Data on the exon-intron organization of genes coding for B-cell receptor-like proteins.

B-cell receptor-associated protein (BAP) family plays important roles in the ER homeostasis and stress responses of eukaryotic cells [1]. We reported the analysis of plant BAP-like (PBL) genes and the encoded proteins of higher land plants [2]. The origin and functional divergence of these genes among all eukaryotes, however, are poorly studied, which impedes our understanding of the functional relationships and diversity among BAP-like proteins. One possible reason for the potential functional diversity may be the differences in the exon-intron structure of PBL genes. In this study, we first performed analysis of the exon-intron organization of these genes in the genome sequences of the Viridiplantae species in addition to previously published data on Angiosperms [2]. To further address the distribution of BAP-like genes in other eukaryotes, we extended our dataset to include the representative genes encoded by non-plant bikonts and unikonts [3].

Specifications Table

Value of the data

The BAP-like genes are usually combined in small gene families and encoded by all well-studied eukaryotic taxons belonging to bikonts and unikonts.

Data on BAP-like gene organizations enable researchers to compare how these genes evolved during progression of different eukaryotic branches resulted, particularly, in appearance of mammals and flowering plants.

Data on BAP-like proteins and genes are intriguing to understand their unique features in different taxons.

Data on gene organizations enable researchers to infer the possible ranges of time frames in the drastic divergence events (particularly, intron gain and loss) of BAP-like genes.

Data and experimental design

Annotation information was obtained for 29 representative genes in bikonts (Table 1) and 81 genes in unikonts (Table 2) [[1], [2], [3]]using Blast2GO program.

Table 1

Features of BAP-like proteins and genes in the selected Biconta speciesa.

Species name	Features of proteins and genes
NCBI accession number	Taxon	Protein length	ProteinpI	Number of introns	Length of introns
Amborella trichopoda (NW_006496807)	Magnoliophyta Amborellales	220 aa	9.18	1	19293 bp
Amborella trichopoda (NW_006499207)	Magnoliophyta Amborellales	220 aa	9.88	1	14781 bp
Pinus lambertiana (LMTP010039273)	Acrogymnospermae Pinales	228 aa	9.61	1	82221 bp
Pseudotsuga menziesii (LPNX010213588)	Acrogymnospermae Pinales	228 aa	9.59	1	71087 bp
Pinus taeda (APFE020507172)	Acrogymnospermae Pinales	230 aa	9.37	1	66410 bp
Selaginella moellendorffii (NW_003314330)	Lycopodiopsida Selaginellales	233 aa	9.46	1	68 bp
Physcomitrella patens (XP_001766710)	Bryopsida Funariales	257 aa	9.40	2	222 bp; 71 bp
Sphagnum fallax (Sphfalx0532s0001b)	Sphagnopsida Sphagnales	238 aa	9.58	2	996 bp; 329 bp
Sphagnum fallax (Sphfalx0012s0168b)	Sphagnopsida Sphagnales	238 aa	9.58	2	992 bp; 329 bp
Sphagnum fallax (Sphfalx0223s0006b)	Sphagnopsida Sphagnales	213 aa	9.90	2	1010 bp; 331 bp
Sphagnum fallax (Sphfalx0012s0164b)	Sphagnopsida Sphagnales	210 aa	9.28	2	1013 bp; 331 bp
Marchantia polymorpha (OAE31879)	Marchantiopsida Marchantiales	189 aa	5.91	2	140 bp 681 bp
Klebsormidium flaccidum (BANV01001480)	Klebsormidiophyceae Klebsormidiales	247 aa	8.67	2	487 bp 330 bp
Chlorella variabilis (XP_005842886)	Chlorophyta Chlorellales	291 aa	5.64	5	176 bp 191 bp 98 bp 189 bp 255 bp
Chlamydomonas reinhardtii (XP_005842886)	Chlorophyta Chlamydomonadales	259 aa	9.11	5	291 bp 264 bp 327 bp 352 bp 171 bp
Monoraphidium neglectum (XP_013903892)	Chlorophyta Sphaeropleales	232 aa	9.48	3	182 bp 190 bp 243 bp
Volvox carteri (XP_002952600)	Chlorophyta Chlamydomonadales	255 aa	9.30	4	166 bp 752 bp 2055 bp 434 bp
Galdieria sulphuraria (XP_002952600)	Rhodophyta Cyanidiales	254 aa	9.91	4	46 bp 51 bp 56 bp 53 bp
Phytophthora infestans (XP_002898022)	Oomycetes Peronosporales	275 aa	5.60	1	114 bp
Saprolegnia diclina (XP_008621469)	Oomycetes Saprolegniales	268 aa	6.75	2	51 bp 47 bp
Aphanomyces invadans (XP_008869471)	Oomycetes Saprolegniales	270 aa	6.32	2	53 bp 88 bp
Albugo candida (CCI47927)	Oomycetes Albuginales	281 aa	7.62	3	49 bp 30 bp 57 bp
Guillardia theta (XP_005830762)	Cryptophyta Pyrenomonadales	200 aa	8.78	8	51 bp 158 bp 49 bp 47 bp 45 bp 50 bp 47 bp 51 bp
Nannochloropsis gaditana (EWM21023)	Eustigmatophyceae Eustigmatales	261 aa	9.78	2	160 bp 263 bp
Ectocarpus siliculosus (CBN78175)	Phaeophyceae Ectocarpales	141 aa	10.28	3	782 bp 1315 bp 1091 bp
Plasmodium fragile (XP_012337233)	Alveolata Aconoidasida	209 aa	9.48	0c	No introns
Toxoplasma gondii (KYF38827)	Alveolata Conoidasida	290 aa	9.39	0	No introns
Perkinsus marinus (XP_002786272)	Alveolata Perkinsida	188 aa	6.33	4	48 bp 59 bp 457 bp 200 bp
Bodo saltans (CUF18891)	Euglenozoa Kinetoplastida	163 aa	10.14	0	No introns

