Development and Application of Genomic Resources in an Endangered Palaeoendemic Tree, Parrotia subaequalis (Hamamelidaceae) From Eastern China

Abstract

Parrotia subaequalis is an endangered palaeoendemic tree from disjunct montane sites in eastern China. Due to the lack of effective genomic resources, the genetic diversity and population structure of this endangered species are not clearly understood. In this study, we conducted paired-end shotgun sequencing (2 × 125 bp) of genomic DNA for two individuals of P. subaequalis on the Illumina HiSeq platform. Based on the resulting sequences, we have successfully assembled the complete chloroplast genome of P. subaequalis, as well as identified the polymorphic chloroplast microsatellites (cpSSRs), nuclear microsatellites (nSSRs) and mutational hotspots of chloroplast. Ten polymorphic cpSSR loci and 12 polymorphic nSSR loci were used to genotype 96 individuals of P. subaequalis from six populations to estimate genetic diversity and population structure. Our results revealed that P. subaequalis exhibited abundant genetic diversity (e.g., cpSSRs: Hcp = 0.862; nSSRs: HT = 0.559) and high genetic differentiation (e.g., cpSSRs: RST = 0.652; nSSRs: RST = 0.331), and characterized by a low pollen-to-seed migration ratio (r ≈ 1.78). These genetic patterns are attributable to its long evolutionary histories and low levels of contemporary inter-population gene flow by pollen and seed. In addition, lack of isolation-by-distance pattern and strong population genetic structuring in both marker systems, suggests that long-term isolation and/or habitat fragmentation as well as genetic drift may have also contributed to the geographic differentiation of P. subaequalis. Therefore, long-term habitat protection is the most important methods to prevent further loss of genetic variation and a decrease in effective population size. Furthermore, both cpSSRs and nSSRs revealed that P. subaequalis populations consisted of three genetic clusters, which should be considered as separated conservation units.

Complete Chloroplast Genome of Calligonum Mongolicum: Genome Organization, Codon Usage Pattern, Phylogenetic Relationships, Comparative Structure and Adaptive Evolution Analysis

“…A number of the codon usage indicators were performed via the program codon W version 1.3 (https://sourceforge.net/projects/codonw/), including the relative synonymous codon usage value (RSCU), the effective number of codons (ENC), G + C content of the gene (GC), the frequency of the nucleotides G + C at the 3rd position of synonymous codons (GC 3s ), and the base compositions (A 3s , T 3s , G 3s , and C 3s ) [28]. The RSCU value and ENC value were used together to describe codon usage patterns [29]. The G + C content at the 1st, 2nd, 3rd of codons (GC 1 , GC 2 , GC 3 ) and the average GC content of the 1st and 2nd (GC 12 ) were calculated by Cusp function from EMBOSS (http://imed.med.ucm.es/EMBOSS/) [30].…”

De Novo Transcriptome Assembly and Population Genetic Analyses for an Endangered Chinese Endemic Acer miaotaiense (Aceraceae)

“…Because of a lack of available genomic information, it was difficult to develop ideal SSR markers and to evaluate the genetic diversity and evolution of endangered species at the genome level [ 20 , 21 , 22 ]. Transcriptome sequencing represents an alternative to whole-genome sequencing because it is more cost-effective and can target genomic regions for important traits through corresponding expressed sequence tag (EST) sequences, which can be selected to develop abundant EST-SSRs [ 23 , 24 ].…”

WITHDRAWN: Complete Chloroplast Genome of Calligonum Mongolicum: Genome Organization, Codon Usage Pattern, Phylogenetic Relationships, Comparative Structure and Adaptive Evolution Analysis

“…A number of the codon usage indicators were performed via the program codon W version 1.3 (https://sourceforge.net/projects/codonw/), including the relative synonymous codon usage value (RSCU), the effective number of codons (ENC), G + C content of the gene (GC), the frequency of the nucleotides G + C at the 3 rd position of synonymous codons (GC 3s ), and the base compositions (A 3s , T 3s , G 3s , and C 3s ) [28]. The RSCU value and ENC value were used together to describe codon usage patterns [29]. The G+C content at the 1 st , 2 nd , 3 rd of codons (GC 1 , GC 2 , GC 3 ) and the average GC content of the 1 st and 2 nd (GC 12 ) were calculated by Cusp function from EMBOSS (http://imed.med.ucm.es/EMBOSS/) [30].…”