Markers + reference

Photinia

27 species · Rosaceae · Rosales

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Species 27
Genome length 159–160 kb
Candidate markers 270
Primer pairs 90

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 274 0.0329 0.95 70.3 yes View details
rps16-trnQ-UUG LSC 825 0.0150 0.97 60.4 yes View details
trnG-UCC-trnR-UCU LSC 206 0.0300 0.87 62.2 yes View details
trnR-UCU-atpA LSC 617 0.0349 0.91 74.8 yes View details
petN-psbM LSC 1274 0.0102 0.90 61.9 yes View details
trnT-GGU-psbD LSC 1585 0.0294 0.93 76.0 yes View details
psbZ-trnG-GCC LSC 410 0.0229 0.96 61.5 yes View details
trnT-UGU-trnL-UAA LSC 1225 0.0131 0.97 72.6 yes View details
ndhC-trnV-UAC LSC 562 0.0427 0.97 88.1 yes View details
ndhF-rpl32 SSC 1111 0.0199 0.96 71.5 yes View details
rpl2-trnH-GUG IRa 304 0.0924 0.79 80.4 no View details
rpl33-rps18 LSC 232 0.0315 0.94 69.7 yes View details
rpl32-trnL-UAG SSC 1456 0.0101 0.95 62.5 yes View details
trnK-UUU-rps16 LSC 949 0.0121 1.00 62.3 yes View details
trnS-GCU-trnG-UCC LSC 653 0.0075 1.00 61.9 yes View details
rps19-rpl2 IRb 70 0.0263 1.00 61.5 yes View details
accD-psaI LSC 688 0.0071 0.96 61.2 yes View details
petG-trnW-CCA LSC 123 0.0499 0.95 61.1 yes View details
psaJ-rpl33 LSC 474 0.0085 0.98 60.5 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 375–396 1.000 89.1
trnH-GUG-psbA_p2 trnH-GUG-psbA ATATTATGGGCGAACGACGG CCTCTAGACCTAGCTGCTGT 386–407 1.000 88.9
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 389–410 1.000 88.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ATATTATGGGCGAACGACGG TTCCCTCTAGACCTAGCTGC 389–410 1.000 88.8
trnH-GUG-psbA_p5 trnH-GUG-psbA ATATTATGGGCGAACGACGG GCGCTAACCTTGGTATGGAA 436–457 1.000 88.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CGGAACTTCGCCCTAATCAA 1009–1054 1.000 87.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGGAACTTCGCCCTAATCAA 1008–1053 1.000 87.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CGGAACTTCGCCCTAATCAA 1018–1063 1.000 86.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTTTTACGGAACTTCGCCCT 1015–1060 1.000 85.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTTTACGGAACTTCGCCCT 1014–1059 1.000 85.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 727–982 0.963 85.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTT GAGGTTCGAATCCTTCCGTC 704–959 0.963 83.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 737–992 0.963 83.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 738–993 0.963 83.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCCACAGCTGATCATGTCC GAGGTTCGAATCCTTCCGTC 739–994 0.963 81.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AATCAAACCGAAAGACCCCT 749–791 1.000 77.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ATCAAACCGAAAGACCCCTT 748–790 1.000 77.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AATCAAACCGAAAGACCCCT 748–790 1.000 77.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ATCAAACCGAAAGACCCCTT 747–789 1.000 77.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ATCAAACCGAAAGACCCCTT 802–844 1.000 76.0
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 262–316 1.000 75.3
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 265–319 1.000 75.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 268–322 1.000 74.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 271–325 1.000 74.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 266–320 1.000 72.9
trnR-UCU-atpA_p1 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT AGACATTTACCGACGAAGCG 246–1042 1.000 76.4
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGACGAAGCG 186–982 1.000 75.5
trnR-UCU-atpA_p3 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT AGACATTTACCGACGAAGCG 221–1017 1.000 72.6
trnR-UCU-atpA_p4 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT GGAAGCCCTTTTGAAAGAAGC 247–1023 1.000 71.1
trnR-UCU-atpA_p5 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT ACCAAGACATTTACCGACGA 246–1046 1.000 70.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (27)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Photinia beauverdiana PQ197389.1 160090 View on NCBI ↗
Photinia beckii NC_045353.1 159230 View on NCBI ↗
Photinia chihsiniana NC_086562.1 159409 View on NCBI ↗
Photinia crassifolia NC_062336.1 160166 View on NCBI ↗
Photinia davidsoniae MT230547.1 160346 View on NCBI ↗
Photinia glabra NC_062337.1 159743 View on NCBI ↗
Photinia hirsuta NC_065652.1 160189 View on NCBI ↗
Photinia hirsuta var. lobulata MN061986.1 160223 View on NCBI ↗
Photinia impressivena NC_065655.1 160200 View on NCBI ↗
Photinia integrifolia NC_045344.1 159654 View on NCBI ↗
Photinia kwangsiensis NC_086563.1 159524 View on NCBI ↗
Photinia lanuginosa NC_045354.1 160184 View on NCBI ↗
Photinia lasiogyna NC_086558.1 160024 View on NCBI ↗
Photinia lasiogyna var. glabrescens OP021695.1 159919 View on NCBI ↗
Photinia lochengensis NC_045352.1 160201 View on NCBI ↗
Photinia loriformis NC_086564.1 159805 View on NCBI ↗
Photinia parvifolia NC_082056.1 160271 View on NCBI ↗
Photinia prionophylla NC_045355.1 160333 View on NCBI ↗
Photinia prunifolia NC_085644.1 159716 View on NCBI ↗
Photinia pustulata NC_065653.1 160258 View on NCBI ↗
Photinia raupingensis NC_086565.1 159730 View on NCBI ↗
Photinia serratifolia NC_045331.1 160254 View on NCBI ↗
Photinia sorbifolia NC_045416.1 160371 View on NCBI ↗
Photinia stenophylla NC_086566.1 159613 View on NCBI ↗
Photinia taishunensis MK920278.1 159572 View on NCBI ↗
Photinia undulata MZ562937.1 160332 View on NCBI ↗
Photinia x fraseri MZ128520.1 160184 View on NCBI ↗