3.1 | Number of in silico mate-pair libraries
using single or multiple references
Mate-pair libraries were generated using multiple reference genomes from
the same genus, family, and order of target species. The quantities of
mate-pair read pairs were counted (Table S7-S8). Referring to mate pairs
generated for C. batrachus , the maximum number of in
silico mate-pair reads was generated using C. magur(600,254,032, same genus) as a reference, and even more using theC. macrocephalus genome as a reference (349,115,222, same genus).
Using A. melas (different genus but same order) as a reference
produced the minimum number of mate pairs (7,048,651). Similar results
were found for in silico mate-pair generation of T.
bimaculatus using different references. Using T. rubripes andT. flavidus as references produced more mate pairs (T.
rubripes : 268,610,220, T. flavidus : 386,830,523, respectively;
same genus) than using T. nigroviridis as a reference
(10,334,324, same family), while using M. mola as a reference
genome produced the minimum number of mate pairs (M. mola :
1,059,534, same order).
The quantities of conserved mate pairs generated using two references
(mag_mac**: 133,670,922) were greater than those obtained using three
references (mag_mac_mel**: 4,474,485) (Table S7). Similar results were
found for the number of conserved mate pairs generated for T.
bimaculatus. Using four references (two from the same genus, one same
family, and one same order) produced fewer number of mate pairs than
using three references or two (rub-fla-nig-mol**: 360,635,
rub-fla-nig**: 7,038,839, rub-fla**: 121,858,574) (Table S8). The number
of conserved in silico mate-pair libraries with different insert
sizes for different target species are shown (Tables S7-S9). The number
of mate pairs was found to decrease with the application of more
reference genomes.