The InBIO Barcoding Initiative Database: contribution to the knowledge of DNA barcodes of the vascular plants of northeastern Portugal

Study Extent

The data were collected in the Trás-os-Montes region (Northeast Portugal), in the municipalities of Aljó, Bragança, Vila Real, Macedo de Cavaleiros, Vila Flor and Vimioso.

Sampling

Plant samples were collected in the northeast of Portugal from traditionally managed olive grove agroecosystems and their surrounding areas. Young olive groves were used as a central point from which a 50m buffer zone was drawn. Every distinct vascular plant species within each patch was collected, photographed, and then herbarised in situ with an assigned specimen number. A portion of leaf tissue was collected from each sample, placed in a paper envelope, and then stored in a zip-lock bag with silica gel until DNA extraction. To minimise contamination between samples, tweezers and scissors were systematically sterilised with 100% ethanol under flame. After morphological identification, all the specimens (vouchers) were deposited in the herbarium of the Natural History and Science Museum of the University of Porto (MHNC-UP) with the codes PO-V72113–PO-V72772.

Quality Control

Collected samples were identified and revised by experts in vascular plant taxonomy. The obtained DNA barcode sequences were compared against the GenBank and BOLD databases, and the top hits were examined to identify potential PCR/ sequencing errors, contaminations or misidentifications.item-0item-0

Method steps

1. 1. Vascular plants were collected in the northeast of Portugal in August 2018, May–June 2019 and June 2020, from traditionally managed olive grove agroecosystems and their surrounding areas. A leaf tissue sample was collected for DNA extraction. 2. Taxonomic identification was carried out, after herborisation, under a stereomicroscope, using mainly the dichotomous keys of Flora Iberica. For some specimens, it was necessary to consult other works namely in cases of possible hybrids, or in cases where the Flora Iberica has a different treatment of the taxon of interest. Whenever possible, the specimens were identified at the infraspecific level. 3. DNA extracts were obtained from collected leaf tissues and DNA barcodes were sequenced using Illumina protocols for two regions: the chloroplast trnL (UAA) intron region (markers e/ f: 147–540 bp and g/ h:10–143 bp) and the nuclear internal transcribed spacer 2 region, ITS2 (marker UniPlantF/ UniPlantR: 187–387 bp). 4. Sequences were submitted to BOLD and GenBank databases.

A total of 659 specimens were collected, of which 647 were morphologically identified to the most specific taxon (species, subspecies or variety). This data set includes 448 species belonging to 69 families, 34 orders, 7 classes and 1 phylum.

1. Plantae
   rank: kingdom
2. Tracheophyta
   rank: phylum
3. Liliopsida
   rank: class
4. Lycopodiopsida
   rank: class
5. Magnoliopsida
   rank: class
6. Pinopsida
   rank: class
7. Polypodiopsida
   rank: class
8. Psilotopsida
   rank: class
9. Pteridopsida
   rank: class
10. Apiales
    rank: order
11. Asparagales
    rank: order
12. Asterales
    rank: order
13. Boraginales
    rank: order
14. Brassicales
    rank: order
15. Caryophyllales
    rank: order
16. Cucurbitales
    rank: order
17. Dioscoreales
    rank: order
18. Dipsacales
    rank: order
19. Equisetales
    rank: order
20. Ericales
    rank: order
21. Fabales
    rank: order
22. Fagales
    rank: order
23. Gentianales
    rank: order
24. Geraniales
    rank: order
25. Isoetales
    rank: order
26. Lamiales
    rank: order
27. Malpighiales
    rank: order
28. Malvales
    rank: order
29. Myrtales
    rank: order
30. Ophioglossales
    rank: order
31. Pinales
    rank: order
32. Piperales
    rank: order
33. Poales
    rank: order
34. Polypodiales
    rank: order
35. Pteridales
    rank: order
36. Ranunculales
    rank: order
37. Rosales
    rank: order
38. Santalales
    rank: order
39. Sapindales
    rank: order
40. Saxifragales
    rank: order
41. Solanales
    rank: order
42. Zygophyllales
    rank: order
43. Amaranthaceae
    rank: family
44. Amaryllidaceae
    rank: family
45. Anacardiaceae
    rank: family
46. Apiaceae
    rank: family
47. Aristolochiaceae
    rank: family
48. Asparagaceae
    rank: family
49. Aspleniaceae
    rank: family
50. Asteraceae
    rank: family
51. Boraginaceae
    rank: family
52. Brassicaceae
    rank: family
53. Campanulaceae
    rank: family
54. Cannabaceae
    rank: family
55. Caprifoliaceae
    rank: family
56. Caryophyllaceae
    rank: family
57. Cistaceae
    rank: family
58. Convolvulaceae
    rank: family
59. Crassulaceae
    rank: family
60. Cucurbitaceae
    rank: family
61. Cupressaceae
    rank: family
62. Cyperaceae
    rank: family
63. Cytinaceae
    rank: family
64. Dennstaedtiaceae
    rank: family
65. Dioscoreaceae
    rank: family
66. Equisetaceae
    rank: family
67. Ericaceae
    rank: family
68. Euphorbiaceae
    rank: family
69. Fabaceae
    rank: family
70. Fagaceae
    rank: family
71. Gentianaceae
    rank: family
72. Geraniaceae
    rank: family
73. Hypericaceae
    rank: family
74. Isoetaceae
    rank: family
75. Juglandaceae
    rank: family
76. Juncaceae
    rank: family
77. Lamiaceae
    rank: family
78. Linaceae
    rank: family
79. Lythraceae
    rank: family
80. Malvaceae
    rank: family
81. Montiaceae
    rank: family
82. Oleaceae
    rank: family
83. Onagraceae
    rank: family
84. Ophioglossaceae
    rank: family
85. Orchidaceae
    rank: family
86. Orobanchaceae
    rank: family
87. Paeoniaceae
    rank: family
88. Papaveraceae
    rank: family
89. Plantaginaceae
    rank: family
90. Plumbaginaceae
    rank: family
91. Poaceae
    rank: family
92. Polygalaceae
    rank: family
93. Polygonaceae
    rank: family
94. Portulacaceae
    rank: family
95. Primulaceae
    rank: family
96. Pteridaceae
    rank: family
97. Ranunculaceae
    rank: family
98. Resedaceae
    rank: family
99. Rosaceae
    rank: family
100. Rubiaceae
     rank: family
101. Rutaceae
     rank: family
102. Salicaceae
     rank: family
103. Santalaceae
     rank: family
104. Saxifragaceae
     rank: family
105. Scrophulariaceae
     rank: family
106. Solanaceae
     rank: family
107. Thymelaeaceae
     rank: family
108. Urticaceae
     rank: family
109. Verbenaceae
     rank: family
110. Violaceae
     rank: family
111. Zygophyllaceae
     rank: family

The study was carried out in the Trás-os-Montes region, specifically in the districts of Bragança and Vila Real in northeastern Portugal.