Development of a Target Enrichment Probe Set for Conifer (REMcon)
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Probe Design
2.2. Taxon Selection
2.3. DNA Extraction, Library Preparation, Hybrid Capture and Sequencing
2.4. Bioinformatics Analyses
3. Results and Discussion
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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S# | Picea abies Gene Name | Arabidopsis thaliana Putative Homolog | Length of the Probe Sequences |
---|---|---|---|
1 | MA_10437158 | AT5G06430 | 195 |
2 | MA_10437143 | AT1G12370 | 480 |
3 | MA_10437077 | AT5G02250 | 621 |
4 | MA_10437070 | AT5G10920 | 720 |
5 | MA_10436603 | AT1G03750 | 945 |
6 | MA_10436489 | AT4G37510 | 878 |
7 | MA_10435966 | AT4G38890 | 822 |
8 | MA_10435879 | AT2G33630 | 613 |
9 | MA_10435851 | AT5G04520 | 510 |
10 | MA_10435433 | AT2G44760 | 426 |
11 | MA_10435005 | AT2G40570 | 787 |
12 | MA_10434812 | AT1G36310 | 1088 |
13 | MA_10434753 | AT1G49380 | 539 |
14 | MA_10433768 | AT2G31955 | 942 |
15 | MA_10433107 | AT5G64150 | 825 |
16 | MA_10432498 | AT1G74640 | 453 |
17 | MA_10431375 | AT2G24830 | 321 |
18 | MA_10430781 | AT4G35910 | 432 |
19 | MA_10429426 | AT1G30070 | 240 |
20 | MA_10428930 | AT1G15390 | 256 |
21 | MA_10428614 | AT2G34640 | 259 |
22 | MA_10428345 | AT1G57770.1 | 315 |
23 | MA_10428134 | AT2G04560 | 273 |
24 | MA_10427767 | AT1G21370 | 291 |
25 | MA_10427729 | AT5G67530 | 1224 |
26 | MA_10427590 | AT1G17160 | 480 |
27 | MA_10427203 | AT2G36740 | 543 |
28 | MA_10426631 | AT4G36390 | 1533 |
29 | MA_10426581 | AT2G33450 | 231 |
30 | MA_10426376 | AT2G38270 | 504 |
31 | MA_9578808 | AT4G18372 | 387 |
32 | MA_9514062 | AT5G20220 | 315 |
33 | MA_9503281 | AT1G48175 | 257 |
34 | MA_8815984 | AT2G346401 | 693 |
35 | MA_8715484 | AT4G38020 | 501 |
36 | MA_8687206 | AT4G26980 | 408 |
37 | MA_8286794 | AT3G17170 | 342 |
38 | MA_8140147 | AT2G28605 | 480 |
39 | MA_7890741 | AT2G44660 | 783 |
40 | MA_5587080 | AT4G20060 | 447 |
41 | MA_957334 | AT1G05055 | 462 |
42 | MA_945784 | AT5G06410 | 380 |
43 | MA_939779 | AT4G27390 | 468 |
44 | MA_938037 | AT5G49570 | 580 |
45 | MA_894439_ | AT2G30100 | 1306 |
46 | MA_824260 | AT4G28020 | 441 |
47 | MA_762004 | AT1G28560 | 675 |
48 | MA_759516 | AT5G08720 | 461 |
49 | MA_749379 | AT4G11980 | 201 |
50 | MA_587488 | AT4G01040 | 377 |
51 | MA_546546 | AT4G17760 | 252 |
52 | MA_537299 | AT5G54840 | 264 |
53 | MA_458270 | AT5G06830 | 690 |
54 | MA_388031 | AT2G20330 | 486 |
55 | MA_341112 | AT5G11980 | 276 |
56 | MA_332596 | AT2G34460 | 333 |
57 | MA_314789 | AT1G56345.1 | 603 |
58 | MA_261436 | AT4G33030 | 1290 |
59 | MA_253636 | AT3G51050 | 768 |
