Fig 1.
Schematic diagram of the CDR3 (AA)-relative analysis and in-frame percent (ORF) statistics.
a-c The CDR3-related analysis of the NO.1, NO.2, and NO.3 camels including CDR3 length (AA) and proportion; d The comparison of in-frame percent of antibody variable region genes between VH and VHH clones of three camels.
Table 1.
Sequencing data overview of three camel samples.
Fig 2.
Box plots of the unique sequence numbers of each sub-region and diversity evaluation.
Unique number represents the number of unique sequences within the reads. a The unique number of sub-regions including FR1, CDR1, FR2, CDR2, FR3, CDR3, and FR4 in three samples. b Diversity evaluation using the normalized unique number by length, which equals to unique number divided by average length of each sub-region. Box plot explanation: upper horizontal line of box, 75th percentile; lower horizontal line of box, 25th percentile; horizontal bar within box, the median of the three samples’ data; upper end of the whisker, maximum of the three samples’ data; lower end of the whisker, minimum of the three samples’ data.
Fig 3.
Box plots of the mutation rate analysis.
a The mutation rates of each sub-region including FR1, CDR1, FR2, CDR2, FR3, and FR4 in three samples before filtering. Mutations are defined as mismatches with the IMGT references on each sample’s sequences. b The mutation rates of each sub-region including FR1, CDR1, FR2, CDR2, FR3, and FR4 in three samples after filtering. c Statistics of specific nucleic acid mutations of the VH and VHH clones before filtering. d Statistics of specific nucleic acid mutations of the VH and VHH clones after filtering. Box plot explanation: upper horizontal line of box, 75th percentile; lower horizontal line of box, 25th percentile; horizontal bar within box, the median of the three samples’ data; upper end of the whisker, maximum of the three samples’ data; lower end of the whisker, minimum of the three samples’ data.
Fig 4.
Amino acids frequency distribution of each position for VH and VHH clones.
The horizontal axis lists the actual positions of the amino acids in IMGT references of the Arabian camel. The vertical axis lists abbreviations of twenty different amino acids. The circles denote VH clones and the triangles, VHHs. The size represents the proportion of clone number. The asterisk-labeled positions represent the amino acids which have little consistency between VH and VHH clones.
Table 2.
Specific amino acids differences between VH and VHH clones of three camels.
Fig 5.
Box plots of the distribution and proportion of Cys codons in VH and VHH clones.
The distribution and proportion of Cys codons (TGC and TGT) in each sub-region including FR1, CDR1, FR2, CDR2, FR3, CDR3, and FR4 in three samples was plotted. The percent equals to the total number of Cys codons divided by the total number of codons in each sub-region. Box plot explanation: upper horizontal line of box, 75th percentile; lower horizontal line of box, 25th percentile; horizontal bar within box, the median of the three samples’ data; upper end of the whisker, maximum of the three samples’ data; lower end of the whisker, minimum of the three samples’ data.
Fig 6.
Box plots of the analysis of non-classical VHH clones.
a The percentage of Trp-clones and Arg-clones (the clones whose first AA of FR4 are Trp and Arg) for classical VHH, non-classical VHH and VH(3) family clones. b Statistics of Cys codons within the Trp-clones and Arg-clones for classical VHH, non-classical VHH, and VH(3) family clones. c The average CDR3 length statistics of Trp-clones and Arg-clones for classical VHH, non-classical VHH and VH(3) family clones. d-f The proportion distribution of CDR3 average length of Trp-clones and Arg-clones. FR4_1st_AA represents the first AA of FR4 sub-region. Classical VHH represents the VHH having four FR2 hallmark amino acids. Non-classical VHH represents the VHH lacking four FR2 hallmark amino acids. VH represents the VH(3) (clan III) family clones. Box plot explanation: upper horizontal line of box, 75th percentile; lower horizontal line of box, 25th percentile; horizontal bar within box, the median of the three samples’ data; upper end of the whisker, maximum of the three samples’ data; lower end of the whisker, minimum of the three samples’ data.