Tables
Table 1. Soil samples collected from suspect’s pants, crime scene and nearby areas.
Table 2. Primers for amplifying diatom rbcL fragments together with oligoes attached to the 5’ ends of the primers for labeling 12 soil samples.
Figures
Fig. 1. Localities of soil samples collected as references for tracking the possible source of the mud on the suspect’s pants and pictures of crime scene, mud from the canal, and suspect’s pants. A: Google map of five sampling sites; B: close-up of Site 1 to 3; C: the crime scene, D: soil from the canal; and E: suspect’s pants.
Fig. 2. Diagram showing how rbcL fragments were labeled by PCR, pooled together and sequenced on Ion Torrent S5xl platform.
Fig. 3. Percentages of the ZOTUs in the mud on suspect’s pants tracked to the 11 candidate source sites by FEAST. A: total ZOTUs with singletons; B: total ZOTUs without singletons; C: annotated ZOTUs with singletons; and D: annotated ZOTUs without singletons.
Fig. S1. Experiment design. Five parts, soil DNA acquisition, amplicon preparation, NGS data sequencing, NGS data processing, and suspect’s mud tracking.
Fig. S2. The ZOTU-rich diatom genera (A) and species (B) found in 12 soil samples.
Refenence
Altschul, S. F. (2012). Basic local alignment search tool (BLAST).Journal of Molecular Biology, 215 (3), 403-410.
Ambers, A., Votrubova, J., Vanek, D., Sajantila, A., & Budowle, B. (2018). Improved Y-STR typing for disaster victim identification, missing persons investigations, and historical human skeletal remains.International Journal of Legal Medicine, 132 (6), 1545-1553.
Bertoglio, B., Grignani, P., Di Simone, P., Polizzi, N., De Angelis, D., Cattaneo, C., . . . Previdere, C. (2020). Disaster victim identification by kinship analysis: the Lampedusa October 3rd, 2013 shipwreck.Forensic Science International-Genetics, 44 .
Dong, W. P., Cheng, T., Li, C. H., Xu, C., Long, P., Chen, C. M., & Zhou, S. L. (2014). Discriminating plants using the DNA barcoderbcL b: an appraisal based on a large data set. Molecular Ecology Resources, 14 (2), 336-343.
Dong, W. P., Xu, C., Li, C. H., Sun, J. H., Zuo, Y. J., Shi, S., . . . Zhou, S. L. (2015). ycf 1, the most promising plastid DNA barcode of land plants. Scientific Reports, 5 (1), 8348.
Edgar, R. C. (2013). UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10 (10), 996.
Edgar, R. C. (2016). UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. bioRxiv , 081257.
Fang, T., Liao, S. P., Chen, X. G., Zhao, Y. C., Zhu, Q., Cao, Y. Y., . . . Zhang, J. (2019). Forensic drowning site inference employing mixed pyrosequencing profile of DNA barcode gene (rbcL ).International Journal of Legal Medicine, 133 (5), 1351-1360.
Ferri, G., Alu, M., Corradini, B., & Beduschi, G. (2009). Forensic botany: species identification of botanical trace evidence using a multigene barcoding approach. International Journal of Legal Medicine, 123 (5), 395-401.
Habibi, S., Ahmadi, A., Behmanesh, M., Miri, A., & Tavallaie, M. (2019). Evaluation of ten SNP Markers for Human Identification and Paternity Analysis in Persian Population. Iranian Journal of Biotechnology, 17 (3), 68-71.
Hebert, P. D. N., Cywinska, A., Ball, S. L., & DeWaard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society B-Biological Sciences, 270 (1512), 313-321.
Hobern, D., & Hebert, P. D. N. (2019). BIOSCAN - Revealing Eukaryote Diversity, Dynamics, and Interactions. Biodiversity Information Science and Standards, 3 .
Irinyi, L., Lackner, M., de Hoog, G. S., & Meyer, W. (2016). DNA barcoding of fungi causing infections in humans and animals.Fungal Biology, 120 (2), 125-136.
Kakizaki, E., Sonoda, A., Sakai, M., & Yukawa, N. (2018). Simple detection of bacterioplankton using a loop-mediated isothermal amplification (LAMP) assay: First practical approach to 72 cases of suspected drowning. Forensic Science International, 289 , 289-303.
Kress, W. J., & Erickson, D. L. (2007). A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-CodingtrnH-psbA Spacer Region. Plos One, 2 (6).
Li, D. Z., Gao, L. M., Li, H. T., Wang, H., Ge, X. J., Liu, J. Q., . . . Grp, C. P. B. (2011). Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proceedings of the National Academy of Sciences of the United States of America, 108 (49), 19641-19646.
