Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads

Table 2 A partial list of P. jirovecii full-length msg isoforms (~3 kb) identified in a clinical sample by PacBio sequencing and clustering-based analysis

Contig no.	Length (bp)	Matched msg gene	Status	Identity to the known (%)	PCR verification
Contig0020	3086	EF371022	Known	98.92	ND
Contig0007	3086	EF371023	Known	99.87	ND
Contig0021	3008	EF371024	Known	99.83	ND
Contig0025	3011	EF371025	Known	99.60	ND
Contig0133	3068	EF371026	Known	99.71	ND
Contig0022	3104	EF371028	Known	99.58	ND
Contig0006	3062	EF371029	Known	99.97	ND
Contig0008	3041	EF371030	Known	99.87	ND
Contig0026	3032	EF371031	Known	98.76	ND
Contig0012	3005	EF371032	Known	99.70	ND
Contig0013	2996	EF371033	Known	99.87	ND
Contig0011	3092	EF371035	Known	99.88	ND
Contig0003	3038	EF371036	Known	99.97	ND
Contig0005	3002	EF371038	Known	99.90	ND
Contig0010	2996	EF371040	Known	99.80	ND
Contig0015	3129	EF371041	Known	99.78	ND
Contig0001	3002	EF371042	Known	99.37	ND
Contig0027	3065	EF371045	Known	99.64	ND
Contig0014	3077	EF371050	Known	99.71	ND
Contig0018	3044	EF371051	Known	99.70	ND
Contig0009	3029	EF371052	Known	99.87	ND
Contig0017	3023	EF371053	Known	99.50	ND
Contig0016	3050	EF371055	Known	99.84	ND
Contig0004	3026	EF371056	Known	99.97	ND
Contig0010b	3060	No	Novel	NA	99.53
Contig0004b	3086	No	Novel	NA	99.45
Contig0015b	3039	No	Novel	NA	99.20
Contig0053b	3077	No	Novel	NA	98.91
Contig0006b	3062	No	Novel	NA	98.50
Contig0054b	3074	No	Novel	NA	98.32
Contig0138b	3041	No	Novel	NA	ND

A total of 72 unique msg isoforms identified in this study, with only 31 of them shown in this table. The first 24 contigs matched in full-length with the 24 previously identified msg genes from the same clinical sample [22] as shown in the third column with GenBank accession no, NA not applicable, ND not determined by PCR. Additional file 4 contains a complete list of sequences for 72 Msg isoforms

ISSN: 1756-0381