De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly

BMC Genomics

Table 1 Descriptive statistics for M. capitata de novo-assembled metatranscriptome, quality filtering criteria and putative coral transcriptome

	Genes^a	Isoforms^b	%GC^c	Total bp^d	Mean bp^e	N50 bp^f
De novo assembly	441,520	660,340	45.5	601,736,076	911	1556
FPKM ≥0.5^g	146,298	237,332	46.5	307,002,357	1293	1916
Complete ORF^h	46,876	91,876	46.4	209,031,715	2275	2689
Internal ORF	23,610	27,492	53.7	24,431,475	888	1177
5′ Partial ORF	53,546	76,197	52.4	124,301,357	1631	1929
3′ Partial ORF	14,368	20,431	49.3	31,264,758	1530	1912
<90% Similarityⁱ	114,925	137,299	50.8	214,880,995	1565	1956
QF assembly^j	76,063	87,085	50.6	143,828,498	1652	1996
Coral transcriptome^k	13,643	20,461	41.6	39,739,502	1942	2409

^aGenes refers to Trinity-assembled contigs. ^bIsoforms refers to Trinity-assembled isotigs. ^c%GC is the percent of nucleotide bases in sequences that are either G or C.^dTotal bp is the total number of basepairs in the given assembly or subset thereof. ^eMean bp is the average length of assembled contig. ^f N50 bp is the mean number of basepairs in all transcripts that, ordered by length, make up 50% of the assembly. ^gFPKM = fragments per kilobase of transcript per million mapped reads; sum of pooled samples ≥0.5. ^hORF = open reading frame; sequences containing a complete, internal or partial ORF were included in the quality-filtered metatranscriptome assembly. ⁱprotein sequences with <90% similarity (for proteins with >90% similarity to each other, the longest sequence was retained as the representative sequence for that cluster). ^jQuality-filtered metatranscriptome assembly. ^kPutative coral transcriptome (see Methods for coral transcript identification criteria)

ISSN: 1471-2164