Abstract
The medicinal woody leguminous genus Archidendron F. Mueller serves as important herbal resources for curing upper respiratory tract infection, acute pharyngitis, tonsillitis, and gastroenteritis. However, genomic resources including transcriptomic sequences and molecular markers remain scarce in the genus. Transcriptome sequencing, genic microsatellite marker development, and population diversity analysis were conducted inArchidendronclypearia (Jack) I.C. Nielsen. Flower and flower bud transcriptomes were de novo assembled into 173,172 transcripts, with an average transcript length of 1597.3bp and an N50 length of 2427bp. A total of 34,701 microsatellite loci were identified from 26,716 (15.4 %) transcripts. Primer pairs were designed for 718 microsatellite loci, of which 456 (63.5 %) were polymorphic. Of the 456 polymorphic markers, 391 (85.7 %) and 402 (88.1 %) were transferable to A. lucidum (Benth.) I.C. Nielsen and A. multifoliolatum (H.Q. Wen) T.L. Wu, respectively. Using a subset of 15 microsatellite markers, relatively high genetic diversity was detected over two A. clypearia populations, with overall mean expected heterozygosity (He) being 0.707 and demonstrating the necessity of conservation. Relatively low differentiation between the two populations was revealed despite the distant separation (about 700km), with overall inbreeding coefficient of sub-population to the total population (Fst) being 8.7 %. This study represents the first attempt to conduct transcriptome sequencing, SSR marker development, and population genetics analysis in the medicinally important genus Archidendron. Our results will offer valuable resources and information for further genetic studies and practical applications in Archidendron and the related taxa.
Highlights
Ne number of effective alleles, Ho observed heterozygosity, He expected heterozygosity, Number of private alleles (Npa) number of private alleles being present only in one population, Nda number of diagnostic alleles being present in only one population at a frequency greater than 10.0%, Fis inbreeding coefficient of individuals relative to the subpopulation, Fit inbreeding coefficient of individuals relative to the total population/species, Fst inbreeding coefficient of sub-population relative to the total population/species, HWE Hardy-Weinberg equilibrium, *** departure at 0.001 significance level with Bonferroni correction
A final number of 173,172 transcripts were retained with an average transcript length of 1597.3 bp and an N50 length of 2427 bp
High quality of flower and flower bud transcriptomes (52,895,540 raw reads, 15.87 Gb in total) were generated and de novo assembled in A. clypearia
Summary
Most species of Pithecellobium Martius [1, 2]. Archidendron species occur widely in tropical Asia [1], ranging from India and southern China to New Guinea (http://www.asianplant.net/). Their leaves, twigs, and branches contain diverse structures such as polyphenols, flavonoids, lignans, and terpenoids that have anti-virus, anti-bacterium, anti-allergy, and/or anti-oxidation functions, and have been long used as herbal resources for curing upper respiratory tract infection, acute pharyngitis, tonsillitis, and gastroenteritis [3]. Pithecellobium clypearia Benth) represents the most important species for medicinal and industrial applications [4]
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