Amborella trichopoda is included as most basal Angiosperm representative.

Phytozome accession number.

Only introns in the protein coding region are counted.

Table 2

Features of BAP-like proteins and genes in the selected Uniconta species.

Species name	Features of proteins and genes
NCBI accession number	Taxon	Protein length	ProteinpI	Number of introns	Length of introns
Homo sapiens BAP 31 (EAW72818)	Chordata	246 aa	8.44	6	2181 bp 5183 bp 11448 bp 901 bp 828 bp 1032 bp
	Mammalia
Homo sapiens BAP 29 (AAP35627)	Chordata	241 aa	9.55	6	3018 bp 9973 bp 1762 bp 4395 bp 2827 bp 8198 bp
	Mammalia
Bos taurus BAP31 (AC_000187)	Chordata	245 aa	9.20	6	1421 bp 3620 bp 19548 bp 856 bp 795 bp 868 bp
	Mammalia
Bos taurus BAP29 (NP_001033164)	Chordata Mammalia	240 aa	9.60	6	5274 bp 8892 bp 1426 bp 4620 bp 21723 bp 4683 bp
Egretta garzetta(NW_009259250)	Chordata Aves	243 aa	9.11	6	3508 bp 2158 bp 4591 bp 2594 bp 7753 bp 1416 bp
Anolis carolinensis(XP_003216939)	Chordata Lepidosauria	247 aa	8.74	6	1679 bp 14262 bp 4948 bp 10491 bp 6440 bp 8714 bp
Xenopus laevis BAP29 (AAH76818)	Chordata Amphibia	243 aa	9.39	6	2408 bp 1685 bp 2474 bp 795 bp 3921 bp 555 bp
Xenopus laevis BAP31 (NP_001086173)	Chordata Amphibia	244 aa	8.65	6	950 bp 4065 bp 3477 bp 273 bp 1233 bp 6242 bp
Danio rerio(AAH49014)	Chordata Actinopterygii	247 aa	8.73	6	1202 bp 1868 bp 15175 bp 18469 bp 3950 bp 12955 bp
	Teleostei
Latimeria chalumnae(XP_005999374)	Chordata Actinopterygii	246 aa	8.90	4	10199 bp 16405 bp 1106 bp 20131 bp
	Coelacanthidae
Ciona savignyi (H2YK40a)	Chordata Tunicata Ascidiacea	251 aa	6.84	6	1005 bp 789 bp 570 bp 469 bp 226 bp 1015 bp
Oikopleura dioica(CBY14290)	Chordata Tunicata Appendicularia	235 aa	7.61	4	179 bp 47 bp 58 bp 47 bp
Branchiostoma floridae(XP_002606682)	Chordata Cephalochordata Branchiostomidae	242 aa	6.98	6	512 bp 3061 bp 1594 bp 869 bp 450 bp 598 bp
Strongylocentrotus purpuratus(XP_791898)	Echinodermata Eleutherozoa Echinozoa	161 aa	7.76	3	386 bp 826 bp 715 bp
Capitella teleta(ELU03196)	Lophotrochozoa Annelida Polychaeta	236 aa	8.87	5	52 bp 105 bp 732 bp 3501 bp 54 bp
Helobdella robusta(XP_009022177)	Lophotrochozoa Annelida Clitellata	234 aa	9.22	6	144 bp 249 bp 91 bp 3212 bp 116 bp 176 bp
Lingula anatine(XP_013411827)	Lophotrochozoa Brachiopoda Linguliformea	244 aa	6.56	7	10030 bp 354 bp 2478 bp 123 bp 243 bp 209 bp 242 bp
Crassostrea gigas(XP_011435954)	Lophotrochozoa Mollusca Bivalvia	237 aa	7.57	6	819 bp 2358 bp 677 bp 403 bp 613 bp 776 bp
Aplysia californica(XP_005090966)	Lophotrochozoa Mollusca Gastropoda	246 aa	6.25	5	1043 bp 921 bp 5421 bp 332 bp 1603 bp
