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.