Zeng-g Qian

The complete mitogenome of the dampwood termite Zootermopsis nevadensis (Insecta: Isoptera: Termopsidae)

Abstract The complete mitogenome of the dampwood termite Zootermopsis nevadensis was reconstructed from whole-genome Illumina sequencing data with an average coverage of 7052×. The circular genome is 15,444 bp in length, and consists of 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs) and one D-loop region. All PCGs are initiated with ATN codons, except for the ND1 and ND5 genes with the start codon GTG. Some PCGs harbor TAG (ND1) or incomplete stop codon T (COII, ND5 & Cytb), while the others use TAA as their stop codons. The nucleotide composition is asymmetric (45.8% A, 19.8% C, 10.9% G, 23.5% T) with an overall GC content of 30.7%. These data would contribute to the design of novel molecular markers for population and evolutionary studies of this and related termite species.

The complete mitogenome of the Cydno Longwing Heliconius cydno (Insecta: Lepidoptera: Nymphalidae)

Abstract The complete mitogenome of the Cydno Longwing Heliconius cydno has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 15,367 bp in length, and consists of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and 1 D-loop region. PCGs are mostly initiated with the ATN codons (COII, COIII, Cytb, ND2, ND3, ND4, ND4L, ND5, ND6, ATP6 & ATP8), except for the ND1 and COI genes with TTG and the unusual CGA as their initiation codons, respectively. Some PCGs harbor TAG (ND3) or incomplete termination codon T (COI, COII & ND4), while all the others use TAA as their termination codons. The nucleotide composition is highly asymmetric (39.3% A, 42.1% T, 7.6% G, 11.0% C) with an overall GC content of 18.6%.

The complete chloroplast genome of Armand pine Pinus armandii, an endemic conifer tree species to China

Abstract The complete chloroplast genome (cpDNA) sequence of an endemic conifer species, Armand pine Pinus armandii Franch., is determined in this study. The cpDNA was 117,265 bp in length, containing a pair of 475 bp inverted repeat (IR) regions those distinguished in large and small single copy (LSC and SSC) regions of 64,548 and 51,767 bp in length, respectively. The cpDNA contained 114 genes, including 74 protein-coding genes (74 PCG species), 4 ribosomal RNA genes (four rRNA species) and 36 transfer RNA genes (33 tRNA species). Out of these genes, 12 harbor a single intron and most of the genes occurred in a single copy. The overall AT content of the Armand pine cpDNA was 61.2%, while the corresponding values of the LSC, SSC and IR regions were 62.0%, 60.2% and 62.7%, respectively. A phylogenetic analysis revealed that P. armandii chloroplast genome is closely related to that of the P. koraiensis within the genus Pinus.

Isolation and characterization of polymorphic microsatellites in the perennial herb Euphorbia kansui using paired-end Illumina shotgun sequencing

Euphorbia kansui is a threatened perennial herb endemic to China, and a good knowledge of its population genetics would be essential to the formulation of effective conservation and management strategies. In this study, 12 novel microsatellite markers were developed for E. kansui using Illumina sequencing technology. The number of alleles varied between 2 and 11, with an average of 4.1 alleles per locus. The expected (HE) and observed heterozygosity (HO) ranged from 0.0950 to 0.7875 and from 0.0500 to 0.9500, with an average of 0.4050 and 0.4083, respectively. Following the false discovery rate controlling procedure, significant deviations from Hardy–Weinberg equilibrium was only detected in a single locus (Ek1073). These informative microsatellite markers can be readily used for genetic analyses of this threatened plant.

Genetic Structure and Evolutionary History of Three Alpine Sclerophyllous Oaks in East Himalaya-Hengduan Mountains and Adjacent Regions

The East Himalaya-Hengduan Mountains (EH-HM) region has a high biodiversity and harbors numerous endemic alpine plants. This is probably the result of combined orographic and climate oscillations occurring since late Tertiary. Here, we determined the genetic structure and evolutionary history of alpine oak species (including Quercus spinosa, Quercus aquifolioides, and Quercus rehderiana) using both cytoplasmic-nuclear markers and ecological niche models (ENMs), and elucidated the impacts of climate oscillations and environmental heterogeneity on their population demography. Our results indicate there were mixed genetic structure and asymmetric contemporary gene flow within them. The ENMs revealed a similar demographic history for the three species expanded their ranges from the last interglacial (LIG) to the last glacial maximum (LGM), which was consistent with effective population sizes changes. Effects of genetic drift and fragmentation of habitats were responsible for the high differentiation and the lack of phylogeographic structure. Our results support that geological and climatic factors since Miocene triggered the differentiation, evolutionary origin and range shifts of the three oak species in the studied area and also emphasize that a multidisciplinary approach combining molecular markers, ENMs and population genetics can yield deep insights into diversification and evolutionary dynamics of species.

Isolation and characterization of polymorphic microsatellites in the Tibetan cypress Cupressus gigantea using paired-end Illumina shotgun sequencing

Cupressus gigantea Cheng et L. K. Fu is an endangered conifer endemic to Tibet of China. In this study, 16 polymorphic microsatellite markers were developed using paired-end Illumina shotgun sequencing. The number of alleles varied between 3 and 18, with an average of 8.063 alleles per locus. The observed (HO) and expected heterozygosities (HE) ranged from 0.227 to 0.902 and from 0.000 to 1.000, respectively. Following the false discovery rate controlling procedure, six loci showed significant deviations from Hardy–Weinberg equilibrium, and linkage disequilibrium was only detected between a pair of loci. These informative microsatellite markers can be readily used for genetic analyses of this endangered plant.