Finding the missing honey bee genes: lessons learned from a genome upgrade

Elsik, Christine G; Worley, Kim C; Bennett, Anna K; Beye, Martin; Camara, Francisco; Childers, Christopher P; de Graaf, Dirk C; Debyser, Griet; Deng, Jixin; Devreese, Bart; Elhaik, Eran; Evans, Jay D; Foster, Leonard J; Graur, Dan; Guigo, Roderic; Hoff, Katharina Jasmin; Holder, Michael E; Hudson, Matthew E; Hunt, Greg J; Jiang, Huaiyang; Joshi, Vandita; Khetani, Radhika S; Kosarev, Peter; Kovar, Christie L; Ma, Jian; Maleszka, Ryszard; Moritz, Robin F A; Munoz-Torres, Monica C; Murphy, Terence D; Muzny, Donna M; Newsham, Irene F; Reese, Justin T; Robertson, Hugh M; Robinson, Gene E; Rueppell, Olav; Solovyev, Victor; Stanke, Mario; Stolle, Eckart; Tsuruda, Jennifer M; Vaerenbergh, Matthias Van; Waterhouse, Robert M; Weaver, Daniel B; Whitfield, Charles W; Wu, Yuanqing; Zdobnov, Evgeny M; Zhang, Lan; Zhu, Dianhui; Gibbs, Richard A

doi:10.1186/1471-2164-15-86

BMC Genomics

Table 6 Repetitive elements in the Apis mellifera genome

From: Finding the missing honey bee genes: lessons learned from a genome upgrade

Type of element	No. elements (no. chimeric/nested insert)^a	No. Ffagments (no. full length copies)^b	Genome coverage (bp)	% of genome (234.087 Mb)	A^c	B^c	C^c	D^c	E^c
Repetitive DNA			22,134,229	9.46
*NON-INTERSPERSED REPEATS*			94,86,745	4.05
SSR	29,697		1,441,651	0.62
Low complexity	31,728		8,001,104	3.42
Satellite	5 (0)	75 (6)	43,990	0.02	0	na	0	0	0
*INTERSPERSED REPEATS*	881 (65)	28,004 (1102)	12,647,484	5.40	25	7	40	2	6
*Class I - Retrotransposons*	758 (13)	21,244 (903)	9,790,204	4.18	4	1	4	0	0
LTR retrotransposons	2 (9)	42 (4)	49,549	0.02	1	1	1	0	0
Copia	1 (3)	29 (3)	43,892	0.02	0	1	1	0	0
Gypsy	0 (2)	0 (0)	0	0.00	0	0	0	0	0
Bel-Pao	0 (4)	0 (0)	0	0.00	0	0	0	0	0
Unclassified LTR retrotransposons	1 (0)	13 (1)	5,657	0.00	1	0	0	0	0
DIRS retrotransposons	2 (0)	9 (3)	12,472	0.01	0	0	2	0	0
LINE (non-LTR) Retrotransposons	3 (4)	140 (3)	83,103	0.04	2	0	1	0	0
R2 (NeSL, R2, R4, CRE)	2 (1)	112 (2)	72,107	0.03	2	0	0	0	0
Jockey (Rex, Jockey, Cr1, Kiri, L2, crack, Daphne)	0 (1)	0 (0)	0	0.00	0	0	0	0	0
I (R1, I, Nimb, outcast, Tad, Loa)	1 (1)	28 (1)	10,996	0.00	0	0	1	0	0
Unclassified LINE	0 (1)	0 (0)	0	0.00	0	0	0	0	0
SINE	19 (0)	222 (29)	69,938	0.03	0	0	0	0	0
SS-Sine	5 (0)	31 (7)	22,660	0.01	0	na	0	0	0
Unclassified SINE	14 (0)	191 (22)	47,278	0.02	0	na	0	0	0
Unclassified retrotransposons	1 (0)	2 (1)	8,526	0.00	0	na	0	0	0
LARD	301 (0)	16,406 (348)	7,256,932	3.10	1	0	0	0	0
TRIM	430 (0)	4,423 (515)	2,309,684	0.99	0	0	0	0	0
*Class II - DNA transposons*	51 (52)	3,209 (93)	1,339,131	0.57	7	6	27	2	5
TIR	50 (46)	3,200 (89)	1,335,380	0.57	7	6	27	2	5
Tc1/Mariner	43 (40)	2,636 (80)	1,147,521	0.49	5	6	25	2	5
PiggyBac	2 (6)	184 (2)	87,963	0.04	2	0	2	0	0
Unclassified TIR DNA transposons	5 (0)	380 (7)	99,896	0.04	0	na	0	0	0
Unclassified DNA-transposons	0 (6)	0 (0)	0	0.00	0	0	0	0	0
MITE	1 (0)	9 (4)	3,751	0.00	0	na	0	0	0
*Unclassified, putative elements*	72 (0)	3,551 (106)	1,518,149	0.65	14	na	9	0	1
Other DNA elements (not repetitive DNA)	158 (0)	13,760 (250)	6,934,063	2.96	17	0	0	0	0
Not categorized	6 (0)	946 (11)	1,233,884	0.53	0	na	0	0	0
Potential host gene^d	152 (0)	12,814 (239)	5,700,179	2.44	17	na	0	0	0

For each group, the number of elements (putative families), the number of element fragments or copies in the genome, the cumulative length, the proportion of the genome and other features (elements containing chimeric or nested inserts of other elements (A), elements that appear to be complete with all typical structural and coding parts present even if stop codons or frameshifts are present (B), elements with a RT or Tase domain detected (C), potentially active elements that contain an intact ORF with all the typical domains although these can lack terminal repeats (D), elements with an intact ORF for the RT domain or parts of the Tase domain that could thus be partly active (E) are shown. The elements that could not be categorized or contained features of A. mellifera coding regions are shown at the bottom, these are probably not transposable elements.
^aThe numbers of chimeric/nested elements within elements of other categories are not included in the total numbers of elements.
^bThe software uses alignments to identify the longest fragment, which it deems as full-length. The number of full-length copies is also included in the total number of fragments.
^cAdditional Columns:
A. No. elements containing inserts
B. No. complete elements
C. No. elements with RT or Tase domains
D. No. potentially active elements
E. No. potentially partially active elements
^dPotential host genes were predicted by software using DNA characteristics, not by overlap analysis with gene predictions. An example of a potential host gene element is a coding sequence for a repeated protein domain or motif.

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ISSN: 1471-2164

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