Lottia gigantea(XP_009058881)	Lophotrochozoa Mollusca Gastropoda	237 aa	9.19	6	611 bp 1442 bp 446 bp 1115 bp 433 bp 591 bp
Biomphalaria glabrata(XP_013084046)	Lophotrochozoa Mollusca Gastropoda	244 aa	6.41	5	988 bp 3021 bp 808 bp 146 bp 499 bp
Octopus bimaculoides(XP_014771618)	Lophotrochozoa Mollusca Cephalopoda	240 aa	9.24	0	No introns
Philodina roseola(ACI90387)	Lophotrochozoa Rotifera Bdelloidea	250 aa	9.44	6	73 bp 60 bp 50 bp 63 bp 95 bp 68 bp
Clonorchis sinensis(GAA53952)	Platyhelminthes Trematoda	256 aa	7.80	7	345 bp 52 bp 4525 bp 415 bp 2538 bp 3249 bp 3650 bp
	Opisthorchiida
Dictyocaulus viviparous(KJH45191)	Ecdysozoa Nematoda Rhabditida	221 aa	8.71	5	171 bp 78 bp 68 bp 50 bp 186 bp
Caenorhabditis elegans(NP_500267)	Ecdysozoa Nematoda Rhabditida	213 aa	9.55	2	109 bp 55 bp
Ascaris suum(ERG85477)	Ecdysozoa Nematoda Ascaridida	235 aa	6.23	6	1187 bp 1089 bp 270 bp 626 bp 711 bp 315 bp
Wuchereria bancrofti(EJW86459)	Ecdysozoa Nematoda Spirurida	210 aa	8.80	5	94 bp 121 bp 190 bp 209 bp 216 bp
Ixodes scapularis(XP_002403043)	Ecdysozoa Arthropoda Acari	243 aa	9.08	7	106 bp 1304 bp 319 bp 248 bp 1219 bp 1795 bp 4918 bp
Parasteatoda tepidariorum(XP_015910252)	Ecdysozoa Arthropoda Araneae	236 aa	8.69	6	2745 bp 2307 bp 2605 bp 2023 bp 2331 bp 7025 bp
Limulus polyphemus(XP_013785233)	Ecdysozoa Arthropoda Merostomata	233 aa	8.39	6	5228 bp 3518 bp 2708 bp 673 bp 10338 bp 1550 bp
Daphnia pulex(EFX80917)	Ecdysozoa Arthropoda Crustacea	236 aa	7.80	4	70 bp 95 bp 62 bp 62 bp
Hyalella azteca(XP_018009243)	Ecdysozoa Arthropoda Crustacea	222 aa	8.84	3	502 bp 354 bp 224 bp
Orchesella cincta(ODM98038)	Ecdysozoa Arthropoda Hexapoda Entomobryomorpha	226 aa	9.34	4	100 bp 78 bp 83 bp 83 bp
Bombyx mori(XP_004923642)	Ecdysozoa Arthropoda Hexapoda Insecta	224 aa	8.51	0	No introns
	Lepidoptera
Papilio machaon(XP_014360347)	Ecdysozoa Arthropoda Hexapoda Insecta	222 aa	7.77	0	No introns
	Lepidoptera
Plutella xylostella(XP_011563833)	Ecdysozoa Arthropoda Hexapoda Insecta Lepidoptera	223 aa	8.81	0	No introns
Agrilus planipennis(XP_018325264)	Ecdysozoa Arthropoda Hexapoda Insecta Coleoptera	228 aa	8.89	3	60 bp 63 bp 719 bp
Nicrophorus vespilloides(XP_017778042)	Ecdysozoa Arthropoda Hexapoda Insecta Coleoptera	230 aa	9.22	2	101 bp 57 bp
Tribolium castaneum(XP_015833546)	Ecdysozoa Arthropoda Hexapoda Insecta Coleoptera	238 aa	9.37	3	47 bp 1864 bp 50 bp
Drosophila elegans(XP_017127683)	Ecdysozoa Arthropoda Hexapoda Insecta Diptera	228 aa	9.04	1	968 bp
Aedes albopictus(KXJ82346)	Ecdysozoa Arthropoda Hexapoda Insecta Diptera	232 aa	9.46	2	9892 bp 208 bp
