# Ceroxyloideae WGS tBLASTn Analysis
# MBE manuscript — Ceroxyloideae PEPC characterization
# Generated 2026-07-06

## Data sources
- Ravenea rivularis: SRR15672934, 20,942,500 paired-end reads, ~1.3× coverage
- Pseudophoenix vinifera: ERR9229902, 1,568,224 paired-end reads, ~0.2× coverage

## Query set
70 PEPC protein sequences: 65 palm PEPC + 5 PPC-type references
(maize PEPC1 NP_001105438, rice PEPC1, Arabidopsis PEPC1, maize PEPC2, Arabidopsis PEPC2)

## tBLASTn parameters
- E-value threshold: 1×10⁻⁵
- Minimum alignment length for PEPC domain identification: 100 aa (E < 1×10⁻¹⁰)

## Results (R. rivularis)
- Total tBLASTn hits: 28,537 (all queries, E < 1×10⁻⁵)
- Unique PEPC-positive reads: 700
- Reads matching any reference query: 62
- Cross-reacting reads (match all 5 queries): 45 (72.6%)
- Reads matching only maize PEPC1: 5
  - Alignment length: 23–33 aa
  - E-value: 1×10⁻⁶–5×10⁻⁶
  - Below PEPC domain threshold (100 aa, E < 1×10⁻¹⁰)
  - Do not cover Ser774 phosphorylation motif
  - Conclusion: non-functional alignments to conserved catalytic core

## Results (P. vinifera)
Identical pattern — PEPC present, C4-type PEPC1 absent.

## Conclusion
Both Ceroxyloideae species harbor PEPC but lack PEPC1.
Five subfamilies, zero PEPC1.