dynamics underlying the evolution of the selfing syndrome remain poorly understood.

METHODS

Here, we characterize differences in the demographic genetic consequences and associated floral-specific traits between two distinct geographical groups of a wild shrub, Daphne kiusiana, endemic to East Asia; plants in the eastern region (southeastern Korea and Kyushu, Japan) exhibit smaller and fewer flowers compared to those of plants in the western region (southwestern Korea). Genetic analyses were conducted using nuclear microsatellites and chloroplast DNA (multiplexed phylogenetic marker sequencing) datasets.

KEY RESULTS

A high selfing rate with significantly increased homozygosity characterized the eastern lineage, associated with lower levels of visibility and herkogamy in the floral traits. The two lineages harboured independent phylogeographical histories. In contrast to the western lineage, the eastern lineage showed a gradual reduction in the effective population size with no signs of a severe bottleneck despite its extreme range contraction during the last glacial period.

CONCLUSIONS

Our results suggest that the selfing-associated morphological changes in D. kiusiana are of relatively old origin (at least 100 000 years ago) and were driven by directional selection for efficient self-pollination. We provide evidence that the evolution of the selfing syndrome in D. kiusiana is not strongly associated with a severe population bottleneck.

Efficient High-throughput Techniques for the Analysis of Disease-Resistant Plant Varieties and Detection of Food Adulteration

Over the past two decades, the advances in the next generation sequencing (NGS) platforms have led to the identification of numerous genes/QTLs at high-resolution for their potential use in crop improvement. The genomic resources generated through these high-throughput sequencing techniques have been efficiently used in screening of particular gene of interest particularly for numerous types of plant stresses and quality traits. Subsequently, the identified-markers linked to a particular trait have been used in marker-assisted backcross breeding (MABB) activities. Besides, these markers are also being used to catalogue the food crops for detection of adulteration to improve the quality of food. With the advancement of technologies, the genomic resources are originating with new markers; however, to use these markers efficiently in crop breeding, high-throughput techniques (HTT) such as multiplex PCR and capillary electrophoresis (CE) can be exploited. Robustness, ease of operation, good reproducibility and low cost are the main advantages of multiplex PCR and CE. The CE is capable of separating and characterizing proteins with simplicity, speed and small sample requirements. Keeping in view the availability of vast data generated through NGS techniques and development of numerous markers, there is a need to use these resources efficiently in crop improvement programmes. In summary, this review describes the use of molecular markers in the screening of resistance genes in breeding programmes and detection of adulterations in food crops using high-throughput techniques.

The complete mitochondrial genome of Atypus karschi (Araneae, Atypidae) with phylogenetic consideration

The complete mitochondrial genome sequence of Atypus karschi has a circular genome of 14,149 bp, comprised of 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region. The nucleotide composition is 35.82% of T, 35.13% of A, 17.19% of G, and 9.16% of C. Most genes are encoded on the heavy strand except seven tRNA genes (Leu, Phe, His, Pro, Leu, Ile, Gln), four protein-coding genes (nad5, nad4, nad4l, nad1), and 16S-rRNA on the light strand. Most protein-coding genes start with TTG, ATT or ATA initiation codon except cox1, cox1’s start codon cannot be determined, and three types of inferred termination codons are TAA, TAG, and an incomplete stop codon. There are four intergenic spacers and 25 gene overlaps. The phylogenetic analysis shows that A. karschi has closer genetic relationship with Cyriopagopus schmidti (von Wirth, 1991) and Phyxioschema suthepium (Raven & Schwendinger, 1898) with high bootstrap support.

Complete mitochondrial genome of Rivularia auriculata (Gastropoda, Viviparidae) with phylogenetic consideration

Complete mitochondrial genome sequence of Rivularia auriculata has a circular genome of 16,552 bp, which is comprised 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. The nucleotide composition of the light strand is 43.16% of A, 26.78% of T, 20.18% of C, and 9.88% of G. All genes are encoded on the heavy strand except seven tRNA genes (Met, Tyr, Cys, Trp, Gln, Gly, and Glu) on the light strand. All the protein-coding genes start with ATC initiation codon except ND4 starts with GTG, and two types of inferred termination codons are TAA and TAG. There are 26 intergenic spacers and 4 gene overlaps. It is indicated that R. auriculata has closer genetic relationship with Viviparus chui (88.64% nucleotide sequence identity between them) than the other snail species.

Complete mitochondrial genome of the apple snail Pomacea diffusa (Gastropoda, Ampullariidae) with phylogenetic consideration

We present the complete mitochondrial genome of Pomacea diffusa in this study. The results show that the mitochondrial genome is 16,640 bp in length, which is comprised of 13 protein-coding genes, two rRNA genes, and 21 tRNA genes. The nucleotide compositions of the light strand are 39.62% of A, 30.13% of T, 16.02% of C, and 14.24% of G. Except eight tRNA (Glu, Gly, Trp, Cys, Tyr, Met, Thr, Val) on the light strand, the rest are encoded on the heavy strand. All the protein-coding genes start with ATC initiation codon, and two types of inferred termination codons are TAA and TAG. There are 26 intergenic spacers and two gene overlaps. The phylogenetic analysis shows that P. diffusa clusters with P. canaliculata and P. maculata with high bootstrap support, which is consistent with the morphological and molecular evidence.

The complete mitochondrial genome of the mudsnail Cipangopaludina cathayensis (Gastropoda: Viviparidae)

We present the complete mitochondrial genome of Cipangopaludina cathayensis in this study. The mitochondrial genome is 17,157 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes. All of them are encoded on the heavy strand except 7 tRNA genes on the light strand. Overall nucleotide compositions of the light strand are 44.51% of A, 26.74% of T, 20.48% of C and 8.28% of G. All the protein-coding genes start with ATG initiation codon except ATP6 with ATA and ND4 with TTG, and 2 types of termination codons are TAA (ATP6, ND2, COX1, COX2, ATP8, ND1, ND6, Cytb, COX3, ND4) and TAG (ND4L, ND5, ND3). There are 29 intergenic spacers and 5 gene overlaps. The tandem repeat sequences are observed in COX2, tRNA(Asp), ATP6, tRNA(Cys), S-rRNA, ND1, Cytb, ND4 and COX3 genes. Gene arrangement and distribution are different from the typical vertebrates. The absence of D-loop is consistent with the Gastropoda, but at least one lengthy non-coding region is essential regulatory element for the initiation of transcription and replication.