Musca domestica(XP_005189051)	Ecdysozoa Arthropoda Hexapoda Insecta Diptera	233 aa	6.86	1	6715 bp
Limnephilus lunatus(JDSM01012005)	Ecdysozoa Arthropoda Hexapoda Insecta Trichoptera	230 aa	9.02	0	No introns
Apis mellifera(XP_397055)	Ecdysozoa Arthropoda Hexapoda Insecta Hymenoptera	229 aa	6.92	1	128 bp
Solenopsis invicta(XP_011173333)	Ecdysozoa Arthropoda Hexapoda Insecta Hymenoptera	232 aa	9.46	1	78 bp
Polistes dominula(XP_015172100)	Ecdysozoa Arthropoda Hexapoda Insecta Hymenoptera	234 aa	9.14	1	571 bp
Zootermopsis nevadensis(KK853387)	Ecdysozoa Arthropoda Hexapoda Insecta Isoptera	231 aa	6.54	0	No introns
Acyrthosiphon pisum(NP_001155477)	Ecdysozoa Arthropoda Hexapoda Insecta Hemiptera	212 aa	7.90	0	No introns
Pediculus humanus corporis(XP_002429237)	Ecdysozoa Arthropoda Hexapoda Insecta Phthiraptera	224 aa	9.32	3	436 bp 92 bp 216 bp
Homalodisca liturata(GECU01024317)	Ecdysozoa Arthropoda Hexapoda Insecta Hemiptera	229 aa	8.89	0	No introns
Exaiptasia pallida(KXJ12234)	Cnidaria Anthozoa Hexacorallia Actiniaria	245 aa	6.39	5	167 bp 801 bp 134 bp 69 bp 454 bp
Acropora digitifera(XP_015771945)	Cnidaria Anthozoa Hexacorallia Scleractinia	178 aa	4.93	5	114 bp 528 bp 3385 bp 456 bp 748 bp
Hydra vulgaris(XP_004209484)	Cnidaria Hydrozoa	242 aa	9.32	4	5752 bp 18903 bp 9438 bp 75 bp
Intoshia linei(OAF65985)	Mesozoa Orthonectida	220 aa	9.62	1	44 bp
Trichoplax adhaerens(XP_002113615)	Placozoa Trichoplax	167 aa	9.34	3	1456 bp 340 bp 267 bp
Amphimedon queenslandica(XP_011406596)	Porifera Demospongiae	172 aa	6.21	5	63 bp 1057 bp 47 bp 54 bp 107 bp
Monosiga brevicollis(XP_001745234)	Choanoflagellida Codonosigidae	230 aa	9.04	4	189 bp 125 bp 139 bp 98 pb
Salpingoeca rosetta(XP_004993388)	Choanoflagellida Salpingoecidae	185 aa	9.74	5	143 bp 251 bp 250 bp 239 bp 162 bp
Capsaspora owczarzaki(XP_004345792)	Ichthyosporea Capsaspora	216 aa	9.43	6	151 bp 181 bp 87 bp 96 bp 171 bp 103 bp
Fonticula alba(XP_009495214)	Nucleariidae and Fonticula group	226 aa	9.24	6	109 bp 176 bp 115 bp 148 bp 313 bp 232 bp
Saccharomyces cerevisiae Yet3p (AJU84316)	Fungi Dikarya Ascomycota Saccharomycotina	203 aa	5.93	0	No introns
Candida glabrata(XP_445444)	Fungi Dikarya Ascomycota Saccharomycotina	191 aa	9.37	0	No introns
Penicillium italicum(KGO75036)	Fungi Dikarya Ascomycota Pezizomycotina	210 aa	9.13	3	140 bp 57 bp 57 bp
Aspergillus calidoustus(CEN62854)	Fungi Dikarya Ascomycota Pezizomycotina	213 aa	8.91	3	66 bp 51 bp 125 bp
Mycena chlorophos(GAT59077)	Fungi Dikarya Basidiomycota Agaricomycotina	208 aa	9.36	6	55 bp 54 bp 54 bp 50 bp 57 bp 52 bp
Ustilago maydis(XP_011388692)	Fungi Dikarya Basidiomycota Ustilaginomycotina	192 aa	9.42	2	82 bp 95 bp