60 | MA_225872 | AT5G14260 | 456 |
61 | MA_224167 | AT2G20790 | 900 |
62 | MA_199851 | AT3G01660 | 350 |
63 | MA_196209 | AT4G36530 | 273 |
64 | MA_187402 | AT4G31460 | 471 |
65 | MA_173127 | AT4G28740 | 548 |
66 | MA_159115 | AT2G27600 | 1191 |
67 | MA_159115 | AT4G27600 | 1056 |
68 | MA_127668 | AT3G15290 | 465 |
69 | MA_123340 | AT2G19870 | 1137 |
70 | MA_121485 | AT1G02410 | 749 |
71 | MA_121026 | AT1G08460 | 570 |
72 | MA_106933 | AT2G266801 | 636 |
73 | MA_104872 | AT3G26580 | 507 |
74 | MA_99242 | AT4G29070 | 412 |
75 | MA_98424 | AT1G07130 | 558 |
76 | MA_95157 | AT5G09820 | 292 |
77 | MA_83545 | AT5G65860 | 514 |
78 | MA_78599 | AT2G40760 | 252 |
79 | MA_73742 | AT2G21840 | 939 |
80 | MA_73742 | AT1G21840 | 939 |
81 | MA_67861 | AT2G26680 | 369 |
82 | MA_66902 | AT2G36145 | 234 |
83 | MA_66902 | AT2G34145 | 234 |
84 | MA_63465 | AT3G24315 | 290 |
85 | MA_61548 | AT1G65030 | 681 |
86 | MA_55048 | AT5G19130 | 858 |
87 | MA_43083 | AT5G48330 | 717 |
88 | MA_41847 | AT3G03790 | 303 |
89 | MA_35149 | AT3G02300 | 431 |
90 | MA_34295 | AT1G43580 | 378 |
91 | MA_30194 | AT5G16210 | 369 |
92 | MA_29076 | AT3G57910 | 513 |
93 | MA_26068 | AT2G37560 | 414 |
94 | MA_25177 | AT1G07970 | 472 |
95 | MA_24252 | AT4G24090 | 600 |
96 | MA_19954 | AT2G02590 | 414 |
97 | MA_11407 | AT3G47860 | 312 |
98 | MA_10909 | AT2G04270 | 318 |
99 | MA_6888 | AT3G24080 | 2286 |
100 | MA_4586 | AT2G22650 | 303 |
Families | N | Average Locus Recovery | Min | Max |
---|---|---|---|---|
Araucariaceae | 5 | 85 | 53 | 97 |
Cupressaceae | 22 | 98 | 89 | 100 |
Pinaceae | 11 | 96 | 95 | 90 |
Podocarpaceae | 26 | 93 | 76 | 97 |
Sciadopityaceae | 1 | 95 | - | - |
Taxaceae | 3 | 97 | 96 | 97 |
Non conifer Gymnosperms | 4 | 81 | 75 | 92 |
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Khan, R.; Biffin, E.; van Dijk, K.-j.; Hill, R.S.; Liu, J.; Waycott, M. Development of a Target Enrichment Probe Set for Conifer (REMcon). Biology 2024, 13, 361. https://doi.org/10.3390/biology13060361
Khan R, Biffin E, van Dijk K-j, Hill RS, Liu J, Waycott M. Development of a Target Enrichment Probe Set for Conifer (REMcon). Biology. 2024; 13(6):361. https://doi.org/10.3390/biology13060361
Chicago/Turabian StyleKhan, Raees, Ed Biffin, Kor-jent van Dijk, Robert S. Hill, Jie Liu, and Michelle Waycott. 2024. "Development of a Target Enrichment Probe Set for Conifer (REMcon)" Biology 13, no. 6: 361. https://doi.org/10.3390/biology13060361
APA StyleKhan, R., Biffin, E., van Dijk, K. -j., Hill, R. S., Liu, J., & Waycott, M. (2024). Development of a Target Enrichment Probe Set for Conifer (REMcon). Biology, 13(6), 361. https://doi.org/10.3390/biology13060361