Li, J. L., Wang, S. S., Yu, J., Wang, L., & Zhou, S. L. (2013). A modified CTAB protocol for plant DNA extraction. Chinese Bulletin of Botany , 48(1), 72-78.
Liu, M. Y., Liu, Y. L., Wu, P., Chen, Q., & Zhou, S. L. (2019). Determination of Place of Residence Using the Gene Information of Plants Carried by the Human Body. Journal of Forensic Medicine, 35 (6), 710-715.
Liu, M. Y., Zhao, Y., Sun, Y. Z., Li, Y. N., Wu, P., Zhou, S. L., & Ren, L. (2020). Comparative study on diatom morphology and molecular identification in drowning cases. Forensic Science International, 317 , 110552.
Liu, M. Y., Zhao, Y., Sun, Y. Z., Wu, P., Zhou, S. L., & Ren, L. (2020). Diatom DNA barcodes for forensic discrimination of drowning incidents. Fems Microbiology Letters, 367 (17).
Liu, Y. L., Xu, C., Sun, Y. Z., Wu, P., Dong, W. P., Yang, X. Y., & Zhou, S. L. (2021). Method for quick DNA barcode reference library construction. Journal of Systematics and Evolution , underview.
Lou, S. K., Wong, K. L., Li, M., But, P. P. H., Tsui, S. K. W., & Shaw, P. C. (2010). An integrated web medicinal materials DNA database: MMDBD (Medicinal Materials DNA Barcode Database). Bmc Genomics, 11 .
Lygo, J. E., Johnson, P. E., Holdaway, D. J., Woodroffe, S., Whitaker, J. P., Clayton, T. M., . . . Gill, P. (1994). The Validation of Short Tandem Repeat (Str) Loci for Use in Forensic Casework.International Journal of Legal Medicine, 107 (2), 77-89.
Meng, H. T., Guo, Y. X., Jin, X. Y., Chen, C., Cui, W., Shi, J. F., . . . Zhu, B. F. (2019). Internal validation study of a newly developed 24-plex Y-STRs genotyping system for forensic application.International Journal of Legal Medicine, 133 (3), 733-743.
Prodan, A., Tremaroli, V., Brolin, H., Zwinderman, A. H., Nieuwdorp, M., & Levin, E. (2020). Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing. Plos One, 15 (1).
Ratnasingham, S., & Hebert, P. D. N. (2007). BOLD: The Barcode of Life Data System (www.barcodinglife.org).Molecular Ecology Notes, 7 (3), 355-364.
Ravi, K., Patel, Mukesh, & Jain. (2012). NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data. Plos One .
Rousseau, D. D., Schevin, P., Duzer, D., Cambon, G., Ferrier, J., Jolly, D., & Poulsen, U. (2006). New evidence of long distance pollen transport to southern Greenland in late spring. Review of Palaeobotany and Palynology, 141 (3-4), 277-286.
Shenhav, L., Thompson, M., Joseph, T. A., Briscoe, L., Furman, O., Bogumil, D., . . . Halperin, E. (2019). FEAST: fast expectation-maximization for microbial source tracking. Nature Methods, 16 (7), 627.
Thomsen, P. F., & Willerslev, E. (2015). Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation, 183 , 4-18.
Thorne, R. F. (2002). How many species of seed plants are there?Taxon, 51 (3), 511-512.
Tnah, L. H., Lee, S. L., Tan, A. L., Lee, C. T., Ng, K. K. S., Ng, C. H., & Nurul Farhanah, Z. (2019). DNA barcode database of common herbal plants in the tropics: a resource for herbal product authentication.Food Control, 95 , 318-326.
Xiong, W., & Zhan, A. B. (2018). Testing clustering strategies for metabarcoding-based investigation of community–environment interactions. Molecular Ecology Resources, 18 (6), 1326-1338.
Xu, C., Dong, W. P., Shi, S., Cheng, T., Li, C., Liu, Y. L., . . . Zhou, S. L. (2015). Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques. Molecular Ecology Resources, 15 (6), 1366-1374.
Yang, X. Y., Song, B. K., Pei, L., & Song, J. Y. (2015). DNA barcoding analysis of plant evidence. Chinese Journal of Forensic Medicine, 30 (2), 189-190.
Young, J. M., Austin, J. J., & Weyrich, L. S. (2017). Soil DNA metabarcoding and high-throughput sequencing as a forensic tool: considerations, potential limitations and recommendations. Fems Microbiology Ecology, 93 (2).
Yu, J., Xue, J. H., & Zhou, S. L. (2011). New universal matKprimers for DNA barcoding angiosperms. Journal of Systematics and Evolution, 49 (3), 176-181.
[dataset] Liu, Y. L; 2020; Determination of a criminal suspect using environmental plant DNA metabarcoding technology; NCBI; SRR13203136.