Allomyces macrogynus(KNE58291)	Fungi Blastocladiomycota Blastocladiomycetes	239 aa	6.99	4	81 bp 73 bp 80 bp 73 bp
Spizellomyces punctatus(XP_016610704)	Fungi Chytridiomycota Chytridiomycetes	210 aa	9.33	9	72 bp 72 bp 61 bp 78 bp 46 bp 64 bp 64 bp 57 bp 62 bp
Gonapodya prolifera(KXS12654)	Fungi Chytridiomycota Monoblepharido- mycetes	197 aa	7.89	6	66 bp 65 bp 76 bp 60 bp 64 bp 64 bp
Conidiobolus coronatus(KXN68246)	Fungi Entomophthoro-mycota	207 aa	7.75	6	63 bp 42 bp 53 bp 54 bp 58 bp 52 bp
Rhizophagus irregularis(ESA18893)	Fungi Glomeromycota Glomeromycetes	211 aa	7.77	8	85 bp 87 bp 72 bp 66 bp 68 bp 72 bp 81 bp 77 bp
Encephalitozoon intestinalis(XP_003072841)	Fungi Microsporidia Unikaryonidae	199 aa	9.34	0	No introns
Edhazardia aedis(EJW03664)	Fungi Microsporidia Edhazardia	192 aa	9.68	0	No introns
Nosema bombycis(EOB11729)	Fungi Microsporidia Nosematidae	197 aa	9.30	0	No introns
Thecamonas trahens(XP_013761453)	Apusozoa Apusomonadidae	150 aa	9.75	1	427 bp
Entamoeba invadens(XP_004260006)	Amoebozoa Archamoebae Entamoebidae	167 aa	6.59	1	121 bp
Acanthamoeba castellanii(XP_004337423)	Amoebozoa Discosea Longamoebia	223 aa	6.06	2	100 bp 280 bp
Polysphondylium pallidum(EFA82930)	Amoebozoa Mycetozoa Dictyosteliida	206 aa	9.40	0	No introns
Acytostelium subglobosum(XP_012752758)	Amoebozoa Mycetozoa Dictyosteliida	203 aa	9.40	0	No introns
Dictyostelium lacteum(KYR02632)	Amoebozoa Mycetozoa Dictyosteliida	206 aa	9.37	0	No introns

UniProt (http://www.uniprot.org/) accession number.

Materials and methods

Annotation of the predicted genes and proteins was mined at the National Center for Biotechnology Information database (NCBI) and Phytozome database, version 11. Additional annotation of other predicted BAP-like proteins and genes was extracted from The UniProt Knowledgebase database (http://www.uniprot.org/).

Subject area	Biology
More specific subject area	Phylogenomics
Type of data	Table
How data was acquired	Gene sequence organizations and protein parameters were derived using ExPASy software, NCBI, Dendrome and Phytozome databases (see below)
Data format	Analyzed
Experimental factors	Amino acid and nucleotide sequences were retrieved from NCBI, Dendrome and Phytozome databases (see below).
Experimental features	Gene and protein sequences were derived using NCBI, Dendrome and Phytozome databases (see below)
Data source location	NCBI: http://www.ncbi.nlm.nih.gov/
	Phytozome v11: http://www.phytozome.net/
	ExPASy: http://www.expasy.org/tools/
	Dendrome: http://dendrome.ucdavis.edu/
Data accessibility	With this article