Zhichai Integrity Report — "Chloroplast Genome Characteristics and Comparative Analysis of Nine Actinidia Species from Guizhou" (DOI: 10.11931/guihaia.gxzw202512031)

Academic fraud report · Geng Detector

Summary

Verdict: Highly suspicious. A routine comparative chloroplast genomics preprint exhibits multiple independent integrity issues. (1) Table 2 arithmetic inconsistency: for A. chinensis var. deliciosa, the sum LSC (88,149) + 2×IR (2×23,542 = 47,084) + SSC (20,331) = 155,564 bp, but the reported total length is 156,048 bp — a 484 bp discrepancy unexplained by the authors, while the other eight species reconcile exactly. (2) Reference mis-attribution in the Methods: MAFFT software is cited as Oliveira et al. 2022, which is in fact a paper on Leishmania (Viannia) shawi nasal swab infection in the Brazilian Amazon — unrelated to phylogenetics or chloroplasts. (3) Fastp is cited as Li et al. 2009, which actually describes the BWA aligner. Confidence in issues 1–3 is high given the unambiguous reporting; image reuse could not be assessed due to text-only PDF. Final determination requires editorial investigation and access to the original assembly data to resolve the 484 bp gap.

Verdict

Highly suspicious based on a correctly-solvable arithmetic inconsistency in core genomic data and demonstrably erroneous software citations. The combination of these distinct issues across data presentation and methods writing points to careless preparation, template reuse, or worse.

Key findings

Arithmetic inconsistency in Table 2 (A. chinensis var. deliciosa): Reported total length (156,048 bp) does not match the sum of the component regions (LSC 88,149 + 2×IR 23,542 + SSC 20,331 = 155,564 bp). The 484 bp discrepancy is not present in the other eight species, which all reconcile correctly.
Cross-domain citation error (MAFFT): The MAFFT multiple alignment tool is cited as Oliveira et al. 2022. The cited reference is *"First report of an asymptomatic Leishmania (Viannia) shawi infection using a nasal swab in Amazon, Brazil"* — a parasitology/epidemiology paper unrelated to chloroplast genomics or sequence alignment. The correct citation for MAFFT is Katoh et al.
Software reference mis-attribution (Fastp): Fastp quality control is cited as Li et al. 2009. The cited reference is the BWA aligner paper (*Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 2009*). The correct Fastp citation is Chen et al. 2018.
Impossible to assess image integrity: Figures 1–7 could not be examined at pixel level from the text-extracted PDF.

Evidence highlights

| Item | Reported value | Expected/explained value | Delta | |---|---|---|---| | LSC (A. chinensis var. deliciosa) | 88,149 bp | — | — | | IR (single copy) | 23,542 bp → ×2 = 47,084 bp | — | — | | SSC | 20,331 bp | — | — | | Computed total | — | 155,564 bp | — | | Reported total | 156,048 bp | — | +484 bp |

Controls: the other eight *Actinidia* taxa in Table 2 reconcile exactly with LSC + 2×IR + SSC.

cited-but-mismatched references:

Oliveira et al., 2022 → nasal swab detection of *Leishmania (Viannia) shawi*, *Int. J. Environ. Res. Public Health* (not MAFFT).
Li et al., 2009 → BWA aligner, *Bioinformatics* (not Fastp).

Notes

DOI: 10.11931/guihaia.gxzw202512031 (preprint, current date 2026-06-03).
Issues 1–3 are independently verifiable from the PDF text and reference list; image-based checks (duplication, splicing, rotation) were not possible and are flagged as untested.
The 484 bp gap could in principle reflect an unannotated region, an alternative IR boundary, or a typographic/compilation error, but the asymmetry across the nine species suggests the report itself is inconsistent with its own definitions. Editorial examination of the original assembly and annotated GenBank files is recommended.
All findings are derived from the text-extracted PDF; no result has been independently re-sequenced or re-assembled here.
This report is AI-assisted and intended for discussion only; final determinations of misconduct require institutional or editorial investigation.