A chromosome-level, haplotype-resolved genome assembly of the impressed tortoise, Manouria impressa

Background. The impressed tortoise, Manouria impressa (Gunther, 1882), is an Endangered, largely fungivorous tortoise of the montane forests of Southeast Asia and one of the two living species of the basal testudinid genus Manouria. It is one of the least-studied tortoises, and no chromosome-level genome was available for the genus. Findings. From 68.5 Gb of PacBio HiFi reads (28x), 9.8 Gb of Hi-C read pairs and RNA-seq of heart and lung from a single female, we assembled a 2.42 Gb primary assembly with a contig N50 of 86.9 Mb and a scaffold N50 of 138.6 Mb. Hi-C scaffolding followed by quantitative curation -- every scaffold join scored against the within-contig contact-decay expectation -- placed 94.5 % of the sequence in 26 chromosomes, matching the testudinid karyotype (2n = 52); the remaining 335 scaffolds are unplaced. Consensus accuracy is QV 67.9 (Merqury), k-mer completeness 95.1 %, and 99.3 % of vertebrate BUSCO genes are complete. Two phased haplotype assemblies (scaffold N50 87.8 and 91.6 Mb; QV 69.1 and 68.5; 99.2 % combined k-mer completeness) and the 18.1-kb mitochondrial genome were assembled from the same data. Repeats mask 48.6 % of the genome (LINEs 11.5 %, LTR retrotransposons 10.0 %, DNA transposons 7.6 %, SINEs 2.6 %, unclassified families 15.4 %); 24,875 protein-coding genes were predicted from RNA-seq and OrthoDB protein evidence (97.6 % complete vertebrate BUSCOs), 89.0 % of them functionally annotated. Conclusions. This haplotype-resolved reference, with its curation evidence and scripts, provides the first chromosome-level genomic resource for Manouria and a foundation for conservation genomics and for studies of the dietary specialisation of this fungivorous tortoise.