Genome survey ofZanthoxylum bungeanumand development of genomic-SSR markers in congeneric species

Abstract

Zanthoxylum bungeanum, a spice and medicinal plant, is cultivated in many parts of China and some countries in Southeast Asia; however, data on its genome are lacking. In the present study, we performed a whole-genome survey and developed novel genomic-SSR markers of Z. bungeanum. Clean data (∼197.16 Gb) were obtained and assembled into 11185221 scaffolds with an N50 of 183 bp. K-mer analysis revealed that Z. bungeanum has an estimated genome size of 3971.92 Mb, and the GC content, heterozygous rate, and repeat sequence rate are 37.21%, 1.73%, and 86.04%, respectively. These results indicate that the genome of Z. bungeanum is complex. Furthermore, 27153 simple sequence repeat (SSR) loci were identified from 57288 scaffolds with a minimum length > 1 kb. Mononucleotide repeats (19706) were the most abundant type, followed by dinucleotide repeats (5154). The most common motifs were A/T, followed by AT/AT; these SSRs accounted for 71.42% and 11.84% of all repeats, respectively. A total of 21243 non-repeating primer pairs were designed, and 100 were randomly selected and validated by PCR analysis using DNA from 10 Z. bungeanum individuals and 5 Zanthoxylum armatum individuals. Finally, 36 polymorphic SSR markers were developed with polymorphism information content (PIC) values ranging from 0.16 to 0.75. Cluster analysis revealed that Z. bungeanum and Z. armatum could be divided into two major clusters, suggesting that these newly developed SSR markers are useful for genetic diversity and germplasm resource identification in Z. bungeanum and Z. armatum.

Whole genome survey and microsatellite motif identification ofArtemia franciscana

“…Overall, the motifs including A or T were more abundant than those including C or G, consistent with the findings of Daphnia pulex genome-wide SSR study (29). These results might be due to the high slippage rate of A/T motifs, addition of 3' poly(A) tail by retrotransposon elements or transition of methylated C to T residues at CpG sites (14,(30)(31)(32). These data for SSRs in A.…”

“…Genome survey sequencing (GSS) using next-generation sequencing (NGS) is a time-and costeffective way to evaluate genome information, such as genome size, heterozygosity level, and repeat content, and can be used to develop molecular markers (13,14). Simple sequence repeats (SSRs) or microsatellites are short tandem repeats of 1-6 nucleotides that have been utilized as genetic markers because of their outstanding abundance and high variability (15).…”

The Complete Chloroplast Genome Sequence of Four Plant Species, Their SSR Identification and Phylogenetic Analysis

“…In nuclear genomes, the mononucleotide SSRs take higher portions in all six classes (mononucleotide, dinucleotide, trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide). In the nuclear genome of Zanthoxylum bungeanum, mononucleotide repeats were the most abundant class, with the value of 19706, which is the four times of dinucleotide repeats (5154) [30]. Similarly, in the nuclear genome, the mononucleotide presents the highest proportion in Chinese jujube (Ziziphus jujuba) [31].…”

Post‐farmland conversion spatio‐temporal dynamics of net soil nitrogen mineralization and availability in a chronosequence of Zanthoxylum bungeanum plantations

“…Forest plantations are not often fertilized, thus the success of afforestation in the absence of fertilization in principle relies on the turnover of soil organic N into plant‐available inorganic N (ION) through mineralization (Reichmann et al, 2013; Xia et al, 2021). The soil N mineralization (N min ) flux is the biggest because, as Li et al (2020) mentioned, as a rule up to 58% of available N for plant production comes from in situ mineralization of native organic matter. Ammonium (NH 4 + ‐N) and nitrate (NO 3 − ‐N) N constitute plant‐available ION pools, and their concentrations in soil solutions govern patterns of N cycle (Cheng et al, 2015).…”

“…Zanthoxylum bungeanum Maxim., a tree also known as ‘Chinese prickly ash', is one of the key species widely cultivated in this region under the CGGP due to its high adaptability to poor habitats, drought stress, and fast growth (Persson et al, 2013). According to an estimation, Z. bungeanum and a closely related species, Z. armatum , occupies about 1.67 million ha, produces an annual output of 3.5 × 10 5 tons of dried pericarp and generates more than 4 billion $US in China (Li et al, 2020). The tremendous economic and ecological benefits offered by Z. bungeanum have resulted in extensive farmland conversions to its economically valued forest plantations (Cheng et al, 2015).…”