3.4 | Genome assemblies of mountain nyala (degenerated
DNA)
Mate-pair generation of T. buxtoni , using B. grunniens as
a reference, yielded the maximum number of mate pairs (B.
grunniens : 416,044,705) while using M. moschiferus produced the
least number of mate pairs (M. moschiferus : 220,576,118). The
number of mate pairs generated using B. grunniens (same
subfamily) as the reference genome was greater than that using T.
scriptus and T. strepsiceros (same genus) as reference genomes
(T. scriptus : 305,670,717, T. strepsiceros : 392,062,745),
and this may be attributed to the high quality of B. grunniensassembly (Table S7-S9).
The mountain nyala (T. buxtoni ) genome, which was generated with
only paired-end reads from the degenerate samples, was not well
assembled (Chen et al., 2019). The quality of the draft genome generated
without using in silico mate-pair libraries was unsatisfactory
(N50: 3.5 Kb, complete BUSCOs: 645) (Table 3). Therefore, we used the
original as well as the optimized in silico method to perform
genome assembly of the mountain nyala. The results showed that when the
original mate pairs were generated using different references (‘scr’:Tragelaphus scriptus , ‘str’: Tragelaphus strepsiceros ,
‘gru’: Bos grunniens , ‘mos’: Moschus moschiferus ), the
draft genomes were improved, showing higher contiguity (N50–scr*: 592
Kb, str*:431 Kb, gru*:2.6 M, mos*:1.5 M) and increased completeness
(Complete BUSCOs: scr*:1,956, str*:1,979, gru*:2,018, mos*:1,697).
Compared to assemblies using the in silico method, genomes
assembled using conserved mate pairs did not increase N50 (scr-str**:
203 Kb, gru-scr**: 474 Kb) or the number of complete BUSCOs (scr-str**:
1,727, gru-scr**: 1,759). Due to the low quality of the mountain nayala
genome, no good reference genome could be used to calculate the
misassembly rate.