Computational protocol: Development and characterization of 15 microsatellite markers for Cephalotaxus fortunei (Cephalotaxaceae)1

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[…] Seventy-five individuals of C. fortunei from five populations were collected in its natural distribution area from 2014 to 2015, and voucher specimens were deposited at the herbarium of Qiannan Normal College for Nationalities (). Young and healthy leaves were preserved in silica gel. All samples were stored at −20°C until processed. Total genomic DNA was extracted using a modified cetyltrimethylammonium bromide (CTAB) protocol with −20°C propanone pretreatment to eliminate polysaccharides ().The FIASCO method was used to develop microsatellite loci using one individual of C. fortunei from the Guizhou population (voucher: CB Wang 201406, JP3 [QNCN]). Approximately 3 μg of DNA was digested with MseI (New England Biolabs, Ipswich, Massachusetts, USA). The DNA digestion fragments were linked to an MseI adapter pair (F: 5′-TACTCAGGACTCAT-3′, R: 5′-GACGATGAGTCCTGAG-3′) with T4 ligase at 4°C overnight (). A diluted digestion-ligation mixture (1:10) was directly amplified using the following program: 95°C for 30 s, 60°C for 20 min, and 72°C for 1.5 min for 23 cycles with MseI-N primers (5′-GATGAGTCCTGAGTAAN-3′). Then, we used 5′-biotinylated (AC)15 and streptavidin-coated magnetic beads (Promega Corporation, Madison, Wisconsin, USA) to hybridize and capture the PCR product (). Enriched fragments were recovered with PCR amplification as described above, using MseI-N as the primers. Purifying with a multifunctional DNA Extraction Kit (OMEGA Bio-Tek, Norcross, Georgia, USA), the PCR products were then ligated into pTA2 vector (Toyobo, Osaka, Japan) and transformed into E. coli DH5α competent cells. A total of 80 clones were selected by blue-white screening and tested by PCR using M13+/M13− as primers. Seventy-six positive clones were chosen to be sequenced on an ABI Prism 3730 automated DNA sequencer (Invitrogen, Guangzhou, China). Out of the 76 clones, 27 clones contained simple sequence repeats, of which 12 were discarded because they were unsuitable for designing primers. Primers for the remaining 15 sequences were designed using Primer Premier 5.0 ().We used 75 individuals from five populations to test the polymorphism of the newly developed primer pairs (). The PCR amplifications were performed in a 20-μL reaction containing 1 μL of genomic DNA, 2 μL of PCR buffer, 0.5 μL 10 mM each primer, 1 μL 10 mM dNTP mixture, and 1 unit Taq DNA polymerase (TaKaRa Biotechnology Co., Dalian, China). PCR profiles were as follows: an initial denaturation at 94°C for 5 min; followed by 35 cycles at 94°C for 45 s, annealing temperature for 30 s, extension at 72°C for 1 min; and final extension at 72°C for 10 min (). PCR products were electrophoresed on 6% polyacrylamide denaturing gels by silver staining using a 50-bp ladder. Thirteen of the 15 loci were found to be polymorphic. The sizes of all amplification products matched the expected lengths.The effective number of alleles (Ae), observed heterozygosity (Ho), expected heterozygosity (He), and departure from Hardy–Weinberg equilibrium (HWE) were estimated by GenAlEx version 6.4 (). Linkage disequilibrium (LD) across all populations was tested using GENEPOP version 4.0.10 (). The occurrence of null alleles was investigated using MICRO-CHECKER version 2.2.3 (). The number of alleles per locus varied from one to seven, with a total of 247 alleles scored across the 75 individuals. He and Ho ranged from 0.108 to 0.738 and from 0.000 to 1.000, respectively. All loci were found to be in HWE. No null alleles were detected, and no significant LD (P > 0.05) was detected (). Furthermore, all 15 loci were successfully amplified in 75 individuals of C. oliveri from five populations (). Of these, 10 loci (CF1–CF10) were polymorphic (). […]

Pipeline specifications

Software tools Primer Premier, GenAlEx, Genepop
Application Population genetic analysis
Organisms Cephalotaxus oliveri